Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 18:43:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpu_9871/04_2023/6jpu_9871_neut.pdb" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 sd= 0.371 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 132 5.16 5 C 17778 2.51 5 N 4734 2.21 5 O 5124 1.98 5 H 2610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ASP 670": "OD1" <-> "OD2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A ASP 735": "OD1" <-> "OD2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A ASP 1129": "OD1" <-> "OD2" Residue "A PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ASP 670": "OD1" <-> "OD2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B ASP 735": "OD1" <-> "OD2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B GLU 1128": "OE1" <-> "OE2" Residue "B ASP 1129": "OD1" <-> "OD2" Residue "B PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C ARG 351": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 657": "OE1" <-> "OE2" Residue "C ASP 670": "OD1" <-> "OD2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C ASP 735": "OD1" <-> "OD2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 764": "NH1" <-> "NH2" Residue "C GLU 1128": "OE1" <-> "OE2" Residue "C ASP 1129": "OD1" <-> "OD2" Residue "C PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1183": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 340": "OD1" <-> "OD2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 442": "OD1" <-> "OD2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D GLU 575": "OE1" <-> "OE2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D ASP 670": "OD1" <-> "OD2" Residue "D GLU 691": "OE1" <-> "OE2" Residue "D GLU 718": "OE1" <-> "OE2" Residue "D ASP 735": "OD1" <-> "OD2" Residue "D ARG 761": "NH1" <-> "NH2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "D GLU 1128": "OE1" <-> "OE2" Residue "D ASP 1129": "OD1" <-> "OD2" Residue "D PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1183": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E ASP 272": "OD1" <-> "OD2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 340": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E ARG 354": "NH1" <-> "NH2" Residue "E ASP 371": "OD1" <-> "OD2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E ARG 425": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E GLU 575": "OE1" <-> "OE2" Residue "E ARG 591": "NH1" <-> "NH2" Residue "E TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "E ASP 670": "OD1" <-> "OD2" Residue "E GLU 691": "OE1" <-> "OE2" Residue "E GLU 718": "OE1" <-> "OE2" Residue "E ASP 735": "OD1" <-> "OD2" Residue "E ARG 761": "NH1" <-> "NH2" Residue "E ARG 764": "NH1" <-> "NH2" Residue "E GLU 1128": "OE1" <-> "OE2" Residue "E ASP 1129": "OD1" <-> "OD2" Residue "E PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1183": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F ASP 272": "OD1" <-> "OD2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 340": "OD1" <-> "OD2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 442": "OD1" <-> "OD2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F GLU 575": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F ASP 670": "OD1" <-> "OD2" Residue "F GLU 691": "OE1" <-> "OE2" Residue "F GLU 718": "OE1" <-> "OE2" Residue "F ASP 735": "OD1" <-> "OD2" Residue "F ARG 761": "NH1" <-> "NH2" Residue "F ARG 764": "NH1" <-> "NH2" Residue "F GLU 1128": "OE1" <-> "OE2" Residue "F ASP 1129": "OD1" <-> "OD2" Residue "F PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1183": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 30378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "B" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "C" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "D" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "E" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "F" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Time building chain proxies: 15.50, per 1000 atoms: 0.51 Number of scatterers: 30378 At special positions: 0 Unit cell: (154.76, 145.22, 142.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 O 5124 8.00 N 4734 7.00 C 17778 6.00 H 2610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.50 Conformation dependent library (CDL) restraints added in 4.5 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 18 sheets defined 46.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 314 through 326 removed outlier: 4.210A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE A1139 " --> pdb=" O LYS A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU A1150 " --> pdb=" O THR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1174 through 1185 removed outlier: 3.624A pdb=" N MET A1185 " --> pdb=" O VAL A1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 386 through 401 removed outlier: 3.759A pdb=" N SER B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 Processing helix chain 'B' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU B 592 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.022A pdb=" N LEU B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 646 through 658 Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 715 through 720 removed outlier: 3.731A pdb=" N TRP B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 720' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE B1139 " --> pdb=" O LYS B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET B1185 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 