Starting phenix.real_space_refine on Mon Mar 25 03:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj3_20086/03_2024/6oj3_20086.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.019 sd= 0.425 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 399 5.16 5 C 47124 2.51 5 N 12704 2.21 5 O 13868 1.98 5 H 74462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 919": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148557 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 12787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12787 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain: "B" Number of atoms: 12787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12787 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain: "C" Number of atoms: 12772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 12772 Classifications: {'peptide': 780} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 751} Chain: "D" Number of atoms: 13574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 13574 Classifications: {'peptide': 827} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 796} Chain: "E" Number of atoms: 13028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 13028 Classifications: {'peptide': 795} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 764} Chain: "F" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "G" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "H" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "I" Number of atoms: 13114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 13114 Classifications: {'peptide': 800} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 769} Chain: "J" Number of atoms: 13391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 13391 Classifications: {'peptide': 816} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 785} Chain: "P" Number of atoms: 17651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 17651 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 34, 'TRANS': 1051} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 46.25, per 1000 atoms: 0.31 Number of scatterers: 148557 At special positions: 0 Unit cell: (287.82, 327.18, 194.34, 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 399 16.00 O 13868 8.00 N 12704 7.00 C 47124 6.00 H 74462 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: 91.61 Conformation dependent library (CDL) restraints added in 10.7 seconds 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17708 Finding SS restraints... Secondary structure from input PDB file: 389 helices and 114 sheets defined 51.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 Creating SS restraints... Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.559A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.787A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 274 through 281 removed outlier: 4.049A pdb=" N PHE A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.653A pdb=" N ARG A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.704A pdb=" N THR A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 361 removed outlier: 3.593A pdb=" N ILE A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.740A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.858A pdb=" N LEU A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.593A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.767A pdb=" N GLY A 448 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 4.063A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.588A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 545 removed outlier: 4.096A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 566 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.763A pdb=" N LEU A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 638 Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.541A pdb=" N LEU A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.551A pdb=" N VAL A 664 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 removed outlier: 4.011A pdb=" N MET A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.751A pdb=" N MET A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.741A pdb=" N ALA A 702 " --> pdb=" O GLN A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.644A pdb=" N VAL A 782 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.799A pdb=" N VAL A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.718A pdb=" N LYS A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 791 through 796' Processing helix chain 'A' and resid 810 through 814 removed outlier: 4.493A pdb=" N ASN A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 823 removed outlier: 4.352A pdb=" N ASP A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.638A pdb=" N ALA A 875 " --> pdb=" O PRO A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.638A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 removed outlier: 3.783A pdb=" N VAL B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.568A pdb=" N GLN B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 removed outlier: 3.825A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.582A pdb=" N ILE B 281 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 321 through 338 removed outlier: 3.889A pdb=" N THR B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 361 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.726A pdb=" N LEU B 374 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 375 " --> pdb=" O GLN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.801A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.627A pdb=" N MET B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 427 through 442 removed outlier: 3.569A pdb=" N LEU B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.611A pdb=" N ILE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.666A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 545 removed outlier: 3.622A pdb=" N LYS B 533 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 Processing helix chain 'B' and resid 585 through 594 removed outlier: 3.703A pdb=" N LEU B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 637 removed outlier: 3.545A pdb=" N ASN B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 655 Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 665 through 678 removed outlier: 3.981A pdb=" N MET B 669 " --> pdb=" O PRO B 665 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 4.881A pdb=" N GLU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN B 698 " --> pdb=" O MET B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing helix chain 'B' and resid 750 through 760 removed outlier: 4.776A pdb=" N ILE B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 784 removed outlier: 3.544A pdb=" N LEU B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.913A pdb=" N VAL B 789 " --> pdb=" O ASP B 786 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 790 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.743A pdb=" N LYS B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 Processing helix chain 'B' and resid 871 through 875 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 165 through 184 Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.267A pdb=" N MET C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.885A pdb=" N ARG C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.601A pdb=" N ARG C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 338 removed outlier: 3.669A pdb=" N SER C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 361 removed outlier: 3.987A pdb=" N LYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.520A pdb=" N PHE C 373 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.992A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 421 removed outlier: 3.554A pdb=" N LEU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 427 through 442 removed outlier: 3.685A pdb=" N LEU C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.645A pdb=" N ILE C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 508 through 522 removed outlier: 3.528A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 545 removed outlier: 3.562A pdb=" N LYS C 533 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 566 Processing helix chain 'C' and resid 585 through 594 Processing helix chain 'C' and resid 603 through 638 removed outlier: 3.516A pdb=" N ASN C 614 " --> pdb=" O TYR C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 655 removed outlier: 3.996A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 664 removed outlier: 4.036A pdb=" N ARG C 663 " --> pdb=" O ASP C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 677 removed outlier: 4.054A pdb=" N TYR C 670 " --> pdb=" O ASP C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 702 removed outlier: 3.671A pdb=" N ASN C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN C 698 " --> pdb=" O MET C 694 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 702 " --> pdb=" O GLN C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 748 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 777 through 783 Processing helix chain 'C' and resid 790 through 796 removed outlier: 4.338A pdb=" N VAL C 794 " --> pdb=" O PHE C 790 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 795 " --> pdb=" O ALA C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.825A pdb=" N ALA C 820 " --> pdb=" O PHE C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.555A pdb=" N LYS D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 4.155A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.563A pdb=" N ASP D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.779A pdb=" N ARG D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.868A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.618A pdb=" N ARG D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 removed outlier: 3.902A pdb=" N SER D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 360 removed outlier: 3.657A pdb=" N LYS D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 Processing helix chain 'D' and resid 381 through 396 removed outlier: 3.691A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.791A pdb=" N LEU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.722A pdb=" N LEU D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 447 Processing helix chain 'D' and resid 461 through 467 removed outlier: 3.641A pdb=" N ILE D 465 " --> pdb=" O THR D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 508 through 523 removed outlier: 3.732A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 545 removed outlier: 3.645A pdb=" N LYS D 533 " --> pdb=" O PRO D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 566 Processing helix chain 'D' and resid 585 through 592 Processing helix chain 'D' and resid 603 through 638 removed outlier: 3.681A pdb=" N ASN D 614 " --> pdb=" O TYR D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 656 Processing helix chain 'D' and resid 660 through 664 removed outlier: 3.817A pdb=" N ARG D 663 " --> pdb=" O ASP D 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 664 " --> pdb=" O ILE D 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 660 through 664' Processing helix chain 'D' and resid 666 through 678 removed outlier: 3.764A pdb=" N TYR D 670 " --> pdb=" O ASP D 666 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 678 " --> pdb=" O ASP D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.764A pdb=" N MET D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLN D 698 " --> pdb=" O MET D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 748 Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 778 through 783 Processing helix chain 'D' and resid 784 through 788 removed outlier: 3.968A pdb=" N ALA D 787 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 788 " --> pdb=" O LEU D 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 784 through 788' Processing helix chain 'D' and resid 791 through 796 Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.633A pdb=" N ALA D 820 " --> pdb=" O PHE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 865 removed outlier: 3.970A pdb=" N PHE D 864 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 875 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 165 through 184 Processing helix chain 'E' and resid 189 through 194 removed outlier: 4.427A pdb=" N MET E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 225 through 235 removed outlier: 3.911A pdb=" N ARG E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 Processing helix chain 'E' and resid 273 through 280 Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 321 through 340 removed outlier: 4.012A pdb=" N LEU E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 361 Processing helix chain 'E' and resid 368 through 375 Processing helix chain 'E' and resid 381 through 396 removed outlier: 3.613A pdb=" N ILE E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 421 removed outlier: 4.061A pdb=" N LEU E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 443 removed outlier: 3.610A pdb=" N LEU E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 443 " --> pdb=" O ILE E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 removed outlier: 4.357A pdb=" N GLN E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 469 " --> pdb=" O ILE E 465 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 470 " --> pdb=" O ALA E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 508 through 522 removed outlier: 3.677A pdb=" N GLN E 512 " --> pdb=" O HIS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 545 removed outlier: 3.608A pdb=" N LEU E 543 " --> pdb=" O GLY E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 566 Processing helix chain 'E' and resid 585 through 594 Processing helix chain 'E' and resid 603 through 637 Processing helix chain 'E' and resid 646 through 656 removed outlier: 3.665A pdb=" N LEU E 656 " --> pdb=" O PHE E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.608A pdb=" N VAL E 664 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 678 removed outlier: 3.756A pdb=" N MET E 669 " --> pdb=" O PRO E 665 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E 678 " --> pdb=" O ASP E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 702 removed outlier: 4.716A pdb=" N GLU E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA E 702 " --> pdb=" O GLN E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 748 Processing helix chain 'E' and resid 751 through 760 Processing helix chain 'E' and resid 778 through 783 removed outlier: 3.641A pdb=" N VAL E 782 " --> pdb=" O VAL E 778 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA E 783 " --> pdb=" O ILE E 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 778 through 783' Processing helix chain 'E' and resid 787 through 790 removed outlier: 3.758A pdb=" N PHE E 790 " --> pdb=" O ALA E 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 787 through 790' Processing helix chain 'E' and resid 791 through 796 removed outlier: 3.795A pdb=" N LYS E 795 " --> pdb=" O ALA