362 removed outlier: 3.881A pdb=" N ALA C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 removed outlier: 4.050A pdb=" N HIS C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 Processing helix chain 'C' and resid 515 through 526 removed outlier: 4.222A pdb=" N MET C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU C 551 " --> pdb=" O PRO C 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 Processing helix chain 'C' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU C 623 " --> pdb=" O GLY C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 646 through 658 Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 715 through 720 removed outlier: 3.729A pdb=" N TRP C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 720' Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 750 through 755 Processing helix chain 'C' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE C1139 " --> pdb=" O LYS C1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1164 removed outlier: 3.742A pdb=" N LEU C1150 " --> pdb=" O THR C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET C1185 " --> pdb=" O VAL C1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 282 through 288 removed outlier: 4.263A pdb=" N LEU D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER D 390 " --> pdb=" O GLN D 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS D 451 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 452 " --> pdb=" O ILE D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 Processing helix chain 'D' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 removed outlier: 6.154A pdb=" N GLU D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 4.022A pdb=" N LEU D 623 " --> pdb=" O GLY D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 646 through 658 Processing helix chain 'D' and resid 679 through 692 Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 715 through 720' Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 750 through 755 Processing helix chain 'D' and resid 1131 through 1139 removed outlier: 3.653A pdb=" N ILE D1139 " --> pdb=" O LYS D1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU D1150 " --> pdb=" O THR D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1167 No H-bonds generated for 'chain 'D' and resid 1165 through 1167' Processing helix chain 'D' and resid 1174 through 1185 removed outlier: 3.624A pdb=" N MET D1185 " --> pdb=" O VAL D1181 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 282 through 288 removed outlier: 4.261A pdb=" N LEU E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 314 through 326 removed outlier: 4.210A pdb=" N SER E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 362 removed outlier: 3.881A pdb=" N ALA E 349 " --> pdb=" O TRP E 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER E 390 " --> pdb=" O GLN E 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 452 " --> pdb=" O ILE E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'E' and resid 515 through 526 removed outlier: 4.222A pdb=" N MET E 526 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 578 Processing helix chain 'E' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU E 592 " --> pdb=" O TYR E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU E 623 " --> pdb=" O GLY E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 646 through 658 Processing helix chain 'E' and resid 679 through 692 Processing helix chain 'E' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 720' Processing helix chain 'E' and resid 722 through 724 No H-bonds generated for 'chain 'E' and resid 722 through 724' Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 743 through 748 Processing helix chain 'E' and resid 750 through 755 Processing helix chain 'E' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE E1139 " --> pdb=" O LYS E1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU E1150 " --> pdb=" O THR E1146 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET E1185 " --> pdb=" O VAL E1181 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 282 through 288 removed outlier: 4.261A pdb=" N LEU F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA F 349 " --> pdb=" O TRP F 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'F' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER F 390 " --> pdb=" O GLN F 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS F 451 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 495 Processing helix chain 'F' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET F 526 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 555 " --> pdb=" O GLU F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 Processing helix chain 'F' and resid 586 through 595 removed outlier: 3.588A pdb=" N LEU F 592 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 646 through 658 Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 715 through 720 removed outlier: 3.729A pdb=" N TRP F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 720 " --> pdb=" O LEU F 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 715 through 720' Processing helix chain 'F' and resid 722 through 724 No H-bonds generated for 'chain 'F' and resid 722 through 724' Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 743 through 748 Processing helix chain 'F' and resid 750 through 755 Processing helix chain 'F' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE F1139 " --> pdb=" O LYS F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1146 