E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 822 Processing helix chain 'E' and resid 841 through 845 Processing helix chain 'E' and resid 860 through 864 removed outlier: 4.035A pdb=" N PHE E 864 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 875 removed outlier: 3.652A pdb=" N ALA E 875 " --> pdb=" O PRO E 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.683A pdb=" N GLU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 117 removed outlier: 3.832A pdb=" N LYS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 184 removed outlier: 3.894A pdb=" N GLN F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 removed outlier: 3.616A pdb=" N ALA F 212 " --> pdb=" O ASP F 208 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 273 through 279 removed outlier: 3.676A pdb=" N ILE F 277 " --> pdb=" O ASN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.690A pdb=" N ARG F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 338 removed outlier: 3.637A pdb=" N SER F 338 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 361 removed outlier: 3.594A pdb=" N GLN F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 365 removed outlier: 4.055A pdb=" N LEU F 365 " --> pdb=" O LEU F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 381 through 396 removed outlier: 3.821A pdb=" N ILE F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 removed outlier: 3.763A pdb=" N LEU F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 440 Processing helix chain 'F' and resid 442 through 448 Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.727A pdb=" N GLN F 468 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.529A pdb=" N ASN F 484 " --> pdb=" O HIS F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 523 removed outlier: 3.931A pdb=" N GLN F 512 " --> pdb=" O HIS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 545 removed outlier: 3.767A pdb=" N SER F 535 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 543 " --> pdb=" O GLY F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 567 removed outlier: 3.912A pdb=" N CYS F 567 " --> pdb=" O THR F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 592 removed outlier: 3.706A pdb=" N LEU F 591 " --> pdb=" O SER F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 638 removed outlier: 3.634A pdb=" N PHE F 608 " --> pdb=" O PRO F 604 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 656 removed outlier: 3.760A pdb=" N ASP F 651 " --> pdb=" O SER F 647 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU F 656 " --> pdb=" O PHE F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 678 Processing helix chain 'F' and resid 682 through 694 removed outlier: 3.654A pdb=" N PHE F 689 " --> pdb=" O ARG F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 700 Processing helix chain 'F' and resid 742 through 748 removed outlier: 3.962A pdb=" N ARG F 747 " --> pdb=" O GLU F 743 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 748 " --> pdb=" O GLU F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 759 removed outlier: 4.848A pdb=" N MET F 757 " --> pdb=" O GLN F 753 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 759 " --> pdb=" O THR F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 784 Processing helix chain 'F' and resid 785 through 789 removed outlier: 4.157A pdb=" N VAL F 789 " --> pdb=" O ASP F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 822 removed outlier: 4.044A pdb=" N TYR F 822 " --> pdb=" O LEU F 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.811A pdb=" N GLN G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 3.883A pdb=" N LEU G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 184 removed outlier: 3.999A pdb=" N GLN G 179 " --> pdb=" O ASN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 221 removed outlier: 3.523A pdb=" N ALA G 212 " --> pdb=" O ASP G 208 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.887A pdb=" N LEU G 264 " --> pdb=" O ASN G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 281 removed outlier: 3.549A pdb=" N ILE G 277 " --> pdb=" O ASN G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 340 removed outlier: 3.745A pdb=" N SER G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 339 " --> pdb=" O LEU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 361 removed outlier: 3.675A pdb=" N GLN G 352 " --> pdb=" O SER G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 365 removed outlier: 3.619A pdb=" N LEU G 365 " --> pdb=" O LEU G 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 362 through 365' Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 381 through 396 removed outlier: 3.826A pdb=" N ILE G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 421 removed outlier: 3.680A pdb=" N LEU G 411 " --> pdb=" O ASN G 407 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP G 416 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 426 removed outlier: 3.501A pdb=" N MET G 425 " --> pdb=" O PRO G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 442 Processing helix chain 'G' and resid 442 through 448 Processing helix chain 'G' and resid 461 through 470 removed outlier: 3.873A pdb=" N GLN G 468 " --> pdb=" O GLN G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 484 removed outlier: 3.894A pdb=" N ASN G 477 " --> pdb=" O PHE G 473 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 522 removed outlier: 3.946A pdb=" N GLN G 512 " --> pdb=" O HIS G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.686A pdb=" N SER G 535 " --> pdb=" O ASP G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 545 Processing helix chain 'G' and resid 546 through 566 Processing helix chain 'G' and resid 584 through 594 removed outlier: 3.714A pdb=" N VAL G 588 " --> pdb=" O GLN G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 639 Processing helix chain 'G' and resid 645 through 655 removed outlier: 3.522A pdb=" N VAL G 649 " --> pdb=" O MET G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 665 through 677 removed outlier: 3.858A pdb=" N MET G 669 " --> pdb=" O PRO G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 694 removed outlier: 3.566A pdb=" N PHE G 689 " --> pdb=" O ARG G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 701 removed outlier: 3.565A pdb=" N ARG G 701 " --> pdb=" O GLU G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 751 through 761 removed outlier: 4.617A pdb=" N MET G 757 " --> pdb=" O GLN G 753 " (cutoff:3.500A) Processing helix chain 'G' and resid 778 through 783 Processing helix chain 'G' and resid 784 through 789 removed outlier: 3.538A pdb=" N ALA G 787 " --> pdb=" O LYS G 784 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 788 " --> pdb=" O LEU G 785 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL G 789 " --> pdb=" O ASP G 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 784 through 789' Processing helix chain 'G' and resid 790 through 796 removed outlier: 3.778A pdb=" N VAL G 794 " --> pdb=" O PHE G 790 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU G 796 " --> pdb=" O GLN G 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 822 removed outlier: 3.688A pdb=" N ALA G 820 " --> pdb=" O PHE G 816 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR G 822 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 100 removed outlier: 3.798A pdb=" N GLN H 94 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 118 removed outlier: 3.968A pdb=" N LEU H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 183 removed outlier: 3.774A pdb=" N GLN H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 removed outlier: 3.589A pdb=" N ASP H 192 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 219 removed outlier: 4.137A pdb=" N ILE H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 235 Processing helix chain 'H' and resid 253 through 266 Processing helix chain 'H' and resid 273 through 281 removed outlier: 3.841A pdb=" N ILE H 277 " --> pdb=" O ASN H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.786A pdb=" N ARG H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 338 removed outlier: 3.895A pdb=" N SER H 338 " --> pdb=" O ILE H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 361 Processing helix chain 'H' and resid 381 through 396 removed outlier: 3.631A pdb=" N ILE H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 421 removed outlier: 3.643A pdb=" N TRP H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 426 removed outlier: 3.641A pdb=" N MET H 425 " --> pdb=" O PRO H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 442 Processing helix chain 'H' and resid 442 through 448 Processing helix chain 'H' and resid 461 through 470 removed outlier: 3.674A pdb=" N GLN H 468 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 4.407A pdb=" N TRP H 478 " --> pdb=" O GLN H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 523 removed outlier: 3.851A pdb=" N GLN H 512 " --> pdb=" O HIS H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 546 removed outlier: 3.906A pdb=" N SER H 535 " --> pdb=" O ASP H 531 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU H 543 " --> pdb=" O GLY H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 566 Processing helix chain 'H' and resid 584 through 594 Processing helix chain 'H' and resid 603 through 638 removed outlier: 3.595A pdb=" N ASN H 614 " --> pdb=" O TYR H 610 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 656 removed outlier: 3.726A pdb=" N ASP H 651 " --> pdb=" O SER H 647 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 656 " --> pdb=" O PHE H 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 666 through 678 Processing helix chain 'H' and resid 682 through 694 Processing helix chain 'H' and resid 695 through 700 Processing helix chain 'H' and resid 742 through 748 removed outlier: 3.620A pdb=" N ARG H 747 " --> pdb=" O GLU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 759 removed outlier: 4.174A pdb=" N MET H 757 " --> pdb=" O GLN H 753 " (cutoff:3.500A) Processing helix chain 'H' and resid 777 through 783 Processing helix chain 'H' and resid 790 through 796 removed outlier: 3.915A pdb=" N VAL H 794 " --> pdb=" O PHE H 790 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 819 removed outlier: 3.503A pdb=" N LEU H 818 " --> pdb=" O ASP H 815 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 865 Processing helix chain 'H' and resid 871 through 875 removed outlier: 3.749A pdb=" N ALA H 875 " --> pdb=" O PRO H 872 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.609A pdb=" N TYR I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'I' and resid 110 through 117 removed outlier: 3.750A pdb=" N LYS I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 183 removed outlier: 3.741A pdb=" N GLN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 Processing helix chain 'I' and resid 208 through 221 removed outlier: 3.781A pdb=" N ALA I 212 " --> pdb=" O ASP I 208 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.553A pdb=" N ARG I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.704A pdb=" N LEU I 264 " --> pdb=" O ASN I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 281 removed outlier: 3.574A pdb=" N ILE I 277 " --> pdb=" O ASN I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 287 removed outlier: 3.771A pdb=" N ARG I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 340 removed outlier: 3.671A pdb=" N SER I 338 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL I 339 " --> pdb=" O LEU I 335 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 361 removed outlier: 3.738A pdb=" N GLN I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 365 removed outlier: 3.576A pdb=" N LEU I 365 " --> pdb=" O LEU I 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 362 through 365' Processing helix chain 'I' and resid 381 through 396 removed outlier: 3.639A pdb=" N ILE I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 421 removed outlier: 3.663A pdb=" N LEU I 411 " --> pdb=" O ASN I 407 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP I 416 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU I 417 " --> pdb=" O SER I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 426 Processing helix chain 'I' and resid 427 through 440 Processing helix chain 'I' and resid 442 through 448 Processing helix chain 'I' and resid 461 through 470 removed outlier: 4.172A pdb=" N GLN I 468 " --> pdb=" O GLN I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 484 removed outlier: 3.684A pdb=" N TRP I 478 " --> pdb=" O GLN I 474 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN I 484 " --> pdb=" O HIS I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 522 removed outlier: 3.996A pdb=" N GLN I 512 " --> pdb=" O HIS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 545 removed outlier: 3.789A pdb=" N SER I 535 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU I 543 " --> pdb=" O GLY I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 566 Processing helix chain 'I' and resid 584 through 594 Processing helix chain 'I' and resid 603 through 637 Processing helix chain 'I' and resid 645 through 656 removed outlier: 3.622A pdb=" N ASP I 651 " --> pdb=" O SER I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 664 removed outlier: 3.671A pdb=" N ARG I 663 " --> pdb=" O ASP I 660 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL I 664 " --> pdb=" O ILE I 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 660 through 664' Processing helix chain 'I' and resid 666 through 678 removed outlier: 4.110A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 700 removed outlier: 4.549A pdb=" N GLU I 697 " --> pdb=" O LEU I 693 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN I 698 " --> pdb=" O MET I 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 742 through 748 removed outlier: 3.753A pdb=" N ARG I 747 " --> pdb=" O GLU I 743 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 760 removed outlier: 4.418A pdb=" N MET I 757 " --> pdb=" O GLN I 753 " (cutoff:3.500A) Processing helix chain 'I' and resid 778 through 783 Processing helix chain 'I' and resid 785 through 789 removed outlier: 3.936A pdb=" N VAL I 789 " --> pdb=" O ASP I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 790 through 796 removed outlier: 4.285A pdb=" N VAL I 794 " --> pdb=" O PHE I 790 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 819 Processing helix chain 'I' and resid 841 through 845 removed outlier: 3.588A pdb=" N SER I 845 " --> pdb=" O ASP I 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 841 through 845' Processing helix chain 'J' and resid 73 through 86 removed outlier: 3.795A pdb=" N LYS J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 100 removed outlier: 3.707A pdb=" N VAL J 93 " --> pdb=" O HIS J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.841A pdb=" N LYS J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 183 removed outlier: 4.017A pdb=" N GLN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 3.516A pdb=" N ASP J 192 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 221 removed outlier: 3.584A pdb=" N ALA J 212 " --> pdb=" O ASP J 208 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 235 removed outlier: 3.719A pdb=" N ARG J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 273 through 281 removed outlier: 3.655A pdb=" N ILE J 277 " --> pdb=" O ASN J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 340 removed outlier: 3.601A pdb=" N SER J 338 " --> pdb=" O ILE J 334 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL J 339 " --> pdb=" O LEU J 335 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 361 removed outlier: 4.125A pdb=" N GLN J 352 " --> pdb=" O SER J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 396 removed outlier: 3.681A pdb=" N ILE J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 421 removed outlier: 3.663A pdb=" N LEU J 411 " --> pdb=" O ASN J 407 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP J 416 " --> pdb=" O ILE J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 442 Processing helix chain 'J' and resid 442 through 448 removed outlier: 3.732A pdb=" N PHE J 447 " --> pdb=" O ILE J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 470 removed outlier: 4.165A pdb=" N GLN J 468 " --> pdb=" O GLN J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 484 Processing helix chain 'J' and resid 508 through 523 removed outlier: 3.985A pdb=" N GLN J 512 " --> pdb=" O HIS J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 545 removed outlier: 3.603A pdb=" N SER J 535 " --> pdb=" O ASP J 531 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE J 536 " --> pdb=" O TYR J 532 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU J 543 " --> pdb=" O GLY J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 566 Processing helix chain 'J' and resid 584 through 592 Processing helix chain 'J' and resid 603 through 638 Processing helix chain 'J' and resid 645 through 655 removed outlier: 3.654A pdb=" N ASP J 651 " --> pdb=" O SER J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 678 removed outlier: 3.696A pdb=" N LEU J 678 " --> pdb=" O ASP J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 694 Processing helix chain 'J' and resid 695 through 702 removed outlier: 3.611A pdb=" N ALA J 702 " --> pdb=" O GLN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 748 removed outlier: 3.799A pdb=" N ARG J 747 " --> pdb=" O GLU J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 760 removed outlier: 3.699A pdb=" N MET J 757 " --> pdb=" O GLN J 753 " (cutoff:3.500A) Processing helix chain 'J' and resid 778 through 783 Processing helix chain 'J' and resid 785 through 789 removed outlier: 3.704A pdb=" N VAL J 789 " --> pdb=" O ASP J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 796 removed outlier: 4.221A pdb=" N LYS J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU J 796 " --> pdb=" O GLN J 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 791 through 796' Processing helix chain 'J' and resid 816 through 821 removed outlier: 3.513A pdb=" N ALA J 820 " --> pdb=" O PHE J 816 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 17 removed outlier: 3.590A pdb=" N ILE P 7 " --> pdb=" O LYS P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.989A pdb=" N GLU P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 68 Processing helix chain 'P' and resid 83 through 90 removed outlier: 3.614A pdb=" N ARG P 87 " --> pdb=" O ASN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 94 removed outlier: 4.099A pdb=" N LYS P 94 " --> pdb=" O LYS P 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 94' Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 121 through 125 removed outlier: 3.536A pdb=" N GLU P 124 " --> pdb=" O THR P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 152 Processing helix chain 'P' and resid 157 through 179 removed outlier: 3.709A pdb=" N ARG P 165 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.525A pdb=" N MET P 196 " --> pdb=" O GLU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 215 removed outlier: 3.817A pdb=" N TRP P 206 " --> pdb=" O TYR P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 231 removed outlier: 3.632A pdb=" N VAL P 231 " --> pdb=" O ARG P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 245 Processing helix chain 'P' and resid 247 through 252 Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 282 through 299 removed outlier: 3.726A pdb=" N GLY P 299 " --> pdb=" O MET P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 309 removed outlier: 3.751A pdb=" N LYS P 305 " --> pdb=" O THR P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 319 through 329 Processing helix chain 'P' and resid 338 through 344 Processing helix chain 'P' and resid 357 through 382 removed outlier: 3.927A pdb=" N GLU P 362 " --> pdb=" O GLU P 358 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU P 377 " --> pdb=" O LYS P 373 " (cutoff:3.500A) Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 383 through 388 removed outlier: 3.589A pdb=" N GLN P 387 " --> pdb=" O ASP P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 388 through 396 Processing helix chain 'P' and resid 397 through 400 Processing helix chain 'P' and resid 419 through 430 removed outlier: 3.864A pdb=" N ALA P 429 " --> pdb=" O MET P 425 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN P 430 " --> pdb=" O ASP P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 466 through 487 removed outlier: 4.550A pdb=" N PHE P 470 " --> pdb=" O PRO P 466 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE P 471 " --> pdb=" O TYR P 467 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA P 475 " --> pdb=" O ILE P 471 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL P 476 " --> pdb=" O ALA P 472 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS P 486 " --> pdb=" O ILE P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 547 removed outlier: 3.710A pdb=" N ARG P 535 " --> pdb=" O THR P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 551 through 570 removed outlier: 3.532A pdb=" N ILE P 555 " --> pdb=" O ASP P 551 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP P 570 " --> pdb=" O ILE P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 595 through 616 removed outlier: 3.518A pdb=" N SER P 613 " --> pdb=" O LYS P 609 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG P 614 " --> pdb=" O THR P 610 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE P 615 " --> pdb=" O VAL P 611 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER P 616 " --> pdb=" O LEU P 612 " (cutoff:3.500A) Processing helix chain 'P' and resid 644 through 661 Processing helix chain 'P' and resid 705 through 724 removed outlier: 3.641A pdb=" N GLN P 709 " --> pdb=" O THR P 705 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA P 710 " --> pdb=" O GLN P 706 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA P 711 " --> pdb=" O TRP P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 741 removed outlier: 3.724A pdb=" N ILE P 732 " --> pdb=" O ASP P 728 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 758 Processing helix chain 'P' and resid 778 through 793 removed outlier: 3.814A pdb=" N VAL P 782 " --> pdb=" O THR P 778 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER P 790 " --> pdb=" O ARG P 786 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER P 793 " --> pdb=" O MET P 789 " (cutoff:3.500A) Processing helix chain 'P' and resid 796 through 803 Processing helix chain 'P' and resid 806 through 820 Processing helix chain 'P' and resid 827 through 840 removed outlier: 3.661A pdb=" N ALA P 837 " --> pdb=" O LEU P 833 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS P 838 " --> pdb=" O THR P 834 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN P 840 " --> pdb=" O LYS P 836 " (cutoff:3.500A) Processing helix chain 'P' and resid 842 through 862 removed outlier: 3.588A pdb=" N SER P 846 " --> pdb=" O TYR P 842 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET P 860 " --> pdb=" O ALA P 856 " (cutoff:3.500A) Processing helix chain 'P' and resid 873 through 882 removed outlier: 3.778A pdb=" N ILE P 877 " --> pdb=" O THR P 873 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP P 880 " --> pdb=" O ASP P 876 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 885 No H-bonds generated for 'chain 'P' and resid 883 through 885' Processing helix chain 'P' and resid 904 through 912 Processing helix chain 'P' and resid 930 through 938 removed outlier: 3.873A pdb=" N ILE P 934 " --> pdb=" O ILE P 930 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS P 936 " --> pdb=" O ARG P 932 " (cutoff:3.500A) Processing helix chain 'P' and resid 943 through 952 removed outlier: 3.755A pdb=" N SER P 952 " --> pdb=" O TYR P 948 " (cutoff:3.500A) Processing helix chain 'P' and resid 956 through 964 removed outlier: 3.610A pdb=" N LEU P 960 " --> pdb=" O ASN P 956 " (cutoff:3.500A) Processing helix chain 'P' and resid 968 through 979 removed outlier: 3.882A pdb=" N ALA P 972 " --> pdb=" O PRO P 968 " (cutoff:3.500A) Processing helix chain 'P' and resid 984 through 997 Processing helix chain 'P' and resid 1002 through 1007 removed outlier: 3.849A pdb=" N PHE P1007 " --> pdb=" O TYR P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1011 through 1017 removed outlier: 3.511A pdb=" N GLU P1015 " --> pdb=" O SER P1011 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU P1017 " --> pdb=" O ASP P1013 " (cutoff:3.500A) Processing helix chain 'P' and resid 1026 through 1049 removed outlier: 3.745A pdb=" N THR P1030 " --> pdb=" O ILE P1026 " (cutoff:3.500A) Processing helix chain 'P' and resid 1059 through 1071 removed outlier: 3.546A pdb=" N LYS P1068 " --> pdb=" O ILE P1064 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS P1069 " --> pdb=" O LYS P1065 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP P1071 " --> pdb=" O TRP P1067 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1082 removed outlier: 3.637A pdb=" N THR P1081 " --> pdb=" O SER P1078 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 141 removed outlier: 3.911A pdb=" N VAL A 140 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG A 150 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.547A pdb=" N TYR A 305 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 304 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.834A pdb=" N SER A 400 " --> pdb=" O LEU A 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 492 Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 712 removed outlier: 3.556A pdb=" N GLY A 709 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 768 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE A 711 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 766 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 740 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ALA A 769 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB1, first strand: chain 'A' and resid 720 through 721 removed outlier: 3.577A pdb=" N VAL A 728 " --> pdb=" O GLU A 720 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AB3, first strand: chain 'A' and resid 773 through 775 Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 141 removed outlier: 4.366A pdb=" N VAL B 140 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG B 150 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB6, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AB7, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.694A pdb=" N TYR B 305 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG B 304 " --> pdb=" O TYR B 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 291 through 294 Processing sheet with id=AB9, first strand: chain 'B' and resid 488 through 492 Processing sheet with id=AC1, first strand: chain 'B' and resid 730 through 731 removed outlier: 6.342A pdb=" N ILE B 740 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 717 through 718 Processing sheet with id=AC3, first strand: chain 'B' and resid 720 through 721 removed outlier: 3.618A pdb=" N VAL B 728 " --> pdb=" O GLU B 720 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.576A pdb=" N ILE B 773 " --> pdb=" O LEU B 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 133 through 141 removed outlier: 4.170A pdb=" N VAL C 140 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG C 150 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC7, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC8, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.507A pdb=" N TYR C 305 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AD1, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AD2, first strand: chain 'C' and resid 488 through 492 Processing sheet with id=AD3, first strand: chain 'C' and resid 706 through 707 Processing sheet with id=AD4, first strand: chain 'C' and resid 710 through 712 removed outlier: 6.338A pdb=" N ILE C 740 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AD6, first strand: chain 'C' and resid 720 through 721 Processing sheet with id=AD7, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AD8, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.933A pdb=" N ILE C 773 " --> pdb=" O LEU C 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 133 through 141 removed outlier: 4.391A pdb=" N VAL D 140 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG D 150 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 195 through 196 Processing sheet with id=AE2, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AE3, first strand: chain 'D' and resid 270 through 271 removed outlier: 3.593A pdb=" N TYR D 305 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG D 304 " --> pdb=" O TYR D 858 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 291 through 294 Processing sheet with id=AE5, first strand: chain 'D' and resid 399 through 402 Processing sheet with id=AE6, first strand: chain 'D' and resid 488 through 492 Processing sheet with id=AE7, first strand: chain 'D' and resid 710 through 712 removed outlier: 6.680A pdb=" N ILE D 740 " --> pdb=" O VAL D 767 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 717 through 718 Processing sheet with id=AE9, first strand: chain 'D' and resid 727 through 728 Processing sheet with id=AF1, first strand: chain 'D' and resid 730 through 731 Processing sheet with id=AF2, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.852A pdb=" N VAL P 580 " --> pdb=" O ASP P 577 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE P 584 " --> pdb=" O VAL P 573 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 133 through 141 removed outlier: 4.127A pdb=" N VAL E 140 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG E 150 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AF5, first strand: chain 'E' and resid 238 through 240 Processing sheet with id=AF6, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AF7, first strand: chain 'E' and resid 291 through 294 Processing sheet with id=AF8, first strand: chain 'E' and resid 400 through 402 removed outlier: 6.428A pdb=" N SER E 400 " --> pdb=" O LEU E 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 