through 1164 removed outlier: 3.742A pdb=" N LEU F1150 " --> pdb=" O THR F1146 " (cutoff:3.500A) Processing helix chain 'F' and resid 1165 through 1167 No H-bonds generated for 'chain 'F' and resid 1165 through 1167' Processing helix chain 'F' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET F1185 " --> pdb=" O VAL F1181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER A 332 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 369 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 334 " --> pdb=" O PHE A 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 664 through 668 Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER B 332 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE B 369 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 334 " --> pdb=" O PHE B 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 664 through 668 Processing sheet with id=AA7, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'C' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER C 332 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE C 369 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 334 " --> pdb=" O PHE C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 664 through 668 Processing sheet with id=AB1, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AB2, first strand: chain 'D' and resid 332 through 336 removed outlier: 6.380A pdb=" N SER D 332 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE D 369 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR D 334 " --> pdb=" O PHE D 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 664 through 668 Processing sheet with id=AB4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER E 332 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 369 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR E 334 " --> pdb=" O PHE E 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 664 through 668 Processing sheet with id=AB7, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER F 332 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE F 369 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR F 334 " --> pdb=" O PHE F 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 664 through 668 966 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 16.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 2610 1.09 - 1.27: 4560 1.27 - 1.45: 8095 1.45 - 1.63: 15515 1.63 - 1.81: 234 Bond restraints: 31014 Sorted by residual: bond pdb=" CG2 ILE B 652 " pdb="HG21 ILE B 652 " ideal model delta sigma weight residual 0.970 1.060 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CB VAL F 379 " pdb=" CG2 VAL F 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.75e+01 bond pdb=" CB VAL E 379 " pdb=" CG2 VAL E 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.75e+01 bond pdb=" CB VAL B 379 " pdb=" CG2 VAL B 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.74e+01 bond pdb=" CB VAL A 379 " pdb=" CG2 VAL A 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.74e+01 ... (remaining 31009 not shown) Histogram of bond angle deviations from ideal: 63.95 - 80.38: 16 80.38 - 96.81: 15 96.81 - 113.24: 21966 113.24 - 129.67: 21766 129.67 - 146.10: 157 Bond angle restraints: 43920 Sorted by residual: angle pdb="HG12 ILE B 652 " pdb=" CG1 ILE B 652 " pdb="HG13 ILE B 652 " ideal model delta sigma weight residual 110.00 63.95 46.05 3.00e+00 1.11e-01 2.36e+02 angle pdb=" CB ILE B 652 " pdb=" CG1 ILE B 652 " pdb="HG12 ILE B 652 " ideal model delta sigma weight residual 109.00 146.10 -37.10 3.00e+00 1.11e-01 1.53e+02 angle pdb="HG22 VAL E 379 " pdb=" CG2 VAL E 379 " pdb="HG23 VAL E 379 " ideal model delta sigma weight residual 110.00 74.08 35.92 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB VAL E 379 " pdb=" CG2 VAL E 379 " pdb="HG22 VAL E 379 " ideal model delta sigma weight residual 109.00 144.27 -35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb="HG11 VAL D 408 " pdb=" CG1 VAL D 408 " pdb="HG12 VAL D 408 " ideal model delta sigma weight residual 110.00 78.34 31.66 3.00e+00 1.11e-01 1.11e+02 ... (remaining 43915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15774 17.47 - 34.95: 1813 34.95 - 52.42: 470 52.42 - 69.90: 182 69.90 - 87.37: 61 Dihedral angle restraints: 18300 sinusoidal: 8136 harmonic: 10164 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N GLY F 258 " pdb=" CA GLY F 258 " ideal model delta harmonic sigma weight residual 180.00 124.14 55.86 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA LEU A 257 " pdb=" C LEU A 257 " pdb=" N GLY A 258 " pdb=" CA GLY A 258 " ideal model delta harmonic sigma weight residual 180.00 124.15 55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA LEU C 257 " pdb=" C LEU C 257 " pdb=" N GLY C 258 " pdb=" CA GLY C 258 " ideal model delta harmonic sigma weight residual 180.00 124.15 55.85 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 18297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3238 0.060 - 0.119: 917 0.119 - 0.179: 111 0.179 - 0.238: 18 0.238 - 0.298: 18 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CB VAL C 282 " pdb=" CA VAL C 282 " pdb=" CG1 VAL C 282 " pdb=" CG2 VAL C 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 282 " pdb=" CA VAL F 282 " pdb=" CG1 VAL F 282 " pdb=" CG2 VAL F 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB VAL B 282 " pdb=" CA VAL B 282 " pdb=" CG1 VAL B 282 " pdb=" CG2 VAL B 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4299 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 