488 through 492 Processing sheet with id=AG1, first strand: chain 'E' and resid 706 through 707 Processing sheet with id=AG2, first strand: chain 'E' and resid 710 through 712 removed outlier: 6.338A pdb=" N ILE E 740 " --> pdb=" O VAL E 767 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 720 through 721 Processing sheet with id=AG4, first strand: chain 'E' and resid 730 through 731 Processing sheet with id=AG5, first strand: chain 'E' and resid 773 through 774 removed outlier: 6.540A pdb=" N ILE E 773 " --> pdb=" O LEU E 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'F' and resid 133 through 138 Processing sheet with id=AG7, first strand: chain 'F' and resid 195 through 196 Processing sheet with id=AG8, first strand: chain 'F' and resid 238 through 240 Processing sheet with id=AG9, first strand: chain 'F' and resid 270 through 271 removed outlier: 3.531A pdb=" N GLU F 270 " --> pdb=" O TYR F 305 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 305 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 291 through 294 Processing sheet with id=AH2, first strand: chain 'F' and resid 488 through 492 Processing sheet with id=AH3, first strand: chain 'F' and resid 706 through 707 Processing sheet with id=AH4, first strand: chain 'F' and resid 710 through 712 removed outlier: 6.342A pdb=" N GLN F 738 " --> pdb=" O ALA F 765 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL F 767 " --> pdb=" O GLN F 738 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE F 740 " --> pdb=" O VAL F 767 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 717 through 718 Processing sheet with id=AH6, first strand: chain 'F' and resid 720 through 721 removed outlier: 3.796A pdb=" N VAL F 728 " --> pdb=" O GLU F 720 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 730 through 731 Processing sheet with id=AH8, first strand: chain 'F' and resid 773 through 774 removed outlier: 6.122A pdb=" N ILE F 773 " --> pdb=" O LEU F 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'G' and resid 133 through 138 Processing sheet with id=AI1, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AI2, first strand: chain 'G' and resid 238 through 240 Processing sheet with id=AI3, first strand: chain 'G' and resid 270 through 271 removed outlier: 3.621A pdb=" N TYR G 305 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 291 through 294 Processing sheet with id=AI5, first strand: chain 'G' and resid 488 through 492 Processing sheet with id=AI6, first strand: chain 'G' and resid 730 through 731 removed outlier: 3.566A pdb=" N LEU G 770 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY G 709 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY G 768 " --> pdb=" O GLY G 709 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE G 711 " --> pdb=" O LEU G 766 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU G 766 " --> pdb=" O ILE G 711 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 717 through 718 Processing sheet with id=AI8, first strand: chain 'G' and resid 720 through 721 Processing sheet with id=AI9, first strand: chain 'H' and resid 133 through 138 Processing sheet with id=AJ1, first strand: chain 'H' and resid 195 through 196 Processing sheet with id=AJ2, first strand: chain 'H' and resid 238 through 240 Processing sheet with id=AJ3, first strand: chain 'H' and resid 270 through 271 removed outlier: 3.665A pdb=" N GLU H 270 " --> pdb=" O TYR H 305 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR H 305 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'H' and resid 291 through 294 Processing sheet with id=AJ5, first strand: chain 'H' and resid 488 through 492 Processing sheet with id=AJ6, first strand: chain 'H' and resid 707 through 712 removed outlier: 6.381A pdb=" N GLY H 768 " --> pdb=" O GLY H 709 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE H 711 " --> pdb=" O LEU H 766 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 766 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN H 738 " --> pdb=" O ALA H 765 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 767 " --> pdb=" O GLN H 738 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE H 740 " --> pdb=" O VAL H 767 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA H 769 " --> pdb=" O ILE H 740 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 720 through 721 Processing sheet with id=AJ8, first strand: chain 'H' and resid 730 through 731 Processing sheet with id=AJ9, first strand: chain 'I' and resid 133 through 141 removed outlier: 4.422A pdb=" N VAL I 140 " --> pdb=" O ARG I 150 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG I 150 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AK2, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AK3, first strand: chain 'I' and resid 270 through 271 removed outlier: 3.555A pdb=" N TYR I 305 " --> pdb=" O GLU I 270 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG I 304 " --> pdb=" O TYR I 858 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 291 through 295 Processing sheet with id=AK5, first strand: chain 'I' and resid 488 through 492 Processing sheet with id=AK6, first strand: chain 'I' and resid 706 through 712 removed outlier: 6.361A pdb=" N GLY I 768 " --> pdb=" O GLY I 709 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE I 711 " --> pdb=" O LEU I 766 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU I 766 " --> pdb=" O ILE I 711 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE I 740 " --> pdb=" O VAL I 767 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ALA I 769 " --> pdb=" O ILE I 740 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'I' and resid 720 through 721 Processing sheet with id=AK8, first strand: chain 'I' and resid 730 through 731 Processing sheet with id=AK9, first strand: chain 'I' and resid 773 through 775 removed outlier: 6.252A pdb=" N ILE I 773 " --> pdb=" O LEU I 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'J' and resid 133 through 138 Processing sheet with id=AL2, first strand: chain 'J' and resid 195 through 196 Processing sheet with id=AL3, first strand: chain 'J' and resid 238 through 240 Processing sheet with id=AL4, first strand: chain 'J' and resid 270 through 271 removed outlier: 7.053A pdb=" N ARG J 304 " --> pdb=" O TYR J 858 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 291 through 295 Processing sheet with id=AL6, first strand: chain 'J' and resid 488 through 492 Processing sheet with id=AL7, first strand: chain 'J' and resid 730 through 731 removed outlier: 3.516A pdb=" N GLY J 709 " --> pdb=" O TYR J 833 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY J 709 " --> pdb=" O GLY J 768 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY J 768 " --> pdb=" O GLY J 709 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE J 711 " --> pdb=" O LEU J 766 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU J 766 " --> pdb=" O ILE J 711 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 720 through 721 removed outlier: 3.888A pdb=" N GLU J 720 " --> pdb=" O VAL J 728 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 728 " --> pdb=" O GLU J 720 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'J' and resid 773 through 774 removed outlier: 6.369A pdb=" N ILE J 773 " --> pdb=" O LEU J 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL9 Processing sheet with id=AM1, first strand: chain 'P' and resid 22 through 28 removed outlier: 6.946A pdb=" N VAL P 22 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER P 76 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE P 24 " --> pdb=" O ILE P 74 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE P 74 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE P 26 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 257 through 260 removed outlier: 4.392A pdb=" N ASN P 258 " --> pdb=" O LYS P 274 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS P 274 " --> pdb=" O ASN P 258 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 450 through 452 Processing sheet with id=AM4, first strand: chain 'P' and resid 621 through 628 removed outlier: 6.025A pdb=" N THR P 623 " --> pdb=" O GLN P 638 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN P 638 " --> pdb=" O THR P 623 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE P 625 " --> pdb=" O VAL P 636 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU P 669 " --> pdb=" O TYR P 518 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'P' and resid 675 through 676 removed outlier: 3.568A pdb=" N ILE P 675 " --> pdb=" O ILE P 682 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE P 682 " --> pdb=" O ILE P 675 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR P 681 " --> pdb=" O PHE P 688 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'P' and resid 888 through 889 removed outlier: 3.722A pdb=" N ASN P 888 " --> pdb=" O SER P1053 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ARG P1019 " --> pdb=" O ILE P1052 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU P1054 " --> pdb=" O ARG P1019 " (cutoff:3.500A) 3182 hydrogen bonds defined for protein. 8994 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: 70.79 Time building geometry restraints manager: 97.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 74406 1.02 - 1.22: 133 1.22 - 1.42: 31235 1.42 - 1.62: 43401 1.62 - 1.82: 742 Bond restraints: 149917 Sorted by residual: bond pdb=" CA ILE B 601 " pdb=" C ILE B 601 " ideal model delta sigma weight residual 1.522 1.449 0.074 7.10e-03 1.98e+04 1.08e+02 bond pdb=" CG1 ILE E 334 " pdb=" CD1 ILE E 334 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.30e+01 bond pdb=" CB PRO C 665 " pdb=" CG PRO C 665 " ideal model delta sigma weight residual 1.492 1.314 0.178 5.00e-02 4.00e+02 1.27e+01 bond pdb=" CA PRO P 439 " pdb=" C PRO P 439 " ideal model delta sigma weight residual 1.517 1.537 -0.020 6.70e-03 2.23e+04 9.09e+00 bond pdb=" C ILE B 601 " pdb=" O ILE B 601 " ideal model delta sigma weight residual 1.232 1.258 -0.025 8.90e-03 1.26e+04 8.03e+00 ... (remaining 149912 not shown) Histogram of bond angle deviations from ideal: 94.04 - 102.06: 395 102.06 - 110.08: 125488 110.08 - 118.10: 75889 118.10 - 126.12: 67544 126.12 - 134.14: 1646 Bond angle restraints: 270962 Sorted by residual: angle pdb=" N VAL E 664 " pdb=" CA VAL E 664 " pdb=" C VAL E 664 " ideal model delta sigma weight residual 108.05 101.50 6.55 1.18e+00 7.18e-01 3.08e+01 angle pdb=" C ALA H 143 " pdb=" N ASN H 144 " pdb=" CA ASN H 144 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N ILE P1026 " pdb=" CA ILE P1026 " pdb=" C ILE P1026 " ideal model delta sigma weight residual 108.88 97.73 11.15 2.16e+00 2.14e-01 2.66e+01 angle pdb=" C ALA G 143 " pdb=" N ASN G 144 " pdb=" CA ASN G 144 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" C ILE A 712 " ideal model delta sigma weight residual 106.61 98.18 8.43 1.78e+00 3.16e-01 2.25e+01 ... (remaining 270957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 64383 16.97 - 33.94: 4723 33.94 - 50.92: 956 50.92 - 67.89: 207 67.89 - 84.86: 31 Dihedral angle restraints: 70300 sinusoidal: 38863 harmonic: 31437 Sorted by residual: dihedral pdb=" CA LYS P 941 " pdb=" C LYS P 941 " pdb=" N PRO P 942 " pdb=" CA PRO P 942 " ideal model delta harmonic sigma weight residual -180.00 -120.13 -59.87 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA ILE D 102 " pdb=" C ILE D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta harmonic sigma weight residual -180.00 -120.85 -59.15 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU F 106 " pdb=" C GLU F 106 " pdb=" N PRO F 107 " pdb=" CA PRO F 107 " ideal model delta harmonic sigma weight residual -180.00 -128.69 -51.31 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 70297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 7833 0.060 - 0.120: 3072 0.120 - 0.180: 699 0.180 - 0.240: 108 0.240 - 0.301: 10 Chirality restraints: 11722 Sorted by residual: chirality pdb=" CA GLN E 368 " pdb=" N GLN E 368 " pdb=" C GLN E 368 " pdb=" CB GLN E 368 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE A 132 " pdb=" CA ILE A 132 " pdb=" CG1 ILE A 132 " pdb=" CG2 ILE A 132 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB THR I 748 " pdb=" CA THR I 748 " pdb=" OG1 THR I 748 " pdb=" CG2 THR I 748 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 11719 not shown) Planarity restraints: 21987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU J 650 " 0.036 2.00e-02 2.50e+03 7.09e-02 5.03e+01 pdb=" C GLU J 650 " -0.123 2.00e-02 2.50e+03 pdb=" O GLU J 650 " 0.045 2.00e-02 2.50e+03 pdb=" N ASP J 651 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 685 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C ARG H 685 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG H 685 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU H 686 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 685 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ARG I 685 " -0.081 2.00e-02 2.50e+03 pdb=" O ARG I 685 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU I 686 " 0.028 2.00e-02 2.50e+03 ... (remaining 21984 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 24634 2.29 - 2.86: 341333 2.86 - 3.44: 382074 3.44 - 4.02: 521800 4.02 - 4.60: 809840 Nonbonded interactions: 2079681 Sorted by model distance: nonbonded pdb=" OD1 ASP F 166 " pdb=" H ALA F 769 " model vdw 1.708 1.850 nonbonded pdb="HH12 ARG B 882 " pdb=" O THR F 527 " model vdw 1.718 1.850 nonbonded pdb=" H SER J 379 " pdb=" OE2 GLU P 358 " model vdw 1.721 1.850 nonbonded pdb=" O LEU H 818 " pdb=" HE1 TRP H 824 " model vdw 1.723 1.850 nonbonded pdb=" O LEU F 818 " pdb=" HE1 TRP F 824 " model vdw 1.725 1.850 ... (remaining 2079676 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' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'B' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = chain 'C' selection = (chain 'D' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'E' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'F' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'G' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'H' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'I' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'J' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) } 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.620 Extract box with map and model: 11.000 Check model and map are aligned: 1.590 Set scattering table: 0.990 Process input model: 370.270 Find NCS groups from input model: 6.960 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 397.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.010 0.178 75455 Z= 0.641 Angle : 1.286 13.954 102320 Z= 0.723 Chirality : 0.065 0.301 11722 Planarity : 0.008 0.109 13254 Dihedral : 10.209 82.675 28629 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 0.01 % Allowed : 1.33 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -3.41 (0.08), residues: 9050 helix: -1.67 (0.07), residues: 4157 sheet: -3.02 (0.14), residues: 862 loop : -2.66 (0.09), residues: 4031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP P1067 HIS 0.027 0.004 HIS I 266 PHE 0.063 0.005 PHE B 373 TYR 0.050 0.005 TYR C 670 ARG 0.021 0.002 ARG F 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 3964 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3963 time to evaluate : 8.350 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8802 (tt0) cc_final: 0.8353 (tm-30) REVERT: A 266 HIS cc_start: 0.7853 (m90) cc_final: 0.7364 (m90) REVERT: A 326 ASP cc_start: 0.8199 (t70) cc_final: 0.7972 (t0) REVERT: A 418 LEU cc_start: 0.8893 (mt) cc_final: 0.8672 (mt) REVERT: A 518 MET cc_start: 0.6866 (mtt) cc_final: 0.6438 (tpp) REVERT: A 565 MET cc_start: 0.8303 (ttm) cc_final: 0.7989 (ttm) REVERT: A 579 THR cc_start: 0.8952 (m) cc_final: 0.8479 (p) REVERT: A 649 VAL cc_start: 0.7615 (t) cc_final: 0.7298 (t) REVERT: A 654 LYS cc_start: 0.8943 (mttt) cc_final: 0.8437 (mtpt) REVERT: A 670 TYR cc_start: 0.8244 (m-10) cc_final: 0.7963 (m-80) REVERT: A 690 ASN cc_start: 0.8503 (m-40) cc_final: 0.7988 (m110) REVERT: A 740 ILE cc_start: 0.7788 (mt) cc_final: 0.7234 (mm) REVERT: A 751 TYR cc_start: 0.7830 (m-80) cc_final: 0.7393 (m-80) REVERT: A 761 ASN cc_start: 0.7926 (m-40) cc_final: 0.6521 (p0) REVERT: A 777 SER cc_start: 0.8151 (t) cc_final: 0.7899 (p) REVERT: A 858 TYR cc_start: 0.7945 (m-80) cc_final: 0.7558 (m-80) REVERT: A 868 ASP cc_start: 0.6934 (t70) cc_final: 0.6573 (t70) REVERT: B 154 TYR cc_start: 0.7428 (m-80) cc_final: 0.7065 (m-80) REVERT: B 177 TYR cc_start: 0.8428 (t80) cc_final: 0.8097 (t80) REVERT: B 178 ASP cc_start: 0.8160 (t0) cc_final: 0.7438 (t0) REVERT: B 182 THR cc_start: 0.8431 (m) cc_final: 0.8216 (p) REVERT: B 227 VAL cc_start: 0.8658 (m) cc_final: 0.8440 (p) REVERT: B 255 ILE cc_start: 0.8324 (mp) cc_final: 0.7936 (tt) REVERT: B 261 GLU cc_start: 0.7695 (tp30) cc_final: 0.7304 (tp30) REVERT: B 266 HIS cc_start: 0.8992 (m90) cc_final: 0.8498 (m170) REVERT: B 267 GLN cc_start: 0.8062 (pt0) cc_final: 0.6711 (pm20) REVERT: B 467 GLU cc_start: 0.7996 (tt0) cc_final: 0.7380 (tt0) REVERT: B 472 ASN cc_start: 0.8640 (t0) cc_final: 0.8404 (t0) REVERT: B 497 ASN cc_start: 0.7930 (m110) cc_final: 0.7662 (m-40) REVERT: B 514 MET cc_start: 0.8203 (mmp) cc_final: 0.7667 (tpp) REVERT: B 519 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8928 (mm-40) REVERT: B 527 THR cc_start: 0.7577 (m) cc_final: 0.6899 (m) REVERT: B 530 VAL cc_start: 0.9025 (t) cc_final: 0.8726 (t) REVERT: B 531 ASP cc_start: 0.6696 (p0) cc_final: 0.5615 (t0) REVERT: B 550 LEU cc_start: 0.9353 (mt) cc_final: 0.8955 (mt) REVERT: B 561 TYR cc_start: 0.8672 (t80) cc_final: 0.8009 (t80) REVERT: B 583 LEU cc_start: 0.8662 (tp) cc_final: 0.8351 (tp) REVERT: B 592 CYS cc_start: 0.6694 (m) cc_final: 0.6278 (t) REVERT: B 625 ILE cc_start: 0.8729 (mt) cc_final: 0.8190 (mt) REVERT: B 629 VAL cc_start: 0.8401 (t) cc_final: 0.7975 (p) REVERT: B 637 ARG cc_start: 0.8529 (mtp180) cc_final: 0.7951 (mtm-85) REVERT: B 688 ILE cc_start: 0.8771 (mm) cc_final: 0.8535 (mm) REVERT: B 712 ILE cc_start: 0.8422 (mt) cc_final: 0.8181 (mt) REVERT: B 724 MET cc_start: 0.7337 (pmm) cc_final: 0.7068 (pmm) REVERT: B 744 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 846 MET cc_start: 0.8458 (tmt) cc_final: 0.7901 (tmt) REVERT: C 130 PHE cc_start: 0.8917 (t80) cc_final: 0.8209 (t80) REVERT: C 151 ASN cc_start: 0.7711 (m-40) cc_final: 0.7182 (m110) REVERT: C 166 ASP cc_start: 0.7733 (m-30) cc_final: 0.7346 (m-30) REVERT: C 183 GLU cc_start: 0.8304 (tt0) cc_final: 0.8075 (tt0) REVERT: C 191 LYS cc_start: 0.8332 (pttp) cc_final: 0.7703 (tptt) REVERT: C 208 ASP cc_start: 0.8544 (t0) cc_final: 0.7377 (t0) REVERT: C 209 SER cc_start: 0.8576 (m) cc_final: 0.8045 (t) REVERT: C 211 THR cc_start: 0.8719 (m) cc_final: 0.8419 (m) REVERT: C 240 GLN cc_start: 0.7068 (pt0) cc_final: 0.6624 (pt0) REVERT: C 256 ASP cc_start: 0.8139 (m-30) cc_final: 0.7581 (m-30) REVERT: C 268 LEU cc_start: 0.7623 (pp) cc_final: 0.7234 (pp) REVERT: C 309 ASN cc_start: 0.8216 (t0) cc_final: 0.7724 (t0) REVERT: C 317 LEU cc_start: 0.9204 (mt) cc_final: 0.8984 (mp) REVERT: C 359 ASP cc_start: 0.7974 (m-30) cc_final: 0.7625 (m-30) REVERT: C 423 ASN cc_start: 0.8559 (m110) cc_final: 0.8212 (p0) REVERT: C 490 VAL cc_start: 0.7939 (p) cc_final: 0.7717 (p) REVERT: C 491 VAL cc_start: 0.8420 (t) cc_final: 0.7993 (p) REVERT: C 556 LEU cc_start: 0.8846 (tt) cc_final: 0.8610 (tt) REVERT: C 639 ASN cc_start: 0.8691 (t0) cc_final: 0.8108 (t0) REVERT: C 641 TYR cc_start: 0.8007 (p90) cc_final: 0.7793 (p90) REVERT: C 683 ILE cc_start: 0.9115 (mm) cc_final: 0.8630 (tp) REVERT: C 687 ASP cc_start: 0.8817 (m-30) cc_final: 0.8261 (m-30) REVERT: C 696 MET cc_start: 0.9096 (ptm) cc_final: 0.8229 (ppp) REVERT: C 697 GLU cc_start: 0.7909 (pm20) cc_final: 0.7640 (pm20) REVERT: C 722 ASP cc_start: 0.7179 (m-30) cc_final: 0.4656 (m-30) REVERT: C 776 SER cc_start: 0.8794 (m) cc_final: 0.7864 (t) REVERT: C 873 ILE cc_start: 0.7406 (tp) cc_final: 0.7004 (tp) REVERT: C 874 ASN cc_start: 0.7589 (m110) cc_final: 0.6930 (t0) REVERT: C 884 MET cc_start: 0.8221 (mtp) cc_final: 0.7979 (mtp) REVERT: D 91 LYS cc_start: 0.8610 (mttt) cc_final: 0.8359 (mttm) REVERT: D 148 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7276 (tp30) REVERT: D 162 LEU cc_start: 0.8500 (mp) cc_final: 0.8099 (tp) REVERT: D 191 LYS cc_start: 0.8620 (pttp) cc_final: 0.8260 (pttm) REVERT: D 201 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8092 (ttm170) REVERT: D 393 MET cc_start: 0.7934 (mtm) cc_final: 0.6996 (mtp) REVERT: D 484 ASN cc_start: 0.8702 (m-40) cc_final: 0.7656 (t0) REVERT: D 556 LEU cc_start: 0.7923 (tt) cc_final: 0.7692 (mm) REVERT: D 561 TYR cc_start: 0.7838 (t80) cc_final: 0.7579 (t80) REVERT: D 586 THR cc_start: 0.8971 (p) cc_final: 0.8650 (p) REVERT: D 588 VAL cc_start: 0.9245 (t) cc_final: 0.8902 (t) REVERT: D 616 ASN cc_start: 0.9012 (m-40) cc_final: 0.8673 (m110) REVERT: D 646 LYS cc_start: 0.8214 (tttt) cc_final: 0.7893 (ttmt) REVERT: D 661 ILE cc_start: 0.7563 (mp) cc_final: 0.6211 (pt) REVERT: D 727 TYR cc_start: 0.8379 (m-80) cc_final: 0.8008 (m-80) REVERT: D 775 ASP cc_start: 0.7010 (t0) cc_final: 0.5195 (m-30) REVERT: D 795 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7152 (tppt) REVERT: D 854 THR cc_start: 0.5949 (m) cc_final: 0.5699 (m) REVERT: D 861 LEU cc_start: 0.8258 (tp) cc_final: 0.8049 (tt) REVERT: E 102 ILE cc_start: 0.7166 (pt) cc_final: 0.6956 (tp) REVERT: E 116 GLU cc_start: 0.8710 (pt0) cc_final: 0.8416 (tt0) REVERT: E 215 CYS cc_start: 0.8931 (m) cc_final: 0.8692 (p) REVERT: E 256 ASP cc_start: 0.8798 (m-30) cc_final: 0.8496 (m-30) REVERT: E 275 ASP cc_start: 0.8537 (m-30) cc_final: 0.8252 (m-30) REVERT: E 378 ASN cc_start: 0.7972 (p0) cc_final: 0.7475 (m-40) REVERT: E 389 LEU cc_start: 0.9099 (mt) cc_final: 0.8764 (mt) REVERT: E 435 GLN cc_start: 0.8614 (mt0) cc_final: 0.8148 (mt0) REVERT: E 450 GLN cc_start: 0.7587 (mp-120) cc_final: 0.7112 (pm20) REVERT: E 468 GLN cc_start: 0.7991 (pt0) cc_final: 0.7695 (tt0) REVERT: E 473 PHE cc_start: 0.7837 (t80) cc_final: 0.7498 (t80) REVERT: E 508 HIS cc_start: 0.8156 (m-70) cc_final: 0.7861 (m90) REVERT: E 514 MET cc_start: 0.8909 (mmp) cc_final: 0.8459 (tpt) REVERT: E 532 TYR cc_start: 0.8489 (t80) cc_final: 0.6417 (t80) REVERT: E 542 LEU cc_start: 0.9258 (mt) cc_final: 0.9040 (mt) REVERT: E 574 HIS cc_start: 0.6928 (t70) cc_final: 0.6646 (t70) REVERT: E 621 TYR cc_start: 0.7979 (t80) cc_final: 0.7668 (t80) REVERT: E 666 ASP cc_start: 0.7251 (m-30) cc_final: 0.6300 (m-30) REVERT: E 710 VAL cc_start: 0.9201 (p) cc_final: 0.8998 (m) REVERT: E 748 THR cc_start: 0.8173 (m) cc_final: 0.7685 (p) REVERT: E 751 TYR cc_start: 0.7439 (m-80) cc_final: 0.7021 (m-10) REVERT: E 803 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8608 (mtpt) REVERT: E 821 ASN cc_start: 0.8528 (m-40) cc_final: 0.8229 (t0) REVERT: E 842 PHE cc_start: 0.9159 (t80) cc_final: 0.8827 (t80) REVERT: E 846 MET cc_start: 0.8349 (tmt) cc_final: 0.8030 (tmm) REVERT: E 862 LEU cc_start: 0.9174 (mt) cc_final: 0.8870 (mt) REVERT: E 868 ASP cc_start: 0.7963 (t70) cc_final: 0.7668 (p0) REVERT: F 198 LYS cc_start: 0.8421 (mppt) cc_final: 0.7999 (mmtm) REVERT: F 234 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7839 (mt-10) REVERT: F 235 MET cc_start: 0.8524 (mtm) cc_final: 0.8175 (mtm) REVERT: F 256 ASP cc_start: 0.8181 (m-30) cc_final: 0.7596 (m-30) REVERT: F 262 TYR cc_start: 0.6612 (t80) cc_final: 0.6090 (t80) REVERT: F 291 TYR cc_start: 0.8583 (m-80) cc_final: 0.8258 (m-80) REVERT: F 385 CYS cc_start: 0.7564 (t) cc_final: 0.7298 (t) REVERT: F 406 THR cc_start: 0.8336 (p) cc_final: 0.7175 (p) REVERT: F 525 PHE cc_start: 0.8346 (m-80) cc_final: 0.7869 (m-80) REVERT: F 563 THR cc_start: 0.9336 (p) cc_final: 0.9131 (t) REVERT: F 564 LEU cc_start: 0.9182 (mt) cc_final: 0.8936 (mm) REVERT: F 581 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7165 (tp30) REVERT: F 607 LEU cc_start: 0.9282 (mt) cc_final: 0.8881 (mt) REVERT: F 611 TYR cc_start: 0.8006 (t80) cc_final: 0.7801 (t80) REVERT: F 621 TYR cc_start: 0.7973 (t80) cc_final: 0.7686 (t80) REVERT: F 636 ASN cc_start: 0.8924 (m-40) cc_final: 0.8661 (t0) REVERT: F 645 MET cc_start: 0.7781 (mtp) cc_final: 0.7365 (mmm) REVERT: F 687 ASP cc_start: 0.8496 (m-30) cc_final: 0.7866 (m-30) REVERT: F 734 LEU cc_start: 0.7966 (tp) cc_final: 0.7574 (tp) REVERT: F 761 ASN cc_start: 0.8844 (m-40) cc_final: 0.7865 (t0) REVERT: F 843 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7855 (mmm160) REVERT: G 104 THR cc_start: 0.8562 (m) cc_final: 0.8164 (t) REVERT: G 119 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8327 (ptpt) REVERT: G 153 TRP cc_start: 0.8520 (m100) cc_final: 0.7963 (m100) REVERT: G 154 TYR cc_start: 0.5088 (m-80) cc_final: 0.4751 (m-80) REVERT: G 179 GLN cc_start: 0.8334 (pt0) cc_final: 0.7914 (tm-30) REVERT: G 256 ASP cc_start: 0.8748 (m-30) cc_final: 0.8417 (m-30) REVERT: G 326 ASP cc_start: 0.9154 (t0) cc_final: 0.8829 (t0) REVERT: G 333 TYR cc_start: 0.8402 (t80) cc_final: 0.7263 (t80) REVERT: G 346 LEU cc_start: 0.7853 (mt) cc_final: 0.7545 (mp) REVERT: G 355 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7703 (tttp) REVERT: G 359 ASP cc_start: 0.6201 (m-30) cc_final: 0.5901 (m-30) REVERT: G 388 THR cc_start: 0.8840 (m) cc_final: 0.8552 (m) REVERT: G 389 LEU cc_start: 0.9584 (mt) cc_final: 0.9382 (mm) REVERT: G 432 VAL cc_start: 0.8483 (t) cc_final: 0.8218 (p) REVERT: G 491 VAL cc_start: 0.8908 (t) cc_final: 0.8673 (p) REVERT: G 582 LYS cc_start: 0.8434 (mmmm) cc_final: 0.7876 (mmtt) REVERT: G 621 TYR cc_start: 0.8664 (t80) cc_final: 0.8312 (t80) REVERT: G 625 ILE cc_start: 0.8842 (mt) cc_final: 0.8300 (tt) REVERT: G 681 VAL cc_start: 0.8076 (t) cc_final: 0.7869 (p) REVERT: G 683 ILE cc_start: 0.8973 (mp) cc_final: 0.8749 (mt) REVERT: G 687 ASP cc_start: 0.8766 (m-30) cc_final: 0.8401 (m-30) REVERT: G 711 ILE cc_start: 0.8921 (mt) cc_final: 0.8627 (mt) REVERT: G 770 LEU cc_start: 0.9030 (pp) cc_final: 0.8536 (tt) REVERT: G 830 THR cc_start: 0.8622 (m) cc_final: 0.8325 (p) REVERT: H 112 LEU cc_start: 0.8494 (tp) cc_final: 0.8122 (tt) REVERT: H 134 GLU cc_start: 0.7644 (pt0) cc_final: 0.7339 (tt0) REVERT: H 140 VAL cc_start: 0.8140 (m) cc_final: 0.7125 (m) REVERT: H 182 THR cc_start: 0.8364 (m) cc_final: 0.8095 (m) REVERT: H 197 ASN cc_start: 0.7633 (t0) cc_final: 0.6958 (t0) REVERT: H 199 ASN cc_start: 0.8709 (m-40) cc_final: 0.8490 (p0) REVERT: H 265 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8308 (mt0) REVERT: H 275 ASP cc_start: 0.9137 (p0) cc_final: 0.7573 (t70) REVERT: H 276 ILE cc_start: 0.8984 (mt) cc_final: 0.8271 (mt) REVERT: H 277 ILE cc_start: 0.9163 (mt) cc_final: 0.8739 (mm) REVERT: H 328 ILE cc_start: 0.9411 (mt) cc_final: 0.9126 (tt) REVERT: H 347 VAL cc_start: 0.7830 (t) cc_final: 0.7418 (t) REVERT: H 350 GLU cc_start: 0.6773 (pm20) cc_final: 0.6384 (pt0) REVERT: H 389 LEU cc_start: 0.9226 (mt) cc_final: 0.8726 (mm) REVERT: H 429 GLU cc_start: 0.8814 (mp0) cc_final: 0.8604 (mp0) REVERT: H 453 HIS cc_start: 0.7986 (m-70) cc_final: 0.7773 (m90) REVERT: H 480 HIS cc_start: 0.8540 (t70) cc_final: 0.8236 (t-170) REVERT: H 498 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7628 (mm-40) REVERT: H 525 PHE cc_start: 0.8551 (m-80) cc_final: 0.8148 (m-80) REVERT: H 531 ASP cc_start: 0.7366 (p0) cc_final: 0.6497 (m-30) REVERT: H 541 LEU cc_start: 0.8323 (mt) cc_final: 0.7881 (mt) REVERT: H 560 ASN cc_start: 0.8879 (m-40) cc_final: 0.8253 (m110) REVERT: H 581 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6767 (mm-30) REVERT: H 621 TYR cc_start: 0.8297 (t80) cc_final: 0.7719 (t80) REVERT: H 729 ASN cc_start: 0.7503 (p0) cc_final: 0.6935 (p0) REVERT: H 759 LEU cc_start: 0.8458 (mt) cc_final: 0.8172 (tp) REVERT: H 818 LEU cc_start: 0.9285 (mt) cc_final: 0.9027 (mm) REVERT: H 852 ASN cc_start: 0.7448 (m110) cc_final: 0.7244 (m110) REVERT: I 100 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8425 (tptp) REVERT: I 130 PHE cc_start: 0.8333 (t80) cc_final: 0.8048 (t80) REVERT: I 132 ILE cc_start: 0.8563 (mm) cc_final: 0.8283 (mm) REVERT: I 142 ARG cc_start: 0.7253 (ptp90) cc_final: 0.6632 (ptm-80) REVERT: I 154 TYR cc_start: 0.6249 (m-80) cc_final: 0.5706 (m-80) REVERT: I 167 TYR cc_start: 0.6541 (t80) cc_final: 0.5917 (t80) REVERT: I 270 GLU cc_start: 0.5975 (mt-10) cc_final: 0.4127 (mt-10) REVERT: I 302 THR cc_start: 0.8674 (p) cc_final: 0.8419 (t) REVERT: I 389 LEU cc_start: 0.8107 (mt) cc_final: 0.7579 (mt) REVERT: I 423 ASN cc_start: 0.8980 (m-40) cc_final: 0.8375 (t0) REVERT: I 470 ILE cc_start: 0.9509 (mm) cc_final: 0.9159 (mm) REVERT: I 519 GLN cc_start: 0.7730 (tp40) cc_final: 0.7403 (tp40) REVERT: I 589 THR cc_start: 0.9225 (m) cc_final: 0.8996 (p) REVERT: I 591 LEU cc_start: 0.9117 (tp) cc_final: 0.8746 (mt) REVERT: I 655 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7129 (mmp80) REVERT: I 666 ASP cc_start: 0.7505 (m-30) cc_final: 0.7155 (m-30) REVERT: I 824 TRP cc_start: 0.5769 (p-90) cc_final: 0.3228 (t60) REVERT: J 140 VAL cc_start: 0.7882 (m) cc_final: 0.7520 (m) REVERT: J 150 ARG cc_start: 0.7308 (ptt180) cc_final: 0.4927 (mtt90) REVERT: J 208 ASP cc_start: 0.8123 (t70) cc_final: 0.7545 (t70) REVERT: J 232 ILE cc_start: 0.8984 (mt) cc_final: 0.8444 (tp) REVERT: J 309 ASN cc_start: 0.8749 (t0) cc_final: 0.8235 (t0) REVERT: J 398 THR cc_start: 0.8859 (m) cc_final: 0.8632 (p) REVERT: J 429 GLU cc_start: 0.9112 (mp0) cc_final: 0.8853 (mp0) REVERT: J 458 ASP cc_start: 0.7818 (t0) cc_final: 0.6653 (m-30) REVERT: J 484 ASN cc_start: 0.8760 (m-40) cc_final: 0.8385 (m-40) REVERT: J 495 VAL cc_start: 0.7465 (m) cc_final: 0.7072 (m) REVERT: J 498 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7848 (mm110) REVERT: J 567 CYS cc_start: 0.8860 (m) cc_final: 0.8457 (m) REVERT: J 571 ASN cc_start: 0.8474 (m-40) cc_final: 0.8192 (m-40) REVERT: J 573 GLN cc_start: 0.7257 (mt0) cc_final: 0.6913 (mt0) REVERT: J 607 LEU cc_start: 0.9267 (mt) cc_final: 0.8821 (tp) REVERT: J 667 ASP cc_start: 0.7723 (p0) cc_final: 0.7337 (p0) REVERT: J 693 LEU cc_start: 0.8886 (mp) cc_final: 0.8355 (mt) REVERT: J 694 MET cc_start: 0.7475 (ptm) cc_final: 0.6821 (ttp) REVERT: J 723 GLU cc_start: 0.6827 (tp30) cc_final: 0.6331 (tp30) REVERT: J 817 TYR cc_start: 0.8255 (p90) cc_final: 0.7490 (m-10) REVERT: J 833 TYR cc_start: 0.7912 (t80) cc_final: 0.6374 (t80) REVERT: P 40 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7448 (mm-30) REVERT: P 61 GLU cc_start: 0.6747 (tt0) cc_final: 0.6200 (mp0) REVERT: P 213 MET cc_start: 0.6691 (mtm) cc_final: 0.6300 (mtm) REVERT: P 215 MET cc_start: 0.8320 (mmp) cc_final: 0.7131 (tpp) REVERT: P 228 GLU cc_start: 0.7606 (tt0) cc_final: 0.6635 (tp30) REVERT: P 308 GLN cc_start: 0.8322 (tt0) cc_final: 0.7989 (tm-30) REVERT: P 468 GLU cc_start: 0.7335 (mp0) cc_final: 0.6596 (mp0) REVERT: P 518 TYR cc_start: 0.6923 (p90) cc_final: 0.6401 (p90) REVERT: P 619 TYR cc_start: 0.7903 (m-80) cc_final: 0.7559 (m-80) REVERT: P 676 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5140 (tm-30) REVERT: P 703 GLN cc_start: 0.5364 (mm110) cc_final: 0.5133 (mm110) REVERT: P 854 ILE cc_start: 0.8859 (mm) cc_final: 0.8427 (tp) REVERT: P 1051 TRP cc_start: 0.8065 (m100) cc_final: 0.7654 (m100) outliers start: 1 outliers final: 0 residues processed: 3964 average time/residue: 1.8542 time to fit residues: 12050.0035 Evaluate side-chains 2695 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2695 time to evaluate : 8.