345 " -0.017 2.00e-02 2.50e+03 1.35e-02 4.56e+00 pdb=" CG TRP C 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 345 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 345 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 345 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 345 " -0.016 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP F 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 345 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 345 " -0.016 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP D 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 345 " -0.002 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.47: 1023 2.47 - 3.00: 25827 3.00 - 3.53: 47036 3.53 - 4.07: 65533 4.07 - 4.60: 93316 Nonbonded interactions: 232735 Sorted by model distance: nonbonded pdb=" OG1 THR A 311 " pdb="HG21 THR A 311 " model vdw 1.933 2.096 nonbonded pdb=" OG1 THR C 314 " pdb=" OD2 ASP C 371 " model vdw 1.984 2.200 nonbonded pdb=" OG1 THR B 314 " pdb=" OD2 ASP B 371 " model vdw 1.984 2.200 nonbonded pdb=" OG1 THR D 314 " pdb=" OD2 ASP D 371 " model vdw 1.984 2.200 nonbonded pdb=" OG1 THR A 314 " pdb=" OD2 ASP A 371 " model vdw 1.984 2.200 ... (remaining 232730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 8.970 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 77.390 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.138 28404 Z= 0.431 Angle : 1.032 11.344 38466 Z= 0.578 Chirality : 0.056 0.298 4302 Planarity : 0.005 0.043 4950 Dihedral : 17.266 86.200 10962 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 70.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.05 % Rotamer Outliers : 9.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.12), residues: 3438 helix: -2.72 (0.11), residues: 1392 sheet: -1.82 (0.29), residues: 288 loop : -2.70 (0.14), residues: 1758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 967 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 667 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 300 outliers final: 91 residues processed: 893 average time/residue: 0.4837 time to fit residues: 650.7877 Evaluate side-chains 554 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 463 time to evaluate : 3.336 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 91 outliers final: 1 residues processed: 91 average time/residue: 0.4166 time to fit residues: 66.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 0.4980 chunk 88 optimal weight: 0.0870 chunk 174 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 103 optimal weight: 0.0470 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN D 615 GLN D 624 GLN E 306 HIS ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 28404 Z= 0.163 Angle : 0.593 8.302 38466 Z= 0.313 Chirality : 0.041 0.173 4302 Planarity : 0.004 0.070 4950 Dihedral : 6.186 49.497 3762 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 76.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.80 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.13), residues: 3438 helix: -1.52 (0.12), residues: 1542 sheet: -1.71 (0.30), residues: 294 loop : -2.71 (0.14), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 587 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 579 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 587 average time/residue: 0.4640 time to fit residues: 420.4938 Evaluate side-chains 451 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 3.495 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3447 time to fit residues: 6.0332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 211 optimal weight: 0.0470 chunk 85 optimal weight: 8.9990 chunk 311 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 overall best weight: 3.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 GLN F 277 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 28404 Z= 0.241 Angle : 0.661 8.260 38466 Z= 0.346 Chirality : 0.041 0.175 4302 Planarity : 0.005 0.046 4950 Dihedral : 5.751 43.133 3762 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 98.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.13), residues: 3438 helix: -1.34 (0.12), residues: 1482 sheet: -1.92 (0.29), residues: 300 loop : -2.23 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 514 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.4828 time to fit residues: 383.9934 Evaluate side-chains 402 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 4.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 8.9990 chunk 233 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 312 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 589 GLN C 615 GLN ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 28404 Z= 0.212 Angle : 0.607 7.606 38466 Z= 0.319 Chirality : 0.041 0.159 4302 Planarity : 0.005 0.053 4950 Dihedral : 5.416 39.739 3762 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 95.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3438 helix: -1.03 (0.12), residues: 1596 sheet: -2.16 (0.26), residues: 354 loop : -2.15 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 502 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.4737 time to fit residues: 368.8900 Evaluate side-chains 385 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 228 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1154 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 28404 Z= 0.320 Angle : 0.767 11.169 38466 Z= 0.400 Chirality : 0.044 0.225 4302 Planarity : 0.006 0.052 4950 Dihedral : 5.791 37.862 3762 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 122.