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 4.9990 chunk 685 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 462 optimal weight: 0.9990 chunk 366 optimal weight: 0.9980 chunk 708 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 430 optimal weight: 0.9980 chunk 527 optimal weight: 3.9990 chunk 820 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN A 574 HIS A 821 ASN A 880 ASN B 260 ASN B 549 GLN B 605 GLN ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN C 352 GLN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 GLN C 839 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 450 GLN D 468 GLN D 549 GLN D 560 ASN D 639 ASN D 668 GLN D 690 ASN ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 HIS E 760 ASN E 762 GLN E 839 GLN E 880 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS F 274 ASN F 480 HIS F 503 ASN F 508 HIS F 519 GLN F 753 GLN G 90 GLN G 361 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 GLN G 835 GLN H 266 HIS H 460 GLN I 94 GLN I 99 GLN I 266 HIS I 298 ASN I 312 GLN I 423 ASN I 480 HIS ** I 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 739 GLN J 287 ASN ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 GLN ** P 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 430 ASN ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 818 GLN P 897 GLN P 908 GLN P 920 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 75455 Z= 0.186 Angle : 0.608 8.059 102320 Z= 0.328 Chirality : 0.041 0.174 11722 Planarity : 0.005 0.094 13254 Dihedral : 6.004 76.829 9999 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.44 % Favored : 93.54 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -2.20 (0.08), residues: 9050 helix: -0.50 (0.08), residues: 4304 sheet: -2.45 (0.16), residues: 793 loop : -2.31 (0.09), residues: 3953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 478 HIS 0.014 0.001 HIS I 266 PHE 0.028 0.002 PHE I 231 TYR 0.029 0.002 TYR I 621 ARG 0.009 0.001 ARG G 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 3047 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3042 time to evaluate : 8.722 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8710 (tt0) cc_final: 0.8433 (tm-30) REVERT: A 297 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.6415 (mmt-90) REVERT: A 693 LEU cc_start: 0.9115 (mt) cc_final: 0.8365 (mt) REVERT: A 751 TYR cc_start: 0.8118 (m-80) cc_final: 0.7752 (m-80) REVERT: A 754 ILE cc_start: 0.9165 (tp) cc_final: 0.8920 (mt) REVERT: A 761 ASN cc_start: 0.8135 (m-40) cc_final: 0.6576 (p0) REVERT: A 777 SER cc_start: 0.8303 (t) cc_final: 0.8017 (p) REVERT: A 822 TYR cc_start: 0.4897 (m-80) cc_final: 0.4552 (m-10) REVERT: A 868 ASP cc_start: 0.6558 (t70) cc_final: 0.6118 (t70) REVERT: B 146 GLU cc_start: 0.7304 (pt0) cc_final: 0.7024 (pt0) REVERT: B 177 TYR cc_start: 0.8295 (t80) cc_final: 0.8022 (t80) REVERT: B 178 ASP cc_start: 0.8375 (t0) cc_final: 0.7729 (t0) REVERT: B 256 ASP cc_start: 0.8720 (m-30) cc_final: 0.8421 (m-30) REVERT: B 266 HIS cc_start: 0.8980 (m90) cc_final: 0.8451 (m90) REVERT: B 346 LEU cc_start: 0.7053 (mt) cc_final: 0.6818 (mp) REVERT: B 427 ILE cc_start: 0.9063 (tt) cc_final: 0.8741 (tt) REVERT: B 467 GLU cc_start: 0.7826 (tt0) cc_final: 0.7622 (tt0) REVERT: B 472 ASN cc_start: 0.8673 (t0) cc_final: 0.8449 (t0) REVERT: B 531 ASP cc_start: 0.6282 (p0) cc_final: 0.5519 (t0) REVERT: B 550 LEU cc_start: 0.9295 (mt) cc_final: 0.8919 (mt) REVERT: B 561 TYR cc_start: 0.8599 (t80) cc_final: 0.7836 (t80) REVERT: B 572 MET cc_start: 0.8830 (ptm) cc_final: 0.8619 (ptm) REVERT: B 576 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7561 (mm-40) REVERT: B 592 CYS cc_start: 0.6708 (m) cc_final: 0.6241 (t) REVERT: B 724 MET cc_start: 0.7820 (pmm) cc_final: 0.7474 (pmm) REVERT: B 730 ILE cc_start: 0.8386 (tt) cc_final: 0.7740 (tt) REVERT: B 821 ASN cc_start: 0.7909 (m-40) cc_final: 0.7681 (m-40) REVERT: B 840 PHE cc_start: 0.7377 (t80) cc_final: 0.7121 (t80) REVERT: C 173 PHE cc_start: 0.8174 (m-80) cc_final: 0.7820 (m-80) REVERT: C 179 GLN cc_start: 0.8274 (mt0) cc_final: 0.8001 (mt0) REVERT: C 189 LEU cc_start: 0.7727 (mm) cc_final: 0.7100 (mm) REVERT: C 191 LYS cc_start: 0.8509 (pttp) cc_final: 0.7738 (tptt) REVERT: C 193 MET cc_start: 0.8097 (ptp) cc_final: 0.7838 (mtt) REVERT: C 211 THR cc_start: 0.8843 (m) cc_final: 0.8367 (m) REVERT: C 223 GLU cc_start: 0.8005 (pm20) cc_final: 0.7705 (pm20) REVERT: C 227 VAL cc_start: 0.8890 (m) cc_final: 0.8643 (p) REVERT: C 228 VAL cc_start: 0.8999 (m) cc_final: 0.8517 (p) REVERT: C 235 MET cc_start: 0.8490 (ppp) cc_final: 0.8021 (ppp) REVERT: C 256 ASP cc_start: 0.7971 (m-30) cc_final: 0.7519 (m-30) REVERT: C 355 LYS cc_start: 0.7227 (ttpt) cc_final: 0.6623 (ttpp) REVERT: C 434 CYS cc_start: 0.8676 (t) cc_final: 0.8293 (t) REVERT: C 519 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8487 (mm-40) REVERT: C 561 TYR cc_start: 0.7966 (t80) cc_final: 0.7703 (t80) REVERT: C 610 TYR cc_start: 0.7986 (t80) cc_final: 0.7721 (t80) REVERT: C 639 ASN cc_start: 0.8632 (t0) cc_final: 0.7763 (t0) REVERT: C 641 TYR cc_start: 0.8376 (p90) cc_final: 0.7781 (p90) REVERT: C 642 GLN cc_start: 0.8656 (mt0) cc_final: 0.7803 (tm-30) REVERT: C 683 ILE cc_start: 0.9159 (mm) cc_final: 0.8659 (tp) REVERT: C 687 ASP cc_start: 0.8856 (m-30) cc_final: 0.8464 (m-30) REVERT: C 696 MET cc_start: 0.8986 (ptm) cc_final: 0.8223 (ppp) REVERT: C 697 GLU cc_start: 0.8314 (pm20) cc_final: 0.7307 (pm20) REVERT: C 701 ARG cc_start: 0.8603 (mmt180) cc_final: 0.8375 (mmt180) REVERT: C 715 ARG cc_start: 0.6492 (ttp-170) cc_final: 0.6172 (ttp-170) REVERT: C 717 MET cc_start: 0.6320 (mtm) cc_final: 0.5930 (mtm) REVERT: C 721 ARG cc_start: 0.8422 (mtt90) cc_final: 0.6278 (ptt-90) REVERT: C 776 SER cc_start: 0.8468 (m) cc_final: 0.8023 (t) REVERT: C 823 ASP cc_start: 0.7794 (t0) cc_final: 0.7474 (t70) REVERT: C 835 GLN cc_start: 0.8879 (mp10) cc_final: 0.8513 (mp10) REVERT: C 873 ILE cc_start: 0.7657 (tp) cc_final: 0.7280 (tp) REVERT: C 874 ASN cc_start: 0.8156 (m110) cc_final: 0.7241 (t0) REVERT: D 91 LYS cc_start: 0.8628 (mttt) cc_final: 0.8411 (mttm) REVERT: D 232 ILE cc_start: 0.9050 (mt) cc_final: 0.8609 (mt) REVERT: D 238 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7278 (ttm-80) REVERT: D 270 GLU cc_start: 0.7818 (mt-10) cc_final: 0.6949 (mt-10) REVERT: D 307 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7124 (ttm-80) REVERT: D 352 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7110 (tp-100) REVERT: D 393 MET cc_start: 0.7969 (mtm) cc_final: 0.7437 (mtp) REVERT: D 484 ASN cc_start: 0.8330 (m-40) cc_final: 0.7529 (t0) REVERT: D 517 LEU cc_start: 0.9226 (mt) cc_final: 0.8964 (mt) REVERT: D 518 MET cc_start: 0.8388 (mmp) cc_final: 0.8130 (mmp) REVERT: D 523 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8706 (mt0) REVERT: D 561 TYR cc_start: 0.8120 (t80) cc_final: 0.7557 (t80) REVERT: D 570 MET cc_start: 0.8887 (mtp) cc_final: 0.8666 (mtm) REVERT: D 586 THR cc_start: 0.8948 (p) cc_final: 0.8685 (p) REVERT: D 592 CYS cc_start: 0.8651 (m) cc_final: 0.8155 (m) REVERT: D 637 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7501 (ttp80) REVERT: D 701 ARG cc_start: 0.8466 (mmt180) cc_final: 0.7739 (mpt-90) REVERT: D 730 ILE cc_start: 0.9088 (tt) cc_final: 0.8642 (mt) REVERT: D 775 ASP cc_start: 0.6971 (t0) cc_final: 0.5279 (m-30) REVERT: D 816 PHE cc_start: 0.8140 (t80) cc_final: 0.7937 (t80) REVERT: D 879 ASP cc_start: 0.9060 (p0) cc_final: 0.8358 (p0) REVERT: E 102 ILE cc_start: 0.7219 (pt) cc_final: 0.6958 (tp) REVERT: E 238 ARG cc_start: 0.6795 (ttp-110) cc_final: 0.6350 (ttp-110) REVERT: E 261 GLU cc_start: 0.7074 (tp30) cc_final: 0.6853 (tm-30) REVERT: E 275 ASP cc_start: 0.8474 (m-30) cc_final: 0.8193 (m-30) REVERT: E 377 ILE cc_start: 0.8951 (mm) cc_final: 0.8724 (mm) REVERT: E 378 ASN cc_start: 0.7943 (p0) cc_final: 0.7574 (m-40) REVERT: E 444 TYR cc_start: 0.6819 (m-10) cc_final: 0.6295 (m-10) REVERT: E 450 GLN cc_start: 0.7761 (mp-120) cc_final: 0.7133 (pm20) REVERT: E 484 ASN cc_start: 0.7395 (t0) cc_final: 0.7042 (t0) REVERT: E 514 MET cc_start: 0.8733 (mmp) cc_final: 0.8297 (tpt) REVERT: E 532 TYR cc_start: 0.8227 (t80) cc_final: 0.7893 (t80) REVERT: E 550 LEU cc_start: 0.9304 (mt) cc_final: 0.9059 (mt) REVERT: E 560 ASN cc_start: 0.8260 (m-40) cc_final: 0.7898 (m110) REVERT: E 578 LEU cc_start: 0.8207 (mp) cc_final: 0.7748 (mp) REVERT: E 626 ASN cc_start: 0.8873 (m-40) cc_final: 0.8257 (m110) REVERT: E 666 ASP cc_start: 0.7247 (m-30) cc_final: 0.6924 (m-30) REVERT: E 751 TYR cc_start: 0.7467 (m-80) cc_final: 0.7211 (m-80) REVERT: E 821 ASN cc_start: 0.8579 (m-40) cc_final: 0.8290 (t0) REVERT: E 848 MET cc_start: 0.8167 (mmm) cc_final: 0.7778 (mmm) REVERT: F 231 PHE cc_start: 0.8648 (t80) cc_final: 0.8416 (t80) REVERT: F 243 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8167 (mtm110) REVERT: F 256 ASP cc_start: 0.8057 (m-30) cc_final: 0.7594 (m-30) REVERT: F 291 TYR cc_start: 0.8534 (m-80) cc_final: 0.8245 (m-80) REVERT: F 406 THR cc_start: 0.8538 (p) cc_final: 0.7313 (p) REVERT: F 460 GLN cc_start: 0.8668 (tp40) cc_final: 0.8318 (tp-100) REVERT: F 488 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7264 (mtt-85) REVERT: F 581 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7185 (tm-30) REVERT: F 594 LEU cc_start: 0.9420 (mt) cc_final: 0.9154 (mm) REVERT: F 609 HIS cc_start: 0.7659 (t-90) cc_final: 0.7316 (t-90) REVERT: F 625 ILE cc_start: 0.8880 (mt) cc_final: 0.8581 (mp) REVERT: F 636 ASN cc_start: 0.8902 (m-40) cc_final: 0.8687 (t0) REVERT: F 645 MET cc_start: 0.7490 (mtp) cc_final: 0.7190 (mmm) REVERT: F 757 MET cc_start: 0.6677 (mtp) cc_final: 0.5947 (mtt) REVERT: F 761 ASN cc_start: 0.8873 (m-40) cc_final: 0.8672 (m110) REVERT: F 793 ILE cc_start: 0.8867 (mm) cc_final: 0.8603 (tp) REVERT: F 843 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7582 (tpt170) REVERT: G 104 THR cc_start: 0.8603 (m) cc_final: 0.8294 (t) REVERT: G 119 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8390 (ptmt) REVERT: G 154 TYR cc_start: 0.4498 (m-80) cc_final: 0.3757 (m-80) REVERT: G 179 GLN cc_start: 0.8467 (pt0) cc_final: 0.7928 (tm-30) REVERT: G 238 ARG cc_start: 0.6021 (mmt180) cc_final: 0.5668 (mmt90) REVERT: G 333 TYR cc_start: 0.7764 (t80) cc_final: 0.7415 (t80) REVERT: G 396 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8507 (mm-40) REVERT: G 486 GLN cc_start: 0.8366 (mp10) cc_final: 0.8080 (mp10) REVERT: G 489 GLN cc_start: 0.7734 (mp10) cc_final: 0.7475 (mp10) REVERT: G 491 VAL cc_start: 0.8811 (t) cc_final: 0.8608 (p) REVERT: G 512 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7493 (tp40) REVERT: G 520 LEU cc_start: 0.8255 (mm) cc_final: 0.7940 (tt) REVERT: G 621 TYR cc_start: 0.8659 (t80) cc_final: 0.8402 (t80) REVERT: G 625 ILE cc_start: 0.8705 (mt) cc_final: 0.8466 (mt) REVERT: G 681 VAL cc_start: 0.8194 (t) cc_final: 0.7884 (p) REVERT: G 683 ILE cc_start: 0.8899 (mp) cc_final: 0.8650 (mt) REVERT: G 687 ASP cc_start: 0.8684 (m-30) cc_final: 0.8320 (m-30) REVERT: G 693 LEU cc_start: 0.8701 (mp) cc_final: 0.8296 (tt) REVERT: G 697 GLU cc_start: 0.7632 (tp30) cc_final: 0.7389 (tp30) REVERT: G 717 MET cc_start: 0.7549 (mmm) cc_final: 0.7347 (mmm) REVERT: G 830 THR cc_start: 0.8655 (m) cc_final: 0.8388 (p) REVERT: G 857 VAL cc_start: 0.8561 (t) cc_final: 0.8143 (m) REVERT: H 140 VAL cc_start: 0.8173 (m) cc_final: 0.6834 (m) REVERT: H 182 THR cc_start: 0.8111 (m) cc_final: 0.7575 (m) REVERT: H 196 GLU cc_start: 0.7223 (tp30) cc_final: 0.7022 (tp30) REVERT: H 277 ILE cc_start: 0.8970 (mt) cc_final: 0.8508 (mm) REVERT: H 293 LEU cc_start: 0.8398 (mt) cc_final: 0.8178 (mt) REVERT: H 389 LEU cc_start: 0.9044 (mt) cc_final: 0.8809 (mm) REVERT: H 498 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7479 (mm-40) REVERT: H 502 ASP cc_start: 0.7371 (m-30) cc_final: 0.6556 (t0) REVERT: H 518 MET cc_start: 0.7799 (tmm) cc_final: 0.7561 (tmm) REVERT: H 531 ASP cc_start: 0.7329 (p0) cc_final: 0.6599 (m-30) REVERT: H 541 LEU cc_start: 0.8092 (mt) cc_final: 0.7829 (mt) REVERT: H 556 LEU cc_start: 0.8617 (tp) cc_final: 0.8024 (tt) REVERT: H 560 ASN cc_start: 0.8794 (m-40) cc_final: 0.8287 (m110) REVERT: H 567 CYS cc_start: 0.7733 (m) cc_final: 0.7286 (m) REVERT: H 593 MET cc_start: 0.7997 (mmm) cc_final: 0.7587 (mmm) REVERT: H 607 LEU cc_start: 0.8983 (mt) cc_final: 0.8446 (tt) REVERT: H 640 LEU cc_start: 0.9175 (mt) cc_final: 0.8245 (mt) REVERT: H 653 LEU cc_start: 0.9309 (mp) cc_final: 0.8842 (mt) REVERT: H 675 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7630 (mtt180) REVERT: H 686 LEU cc_start: 0.7828 (tt) cc_final: 0.7623 (tt) REVERT: H 690 ASN cc_start: 0.8080 (m110) cc_final: 0.7757 (m110) REVERT: H 727 TYR cc_start: 0.8013 (m-10) cc_final: 0.7800 (m-10) REVERT: H 729 ASN cc_start: 0.7574 (p0) cc_final: 0.6681 (p0) REVERT: H 759 LEU cc_start: 0.8724 (mt) cc_final: 0.8394 (tp) REVERT: H 772 PHE cc_start: 0.8581 (p90) cc_final: 0.8353 (p90) REVERT: H 861 LEU cc_start: 0.6870 (pp) cc_final: 0.6457 (mt) REVERT: I 142 ARG cc_start: 0.7222 (ptp90) cc_final: 0.6455 (ptm-80) REVERT: I 157 LEU cc_start: 0.8458 (mt) cc_final: 0.7652 (mt) REVERT: I 167 TYR cc_start: 0.6090 (t80) cc_final: 0.5644 (t80) REVERT: I 175 ASN cc_start: 0.8875 (t0) cc_final: 0.8657 (t0) REVERT: I 277 ILE cc_start: 0.8955 (mt) cc_final: 0.8753 (mm) REVERT: I 312 GLN cc_start: 0.6512 (mt0) cc_final: 0.6301 (mt0) REVERT: I 356 MET cc_start: 0.7861 (mtt) cc_final: 0.7630 (mtt) REVERT: I 389 LEU cc_start: 0.7974 (mt) cc_final: 0.7618 (mt) REVERT: I 396 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7783 (mm-40) REVERT: I 423 ASN cc_start: 0.8897 (m110) cc_final: 0.8610 (t0) REVERT: I 572 MET cc_start: 0.6244 (ptm) cc_final: 0.5915 (ptp) REVERT: I 655 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7294 (mmp80) REVERT: I 671 ARG cc_start: 0.6920 (ttm110) cc_final: 0.6717 (ttm170) REVERT: I 696 MET cc_start: 0.6651 (ptm) cc_final: 0.6260 (tmm) REVERT: I 738 GLN cc_start: 0.8250 (tt0) cc_final: 0.8039 (mt0) REVERT: I 739 GLN cc_start: 0.6487 (tm130) cc_final: 0.6130 (tm-30) REVERT: I 809 ILE cc_start: 0.4640 (mm) cc_final: 0.4364 (mm) REVERT: J 150 ARG cc_start: 0.7340 (ptt180) cc_final: 0.4990 (mtm-85) REVERT: J 232 ILE cc_start: 0.8987 (mt) cc_final: 0.8759 (tp) REVERT: J 274 ASN cc_start: 0.8258 (m-40) cc_final: 0.7956 (m-40) REVERT: J 309 ASN cc_start: 0.8659 (t0) cc_final: 0.8247 (t0) REVERT: J 356 MET cc_start: 0.8413 (mmm) cc_final: 0.7951 (mmm) REVERT: J 398 THR cc_start: 0.8903 (m) cc_final: 0.8661 (p) REVERT: J 454 TYR cc_start: 0.8133 (t80) cc_final: 0.7846 (t80) REVERT: J 485 ASN cc_start: 0.7993 (t0) cc_final: 0.7708 (t0) REVERT: J 511 ASN cc_start: 0.7396 (m-40) cc_final: 0.7136 (t0) REVERT: J 567 CYS cc_start: 0.9002 (m) cc_final: 0.8660 (m) REVERT: J 571 ASN cc_start: 0.8576 (m-40) cc_final: 0.8215 (m-40) REVERT: J 607 LEU cc_start: 0.9213 (mt) cc_final: 0.8777 (tp) REVERT: J 670 TYR cc_start: 0.7163 (m-10) cc_final: 0.6919 (m-10) REVERT: J 694 MET cc_start: 0.6868 (ptm) cc_final: 0.6570 (ttt) REVERT: J 817 TYR cc_start: 0.8370 (p90) cc_final: 0.7393 (m-10) REVERT: J 831 LYS cc_start: 0.7911 (mttt) cc_final: 0.7523 (mttp) REVERT: J 833 TYR cc_start: 0.7601 (t80) cc_final: 0.5931 (t80) REVERT: J 881 MET cc_start: 0.7735 (tpp) cc_final: 0.7048 (tpp) REVERT: P 213 MET cc_start: 0.7187 (mtm) cc_final: 0.6935 (mtm) REVERT: P 215 MET cc_start: 0.8252 (mmp) cc_final: 0.7194 (tpp) REVERT: P 294 ASN cc_start: 0.8348 (m110) cc_final: 0.8125 (m110) REVERT: P 308 GLN cc_start: 0.8513 (tt0) cc_final: 0.8027 (tm-30) REVERT: P 322 MET cc_start: 0.7739 (mmt) cc_final: 0.7049 (mmp) REVERT: P 362 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7490 (tt0) REVERT: P 363 TYR cc_start: 0.7493 (t80) cc_final: 0.6974 (t80) REVERT: P 468 GLU cc_start: 0.7142 (mp0) cc_final: 0.6373 (mp0) REVERT: P 518 TYR cc_start: 0.6609 (p90) cc_final: 0.6212 (p90) REVERT: P 568 LEU cc_start: 0.9180 (mt) cc_final: 0.8863 (mt) REVERT: P 645 LYS cc_start: 0.8130 (mttt) cc_final: 0.7836 (mtpp) REVERT: P 676 GLU cc_start: 0.5748 (tm-30) cc_final: 0.5091 (tm-30) REVERT: P 734 THR cc_start: 0.8716 (m) cc_final: 0.8434 (m) REVERT: P 818 GLN cc_start: 0.9116 (tp40) cc_final: 0.8812 (tm-30) REVERT: P 914 ILE cc_start: 0.7712 (pt) cc_final: 0.7115 (mp) REVERT: P 946 GLU cc_start: 0.7411 (mp0) cc_final: 0.6966 (mp0) REVERT: P 995 ASN cc_start: 0.8736 (t0) cc_final: 0.8054 (t0) REVERT: P 1051 TRP cc_start: 0.8025 (m100) cc_final: 0.7709 (m100) outliers start: 5 outliers final: 0 residues processed: 3045 average time/residue: 1.8792 time to fit residues: 9511.3604 Evaluate side-chains 2508 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2507 time to evaluate : 8.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 683 optimal weight: 10.0000 chunk 559 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 822 optimal weight: 0.9990 chunk 888 optimal weight: 4.9990 chunk 732 optimal weight: 6.9990 chunk 815 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 659 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 642 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 287 ASN B 549 GLN B 622 ASN B 760 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 874 ASN D 199 ASN D 247 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN D 708 GLN E 137 GLN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 GLN E 622 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN F 266 HIS F 480 HIS ** F 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN F 874 ASN G 90 GLN ** G 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN G 287 ASN ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN G 484 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** H 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 537 GLN H 616 ASN H 642 GLN I 94 GLN I 257 HIS ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 460 GLN I 480 HIS ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 616 ASN I 760 ASN ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 657 GLN P 430 ASN ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 794 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 75455 Z= 0.343 Angle : 0.687 9.240 102320 Z= 0.376 Chirality : 0.042 0.286 11722 Planarity : 0.006 0.111 13254 Dihedral : 5.803 70.120 9999 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.07 % Favored : 91.91 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.79 (0.08), residues: 9050 helix: -0.12 (0.08), residues: 4316 sheet: -2.11 (0.16), residues: 758 loop : -2.20 (0.09), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 325 HIS 0.014 0.002 HIS F 266 PHE 0.040 0.002 PHE D 689 TYR 0.027 0.002 TYR J 822 ARG 0.013 0.001 ARG J 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2810 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2803 time to evaluate : 8.690 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 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8936 (tt0) cc_final: 0.8547 (tm-30) REVERT: A 267 GLN cc_start: 0.8548 (pt0) cc_final: 0.8096 (pt0) REVERT: A 304 ARG cc_start: 0.7449 (mpt180) cc_final: 0.7211 (mpt180) REVERT: A 355 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8683 (tppt) REVERT: A 416 TRP cc_start: 0.8900 (t60) cc_final: 0.8698 (t60) REVERT: A 455 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7977 (mpt-90) REVERT: A 498 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8364 (mm-40) REVERT: A 518 MET cc_start: 0.6441 (tpp) cc_final: 0.5871 (tpp) REVERT: A 549 GLN cc_start: 0.8174 (mp10) cc_final: 0.7943 (mp10) REVERT: A 667 ASP cc_start: 0.8279 (p0) cc_final: 0.7999 (p0) REVERT: A 724 MET cc_start: 0.8552 (pmm) cc_final: 0.8311 (pmm) REVERT: A 751 TYR cc_start: 0.8477 (m-80) cc_final: 0.7848 (m-80) REVERT: A 761 ASN cc_start: 0.8427 (m-40) cc_final: 0.7141 (p0) REVERT: A 777 SER cc_start: 0.8381 (t) cc_final: 0.8012 (p) REVERT: A 868 ASP cc_start: 0.6567 (t70) cc_final: 0.6160 (t70) REVERT: B 178 ASP cc_start: 0.8242 (t0) cc_final: 0.7889 (t0) REVERT: B 266 HIS cc_start: 0.9262 (m90) cc_final: 0.8735 (m90) REVERT: B 284 ARG cc_start: 0.6680 (mpt-90) cc_final: 0.6408 (mpt-90) REVERT: B 427 ILE cc_start: 0.9137 (tt) cc_final: 0.8848 (tt) REVERT: B 514 MET cc_start: 0.8412 (mmp) cc_final: 0.7912 (mmt) REVERT: B 518 MET cc_start: 0.8212 (mtt) cc_final: 0.7999 (mpp) REVERT: B 531 ASP cc_start: 0.7157 (p0) cc_final: 0.6268 (t0) REVERT: B 549 GLN cc_start: 0.8022 (mp10) cc_final: 0.7792 (mm-40) REVERT: B 561 TYR cc_start: 0.8676 (t80) cc_final: 0.8304 (t80) REVERT: B 688 ILE cc_start: 0.8780 (mm) cc_final: 0.8513 (mm) REVERT: B 730 ILE cc_start: 0.8712 (tt) cc_final: 0.8221 (tt) REVERT: B 821 ASN cc_start: 0.7961 (m-40) cc_final: 0.7758 (m-40) REVERT: C 191 LYS cc_start: 0.8694 (pttp) cc_final: 0.7771 (tptt) REVERT: C 209 SER cc_start: 0.8784 (m) cc_final: 0.8466 (t) REVERT: C 211 THR cc_start: 0.8820 (m) cc_final: 0.8590 (m) REVERT: C 228 VAL cc_start: 0.9154 (m) cc_final: 0.8779 (p) REVERT: C 289 VAL cc_start: 0.9037 (m) cc_final: 0.8573 (p) REVERT: C 355 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6711 (ttpp) REVERT: C 359 ASP cc_start: 0.7701 (m-30) cc_final: 0.7444 (m-30) REVERT: C 386 PHE cc_start: 0.8218 (t80) cc_final: 0.7977 (t80) REVERT: C 423 ASN cc_start: 0.8642 (m110) cc_final: 0.8264 (p0) REVERT: C 434 CYS cc_start: 0.8648 (t) cc_final: 0.8266 (t) REVERT: C 491 VAL cc_start: 0.8202 (p) cc_final: 0.7975 (p) REVERT: C 626 ASN cc_start: 0.8565 (m-40) cc_final: 0.7358 (m110) REVERT: C 639 ASN cc_start: 0.8757 (t0) cc_final: 0.8130 (t0) REVERT: C 641 TYR cc_start: 0.8708 (p90) cc_final: 0.8328 (p90) REVERT: C 677 ARG cc_start: 0.8547 (mtp180) cc_final: 0.8333 (mtm180) REVERT: C 696 MET cc_start: 0.9008 (ptm) cc_final: 0.8192 (ppp) REVERT: C 697 GLU cc_start: 0.8212 (pm20) cc_final: 0.7194 (pm20) REVERT: C 721 ARG cc_start: 0.8561 (mtt90) cc_final: 0.6315 (ptt-90) REVERT: C 776 SER cc_start: 0.8986 (m) cc_final: 0.8619 (t) REVERT: D 215 CYS cc_start: 0.9039 (m) cc_final: 0.8362 (t) REVERT: D 232 ILE cc_start: 0.9111 (mt) cc_final: 0.8183 (mt) REVERT: D 307 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7259 (ttm-80) REVERT: D 393 MET cc_start: 0.8037 (mtm) cc_final: 0.7512 (mtp) REVERT: D 484 ASN cc_start: 0.8585 (m-40) cc_final: 0.7811 (t0) REVERT: D 523 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8712 (mt0) REVERT: D 561 TYR cc_start: 0.8320 (t80) cc_final: 0.7890 (t80) REVERT: D 588 VAL cc_start: 0.9279 (t) cc_final: 0.9007 (t) REVERT: D 696 MET cc_start: 0.8630 (ptp) cc_final: 0.8414 (ptp) REVERT: D 730 ILE cc_start: 0.8967 (tt) cc_final: 0.8525 (mt) REVERT: D 879 ASP cc_start: 0.9330 (p0) cc_final: 0.8652 (p0) REVERT: E 102 ILE cc_start: 0.7071 (pt) cc_final: 0.6866 (tp) REVERT: E 160 ASP cc_start: 0.7244 (m-30) cc_final: 0.7007 (m-30) REVERT: E 248 TYR cc_start: 0.7269 (m-80) cc_final: 0.6920 (m-10) REVERT: E 261 GLU cc_start: 0.8196 (tp30) cc_final: 0.7863 (tm-30) REVERT: E 450 GLN cc_start: 0.7559 (mp-120) cc_final: 0.6982 (pm20) REVERT: E 467 GLU cc_start: 0.8582 (tt0) cc_final: 0.8303 (tt0) REVERT: E 488 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6973 (mtm110) REVERT: E 514 MET cc_start: 0.8771 (mmp) cc_final: 0.8273 (tpt) REVERT: E 550 LEU cc_start: 0.9391 (mt) cc_final: 0.9144 (mt) REVERT: E 568 ILE cc_start: 0.8629 (mm) cc_final: 0.8394 (mm) REVERT: E 578 LEU cc_start: 0.8276 (mp) cc_final: 0.7979 (mp) REVERT: E 666 ASP cc_start: 0.7416 (m-30) cc_final: 0.6799 (m-30) REVERT: E 748 THR cc_start: 0.7955 (p) cc_final: 0.7525 (p) REVERT: E 821 ASN cc_start: 0.8671 (m-40) cc_final: 0.8252 (t0) REVERT: E 846 MET cc_start: 0.8371 (tmm) cc_final: 0.8146 (tmm) REVERT: F 99 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7323 (tm-30) REVERT: F 168 ASP cc_start: 0.8377 (m-30) cc_final: 0.8164 (m-30) REVERT: F 231 PHE cc_start: 0.8717 (t80) cc_final: 0.8496 (t80) REVERT: F 243 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8216 (mtm110) REVERT: F 256 ASP cc_start: 0.7981 (m-30) cc_final: 0.7537 (m-30) REVERT: F 262 TYR cc_start: 0.6940 (t80) cc_final: 0.6277 (t80) REVERT: F 309 ASN cc_start: 0.6632 (t0) cc_final: 0.6401 (t0) REVERT: F 355 LYS cc_start: 0.8450 (ptmm) cc_final: 0.7986 (ttmt) REVERT: F 581 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7209 (tp30) REVERT: F 636 ASN cc_start: 0.8968 (m-40) cc_final: 0.8704 (t0) REVERT: F 645 MET cc_start: 0.7596 (mtp) cc_final: 0.7265 (mmm) REVERT: F 687 ASP cc_start: 0.8534 (m-30) cc_final: 0.8139 (m-30) REVERT: F 696 MET cc_start: 0.8178 (ptm) cc_final: 0.7759 (ptm) REVERT: F 757 MET cc_start: 0.7783 (mtp) cc_final: 0.7551 (mmt) REVERT: F 843 ARG cc_start: 0.8630 (mtt90) cc_final: 0.7765 (tpt170) REVERT: G 179 GLN cc_start: 0.8504 (pt0) cc_final: 0.7861 (tm-30) REVERT: G 256 ASP cc_start: 0.8604 (m-30) cc_final: 0.8355 (m-30) REVERT: G 262 TYR cc_start: 0.7703 (t80) cc_final: 0.7349 (t80) REVERT: G 265 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7990 (tt0) REVERT: G 396 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8518 (mm-40) REVERT: G 484 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7760 (t0) REVERT: G 582 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8336 (mmtm) REVERT: G 621 TYR cc_start: 0.8805 (t80) cc_final: 0.8544 (t80) REVERT: G 687 ASP cc_start: 0.8879 (m-30) cc_final: 0.8528 (m-30) REVERT: G 697 GLU cc_start: 0.7806 (tp30) cc_final: 0.7465 (tp30) REVERT: G 715 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.8279 (ptt-90) REVERT: G 746 MET cc_start: 0.6866 (tmm) cc_final: 0.6653 (tmm) REVERT: G 885 ASN cc_start: 0.7852 (t0) cc_final: 0.7446 (t0) REVERT: H 140 VAL cc_start: 0.8288 (m) cc_final: 0.5701 (m) REVERT: H 567 CYS cc_start: 0.8078 (m) cc_final: 0.7464 (m) REVERT: H 593 MET cc_start: 0.8067 (mmm) cc_final: 0.7595 (mmm) REVERT: H 607 LEU cc_start: 0.9021 (mt) cc_final: 0.8479 (tt) REVERT: H 690 ASN cc_start: 0.8251 (m110) cc_final: 0.7940 (m110) REVERT: H 724 MET cc_start: 0.6943 (mmt) cc_final: 0.6044 (tpp) REVERT: H 759 LEU cc_start: 0.8771 (mt) cc_final: 0.8413 (tp) REVERT: I 132 ILE cc_start: 0.8316 (mm) cc_final: 0.7827 (pt) REVERT: I 142 ARG cc_start: 0.7563 (ptp90) cc_final: 0.6025 (ptm-80) REVERT: I 167 TYR cc_start: 0.6590 (t80) cc_final: 0.6120 (t80) REVERT: I 175 ASN cc_start: 0.9007 (t0) cc_final: 0.8790 (t0) REVERT: I 283 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7942 (mm-30) REVERT: I 305 TYR cc_start: 0.8666 (p90) cc_final: 0.8367 (p90) REVERT: I 322 GLU cc_start: 0.9011 (pm20) cc_final: 0.8724 (pm20) REVERT: I 389 LEU cc_start: 0.7897 (mt) cc_final: 0.7674 (mt) REVERT: I 394 LEU cc_start: 0.8506 (mt) cc_final: 0.7984 (mt) REVERT: I 396 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7965 (mm-40) REVERT: I 423 ASN cc_start: 0.8960 (m110) cc_final: 0.8707 (t0) REVERT: I 438 ILE cc_start: 0.8984 (mt) cc_final: 0.8734 (mt) REVERT: I 440 ASN cc_start: 0.8730 (m110) cc_final: 0.7901 (p0) REVERT: I 480 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7542 (t-90) REVERT: I 567 CYS cc_start: 0.8756 (m) cc_final: 0.8554 (m) REVERT: I 637 ARG cc_start: 0.8274 (mtt180) cc_final: 0.6645 (tpt170) REVERT: I 663 ARG cc_start: 0.7497 (tpp80) cc_final: 0.7223 (tpp80) REVERT: I 809 ILE cc_start: 0.5317 (mm) cc_final: 0.4911 (mm) REVERT: I 848 MET cc_start: 0.6485 (mmm) cc_final: 0.6277 (mmm) REVERT: J 150 ARG cc_start: 0.7742 (ptt180) cc_final: 0.5267 (mtt180) REVERT: J 154 TYR cc_start: 0.6733 (m-80) cc_final: 0.6188 (m-80) REVERT: J 238 ARG cc_start: 0.7053 (mtt90) cc_final: 0.6126 (ttm110) REVERT: J 356 MET cc_start: 0.8799 (mmm) cc_final: 0.8540 (mmm) REVERT: J 399 MET cc_start: 0.7930 (ptt) cc_final: 0.7680 (ptt) REVERT: J 425 MET cc_start: 0.8476 (tmm) cc_final: 0.7458 (ppp) REVERT: J 495 VAL cc_start: 0.7638 (m) cc_final: 0.7281 (m) REVERT: J 538 ARG cc_start: 0.8444 (mpt-90) cc_final: 0.8120 (mpt-90) REVERT: J 567 CYS cc_start: 0.9291 (m) cc_final: 0.8678 (m) REVERT: J 571 ASN cc_start: 0.8559 (m-40) cc_final: 0.8094 (m-40) REVERT: J 578 LEU cc_start: 0.8664 (mp) cc_final: 0.8398 (mp) REVERT: J 607 LEU cc_start: 0.9208 (mt) cc_final: 0.8929 (tp) REVERT: J 817 TYR cc_start: 0.8513 (p90) cc_final: 0.7163 (m-80) REVERT: J 833 TYR cc_start: 0.7883 (t80) cc_final: 0.6136 (t80) REVERT: P 215 MET cc_start: 0.8658 (mmp) cc_final: 0.8300 (tpp) REVERT: P 293 ASP cc_start: 0.7515 (m-30) cc_final: 0.7134 (t0) REVERT: P 294 ASN cc_start: 0.8539 (m110) cc_final: 0.8273 (m110) REVERT: P 308 GLN cc_start: 0.8882 (tt0) cc_final: 0.8279 (tm-30) REVERT: P 322 MET cc_start: 0.8083 (mmt) cc_final: 0.7599 (mmp) REVERT: P 337 GLN cc_start: 0.8999 (pm20) cc_final: 0.8798 (pm20) REVERT: P 365 MET cc_start: 0.7621 (ttt) cc_final: 0.6771 (ttt) REVERT: P 518 TYR cc_start: 0.7049 (p90) cc_final: 0.6432 (p90) REVERT: P 548 MET cc_start: 0.8057 (ttm) cc_final: 0.7761 (ttp) REVERT: P 561 TYR cc_start: 0.7441 (t80) cc_final: 0.7198 (t80) REVERT: P 568 LEU cc_start: 0.9414 (mt) cc_final: 0.9213 (mt) REVERT: P 646 GLN cc_start: 0.8404 (mt0) cc_final: 0.8112 (tp40) REVERT: P 651 VAL cc_start: 0.9353 (m) cc_final: 0.8452 (m) REVERT: P 811 TYR cc_start: 0.8402 (t80) cc_final: 0.8164 (t80) REVERT: P 818 GLN cc_start: 0.9135 (tp40) cc_final: 0.8774 (tm-30) REVERT: P 863 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8080 (mmmt) REVERT: P 914 ILE cc_start: 0.8007 (pt) cc_final: 0.7344 (mp) REVERT: P 928 SER cc_start: 0.7298 (t) cc_final: 0.7095 (m) REVERT: P 946 GLU cc_start: 0.7603 (mp0) cc_final: 0.7393 (mp0) REVERT: P 955 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6700 (mm-30) REVERT: P 1051 TRP cc_start: 0.8181 (m100) cc_final: 0.7796 (m100) outliers start: 7 outliers final: 5 residues processed: 2808 average time/residue: 1.8176 time to fit residues: 8458.8959 Evaluate side-chains 2365 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2358 time to evaluate : 7.