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3438 helix: -1.31 (0.12), residues: 1500 sheet: -2.18 (0.24), residues: 384 loop : -2.16 (0.16), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 475 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.4652 time to fit residues: 345.1457 Evaluate side-chains 378 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 4.9990 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 153 optimal weight: 0.0570 chunk 27 optimal weight: 0.0070 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 GLN ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 306 HIS F 489 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 28404 Z= 0.153 Angle : 0.561 7.462 38466 Z= 0.295 Chirality : 0.041 0.202 4302 Planarity : 0.005 0.082 4950 Dihedral : 5.281 34.839 3762 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 92.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3438 helix: -0.71 (0.13), residues: 1494 sheet: -2.07 (0.25), residues: 384 loop : -1.75 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.4659 time to fit residues: 365.9718 Evaluate side-chains 389 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 188 optimal weight: 0.0670 chunk 241 optimal weight: 20.0000 chunk 187 optimal weight: 0.0030 chunk 278 optimal weight: 5.9990 chunk 184 optimal weight: 0.0470 chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.0230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C1136 GLN ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 28404 Z= 0.171 Angle : 0.569 10.748 38466 Z= 0.299 Chirality : 0.041 0.235 4302 Planarity : 0.005 0.081 4950 Dihedral : 5.038 32.583 3762 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 97.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3438 helix: -0.55 (0.13), residues: 1476 sheet: -2.03 (0.25), residues: 384 loop : -1.59 (0.17), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 492 average time/residue: 0.4608 time to fit residues: 354.1725 Evaluate side-chains 383 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 196 optimal weight: 50.0000 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 259 optimal weight: 0.0570 overall best weight: 2.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28404 Z= 0.183 Angle : 0.578 8.936 38466 Z= 0.304 Chirality : 0.041 0.231 4302 Planarity : 0.005 0.070 4950 Dihedral : 5.006 30.959 3762 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 100.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3438 helix: -0.53 (0.13), residues: 1476 sheet: -2.21 (0.28), residues: 306 loop : -1.55 (0.16), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.4545 time to fit residues: 344.8135 Evaluate side-chains 381 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 277 optimal weight: 9.9990 chunk 290 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 GLN ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 742 GLN ** F1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 28404 Z= 0.194 Angle : 0.588 12.083 38466 Z= 0.312 Chirality : 0.041 0.264 4302 Planarity : 0.005 0.068 4950 Dihedral : 4.954 29.428 3762 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 101.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3438 helix: -0.59 (0.13), residues: 1482 sheet: -2.15 (0.25), residues: 384 loop : -1.48 (0.17), residues: 1572 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.4583 time to fit residues: 345.9652 Evaluate side-chains 372 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.728 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 0.0870 chunk 324 optimal weight: 6.9990 chunk 198 optimal weight: 0.0050 chunk 154 optimal weight: 0.0070 chunk 225 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 209 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.104 28404 Z= 0.141 Angle : 0.540 9.565 38466 Z= 0.280 Chirality : 0.042 0.181 4302 Planarity : 0.004 0.077 4950 Dihedral : 4.679 26.020 3762 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 84.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3438 helix: 0.01 (0.13), residues: 1434 sheet: -2.07 (0.25), residues: 384 loop : -1.24 (0.17), residues: 1620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 502 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.4953 time to fit residues: 395.3728 Evaluate side-chains 395 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 271 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 279 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1152 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.095644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061480 restraints weight = 173799.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063375 restraints weight = 123496.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064587 restraints weight = 94633.942| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28404 Z= 0.186 Angle : 0.581 7.838 38466 Z= 0.303 Chirality : 0.041 0.193 4302 Planarity : 0.005 0.077 4950 Dihedral : 4.694 25.195 3762 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 100.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3438 helix: -0.28 (0.13), residues: 1476 sheet: -2.12 (0.25), residues: 384 loop : -1.25 (0.18), residues: 1578 =============================================================================== Job complete usr+sys time: 7302.43 seconds wall clock time: 134 minutes 23.19 seconds (8063.19 seconds total)