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 7.9990 chunk 618 optimal weight: 8.9990 chunk 426 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 552 optimal weight: 6.9990 chunk 825 optimal weight: 5.9990 chunk 873 optimal weight: 7.9990 chunk 431 optimal weight: 5.9990 chunk 782 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 290 ASN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN B 279 ASN B 483 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN B 668 GLN B 760 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 821 ASN D 72 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 ASN F 480 HIS ** F 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN G 199 ASN G 279 ASN ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 358 GLN ** H 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 GLN ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN ** H 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 GLN ** I 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 560 ASN I 739 GLN ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 614 ASN J 761 ASN P 208 ASN ** P 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 824 ASN P 908 GLN P1048 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 75455 Z= 0.528 Angle : 0.849 10.978 102320 Z= 0.469 Chirality : 0.046 0.207 11722 Planarity : 0.007 0.113 13254 Dihedral : 6.370 58.177 9999 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.20 % Favored : 89.78 % Rotamer: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -2.59 (0.08), residues: 9050 helix: -0.89 (0.07), residues: 4325 sheet: -2.14 (0.17), residues: 727 loop : -2.56 (0.09), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 325 HIS 0.011 0.003 HIS F 253 PHE 0.041 0.003 PHE H 487 TYR 0.039 0.003 TYR B 532 ARG 0.015 0.001 ARG I 882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2661 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2650 time to evaluate : 8.610 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: 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REVERT: A 122 GLN cc_start: 0.9052 (tt0) cc_final: 0.8546 (tm-30) REVERT: A 236 ARG cc_start: 0.8239 (ptm160) cc_final: 0.8002 (ptm160) REVERT: A 393 MET cc_start: 0.8098 (mtm) cc_final: 0.7882 (mtm) REVERT: A 452 MET cc_start: 0.8564 (tpt) cc_final: 0.8332 (tpt) REVERT: A 593 MET cc_start: 0.8695 (tpp) cc_final: 0.8446 (tpp) REVERT: A 666 ASP cc_start: 0.7473 (p0) cc_final: 0.7066 (p0) REVERT: A 751 TYR cc_start: 0.8464 (m-80) cc_final: 0.7970 (m-80) REVERT: A 761 ASN cc_start: 0.8550 (m-40) cc_final: 0.7311 (p0) REVERT: A 762 GLN cc_start: 0.9124 (mt0) cc_final: 0.8736 (mt0) REVERT: A 777 SER cc_start: 0.8821 (t) cc_final: 0.8553 (p) REVERT: B 266 HIS cc_start: 0.9319 (m90) cc_final: 0.8780 (m90) REVERT: B 324 LEU cc_start: 0.9376 (mt) cc_final: 0.9063 (tt) REVERT: B 361 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 410 SER cc_start: 0.9119 (m) cc_final: 0.8890 (p) REVERT: B 467 GLU cc_start: 0.8495 (tt0) cc_final: 0.8086 (tt0) REVERT: B 514 MET cc_start: 0.8681 (mmp) cc_final: 0.7822 (tpp) REVERT: B 561 TYR cc_start: 0.8672 (t80) cc_final: 0.8084 (t80) REVERT: B 576 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8609 (mm-40) REVERT: B 727 TYR cc_start: 0.7704 (m-10) cc_final: 0.7455 (m-10) REVERT: C 209 SER cc_start: 0.8786 (m) cc_final: 0.8516 (t) REVERT: C 211 THR cc_start: 0.8881 (m) cc_final: 0.8632 (m) REVERT: C 228 VAL cc_start: 0.9314 (m) cc_final: 0.8938 (p) REVERT: C 289 VAL cc_start: 0.9199 (m) cc_final: 0.8854 (p) REVERT: C 386 PHE cc_start: 0.8339 (t80) cc_final: 0.8127 (t80) REVERT: C 423 ASN cc_start: 0.8803 (m110) cc_final: 0.8461 (p0) REVERT: C 518 MET cc_start: 0.8275 (mmt) cc_final: 0.8059 (mmm) REVERT: C 531 ASP cc_start: 0.7740 (p0) cc_final: 0.7519 (p0) REVERT: C 626 ASN cc_start: 0.8614 (m-40) cc_final: 0.8398 (m110) REVERT: C 677 ARG cc_start: 0.8500 (mtp180) cc_final: 0.8294 (mtm110) REVERT: C 683 ILE cc_start: 0.9046 (mm) cc_final: 0.8739 (tp) REVERT: C 696 MET cc_start: 0.8879 (ptm) cc_final: 0.8233 (ppp) REVERT: C 697 GLU cc_start: 0.8068 (pm20) cc_final: 0.7041 (pm20) REVERT: C 720 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7044 (tm-30) REVERT: C 721 ARG cc_start: 0.8071 (mtt90) cc_final: 0.6478 (ptt-90) REVERT: C 722 ASP cc_start: 0.7133 (m-30) cc_final: 0.6086 (m-30) REVERT: C 784 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8438 (mtpt) REVERT: C 790 PHE cc_start: 0.8241 (m-80) cc_final: 0.7948 (m-80) REVERT: C 860 ASP cc_start: 0.8731 (t0) cc_final: 0.8506 (t0) REVERT: D 142 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7114 (mmt180) REVERT: D 184 MET cc_start: 0.7882 (tmm) cc_final: 0.7469 (tmm) REVERT: D 215 CYS cc_start: 0.9149 (m) cc_final: 0.8660 (t) REVERT: D 232 ILE cc_start: 0.9123 (mt) cc_final: 0.8373 (mt) REVERT: D 305 TYR cc_start: 0.8619 (p90) cc_final: 0.8350 (p90) REVERT: D 352 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8453 (tm-30) REVERT: D 393 MET cc_start: 0.8178 (mtm) cc_final: 0.7101 (mtm) REVERT: D 484 ASN cc_start: 0.8672 (m-40) cc_final: 0.8108 (t0) REVERT: D 515 GLU cc_start: 0.8977 (tp30) cc_final: 0.8736 (tt0) REVERT: D 561 TYR cc_start: 0.8256 (t80) cc_final: 0.7752 (t80) REVERT: D 588 VAL cc_start: 0.9358 (t) cc_final: 0.9092 (t) REVERT: D 615 VAL cc_start: 0.9730 (t) cc_final: 0.9514 (m) REVERT: D 637 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7979 (ttp-110) REVERT: D 701 ARG cc_start: 0.8822 (mmt180) cc_final: 0.8509 (mtt90) REVERT: D 730 ILE cc_start: 0.9003 (tt) cc_final: 0.8544 (mt) REVERT: D 741 ASN cc_start: 0.8755 (t0) cc_final: 0.8476 (t0) REVERT: D 764 VAL cc_start: 0.6976 (p) cc_final: 0.6578 (p) REVERT: D 854 THR cc_start: 0.6345 (m) cc_final: 0.5851 (m) REVERT: D 881 MET cc_start: 0.8171 (mmp) cc_final: 0.7735 (mmm) REVERT: E 102 ILE cc_start: 0.7238 (pt) cc_final: 0.6939 (tp) REVERT: E 160 ASP cc_start: 0.7490 (m-30) cc_final: 0.6695 (t0) REVERT: E 168 ASP cc_start: 0.8966 (m-30) cc_final: 0.8676 (m-30) REVERT: E 193 MET cc_start: 0.8471 (ptp) cc_final: 0.7923 (mtp) REVERT: E 261 GLU cc_start: 0.8599 (tp30) cc_final: 0.8052 (tm-30) REVERT: E 270 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7699 (mt-10) REVERT: E 326 ASP cc_start: 0.8796 (t70) cc_final: 0.8478 (t70) REVERT: E 362 LEU cc_start: 0.7574 (mt) cc_final: 0.7276 (pp) REVERT: E 409 MET cc_start: 0.9140 (tpp) cc_final: 0.8882 (tpp) REVERT: E 423 ASN cc_start: 0.8205 (m110) cc_final: 0.7405 (m-40) REVERT: E 488 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7451 (mtm110) REVERT: E 514 MET cc_start: 0.8882 (mmp) cc_final: 0.8153 (tpt) REVERT: E 550 LEU cc_start: 0.9446 (mt) cc_final: 0.9197 (mt) REVERT: E 625 ILE cc_start: 0.8890 (mt) cc_final: 0.8689 (mt) REVERT: E 666 ASP cc_start: 0.7510 (m-30) cc_final: 0.6935 (m-30) REVERT: E 821 ASN cc_start: 0.8763 (m-40) cc_final: 0.8378 (t0) REVERT: F 87 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5880 (pt0) REVERT: F 99 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7614 (tm-30) REVERT: F 168 ASP cc_start: 0.8696 (m-30) cc_final: 0.8457 (m-30) REVERT: F 177 TYR cc_start: 0.8252 (t80) cc_final: 0.7976 (t80) REVERT: F 179 GLN cc_start: 0.8654 (pp30) cc_final: 0.8429 (pp30) REVERT: F 199 ASN cc_start: 0.9243 (m-40) cc_final: 0.8913 (m-40) REVERT: F 216 ASP cc_start: 0.9240 (m-30) cc_final: 0.8800 (m-30) REVERT: F 243 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8299 (mtm110) REVERT: F 256 ASP cc_start: 0.7965 (m-30) cc_final: 0.7511 (m-30) REVERT: F 355 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8115 (ttmt) REVERT: F 356 MET cc_start: 0.8551 (mmt) cc_final: 0.8236 (mmt) REVERT: F 415 MET cc_start: 0.8676 (ptp) cc_final: 0.8409 (ptp) REVERT: F 581 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7398 (tp30) REVERT: F 636 ASN cc_start: 0.9041 (m-40) cc_final: 0.8690 (t0) REVERT: F 696 MET cc_start: 0.8417 (ptm) cc_final: 0.8030 (ttp) REVERT: F 744 GLU cc_start: 0.8895 (mp0) cc_final: 0.7662 (tp30) REVERT: F 745 LEU cc_start: 0.8154 (tp) cc_final: 0.7881 (tp) REVERT: F 843 ARG cc_start: 0.8707 (mtt90) cc_final: 0.7947 (tpt170) REVERT: F 874 ASN cc_start: 0.9122 (m-40) cc_final: 0.8836 (m-40) REVERT: G 179 GLN cc_start: 0.8516 (pt0) cc_final: 0.7997 (tm-30) REVERT: G 256 ASP cc_start: 0.8603 (m-30) cc_final: 0.8364 (m-30) REVERT: G 265 GLN cc_start: 0.8680 (mm-40) cc_final: 0.7874 (tt0) REVERT: G 284 ARG cc_start: 0.8190 (ptt180) cc_final: 0.7743 (ptt180) REVERT: G 304 ARG cc_start: 0.7870 (mpt-90) cc_final: 0.7565 (mpt-90) REVERT: G 316 ASN cc_start: 0.8022 (m-40) cc_final: 0.7642 (m-40) REVERT: G 394 LEU cc_start: 0.9198 (mt) cc_final: 0.8840 (tt) REVERT: G 396 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8610 (mm-40) REVERT: G 402 ASP cc_start: 0.8518 (m-30) cc_final: 0.8193 (m-30) REVERT: G 515 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6748 (mt-10) REVERT: G 582 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8059 (mmtm) REVERT: G 611 TYR cc_start: 0.8881 (t80) cc_final: 0.8415 (t80) REVERT: G 620 ASN cc_start: 0.8363 (t0) cc_final: 0.8057 (t0) REVERT: G 625 ILE cc_start: 0.8972 (mt) cc_final: 0.8548 (tt) REVERT: G 687 ASP cc_start: 0.9092 (m-30) cc_final: 0.8682 (m-30) REVERT: G 694 MET cc_start: 0.7189 (mtp) cc_final: 0.6930 (mtm) REVERT: G 746 MET cc_start: 0.7880 (tmm) cc_final: 0.7393 (tmm) REVERT: H 121 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7331 (mm-30) REVERT: H 137 GLN cc_start: 0.7958 (tt0) cc_final: 0.7499 (pt0) REVERT: H 152 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: H 277 ILE cc_start: 0.9127 (mt) cc_final: 0.8796 (mm) REVERT: H 404 VAL cc_start: 0.8580 (t) cc_final: 0.8341 (m) REVERT: H 470 ILE cc_start: 0.8920 (mm) cc_final: 0.8696 (mt) REVERT: H 560 ASN cc_start: 0.8940 (m-40) cc_final: 0.8345 (m110) REVERT: H 593 MET cc_start: 0.8096 (mmm) cc_final: 0.7680 (mmm) REVERT: H 689 PHE cc_start: 0.8164 (t80) cc_final: 0.7775 (t80) REVERT: H 690 ASN cc_start: 0.8446 (m110) cc_final: 0.8193 (m110) REVERT: H 723 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6995 (tm-30) REVERT: H 727 TYR cc_start: 0.8655 (m-10) cc_final: 0.8440 (m-10) REVERT: H 759 LEU cc_start: 0.8591 (mt) cc_final: 0.8290 (tp) REVERT: H 807 TYR cc_start: 0.7828 (m-80) cc_final: 0.7330 (m-80) REVERT: H 874 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7219 (p0) REVERT: I 295 MET cc_start: 0.8540 (mmm) cc_final: 0.8315 (mmm) REVERT: I 305 TYR cc_start: 0.9003 (p90) cc_final: 0.8798 (p90) REVERT: I 389 LEU cc_start: 0.8261 (mt) cc_final: 0.7981 (mt) REVERT: I 394 LEU cc_start: 0.8667 (mt) cc_final: 0.8257 (mt) REVERT: I 396 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8231 (mm-40) REVERT: I 423 ASN cc_start: 0.9009 (m110) cc_final: 0.8705 (t0) REVERT: I 426 PHE cc_start: 0.8612 (m-80) cc_final: 0.8371 (m-10) REVERT: I 443 ILE cc_start: 0.9361 (mm) cc_final: 0.9153 (mp) REVERT: I 521 SER cc_start: 0.8500 (m) cc_final: 0.8256 (p) REVERT: I 567 CYS cc_start: 0.8920 (m) cc_final: 0.8707 (m) REVERT: I 610 TYR cc_start: 0.8714 (t80) cc_final: 0.8424 (t80) REVERT: I 623 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8378 (mm-30) REVERT: I 637 ARG cc_start: 0.8810 (mtt180) cc_final: 0.6891 (tpt170) REVERT: J 168 ASP cc_start: 0.8962 (m-30) cc_final: 0.8705 (m-30) REVERT: J 191 LYS cc_start: 0.8916 (pptt) cc_final: 0.8714 (pptt) REVERT: J 305 TYR cc_start: 0.8675 (p90) cc_final: 0.8402 (p90) REVERT: J 396 GLN cc_start: 0.8896 (mp10) cc_final: 0.8668 (mp10) REVERT: J 567 CYS cc_start: 0.9316 (m) cc_final: 0.8888 (m) REVERT: J 572 MET cc_start: 0.6510 (ptp) cc_final: 0.6232 (ptp) REVERT: J 658 ILE cc_start: 0.8868 (pt) cc_final: 0.8566 (mp) REVERT: J 706 ILE cc_start: 0.8867 (pt) cc_final: 0.8649 (tt) REVERT: J 742 LEU cc_start: 0.9354 (tt) cc_final: 0.9015 (tt) REVERT: J 833 TYR cc_start: 0.7867 (t80) cc_final: 0.6001 (t80) REVERT: J 835 GLN cc_start: 0.7719 (mm110) cc_final: 0.6613 (mm110) REVERT: P 215 MET cc_start: 0.8827 (mmp) cc_final: 0.8036 (tpp) REVERT: P 283 GLN cc_start: 0.8000 (pp30) cc_final: 0.7732 (pp30) REVERT: P 293 ASP cc_start: 0.7390 (m-30) cc_final: 0.7055 (t0) REVERT: P 294 ASN cc_start: 0.8406 (m110) cc_final: 0.8143 (m110) REVERT: P 308 GLN cc_start: 0.8958 (tt0) cc_final: 0.8321 (tm-30) REVERT: P 363 TYR cc_start: 0.8214 (t80) cc_final: 0.7956 (t80) REVERT: P 365 MET cc_start: 0.7444 (ttt) cc_final: 0.6662 (ttt) REVERT: P 384 HIS cc_start: 0.8529 (p-80) cc_final: 0.8265 (p-80) REVERT: P 518 TYR cc_start: 0.7568 (p90) cc_final: 0.7136 (p90) REVERT: P 540 MET cc_start: 0.8416 (mtp) cc_final: 0.8141 (mtm) REVERT: P 646 GLN cc_start: 0.8573 (mt0) cc_final: 0.8006 (tp40) REVERT: P 653 ASN cc_start: 0.7641 (m110) cc_final: 0.7084 (t0) REVERT: P 763 PHE cc_start: 0.8492 (m-10) cc_final: 0.8090 (m-10) REVERT: P 818 GLN cc_start: 0.9211 (tp40) cc_final: 0.8855 (tm-30) REVERT: P 863 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8119 (mmmm) REVERT: P 1039 LEU cc_start: 0.9162 (mp) cc_final: 0.8538 (tp) REVERT: P 1051 TRP cc_start: 0.8137 (m100) cc_final: 0.7709 (m100) outliers start: 11 outliers final: 5 residues processed: 2660 average time/residue: 1.7830 time to fit residues: 7847.3845 Evaluate side-chains 2256 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2250 time to evaluate : 8.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 6.9990 chunk 496 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 650 optimal weight: 0.5980 chunk 360 optimal weight: 4.9990 chunk 745 optimal weight: 0.5980 chunk 604 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 446 optimal weight: 2.9990 chunk 784 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 549 GLN B 874 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN C 614 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 ASN D 484 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 480 HIS F 874 ASN G 267 GLN ** G 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 657 GLN I 94 GLN I 240 GLN I 480 HIS I 486 GLN I 523 GLN I 549 GLN ** I 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 739 GLN I 852 ASN J 247 ASN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1048 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 75455 Z= 0.187 Angle : 0.582 7.983 102320 Z= 0.314 Chirality : 0.041 0.225 11722 Planarity : 0.005 0.215 13254 Dihedral : 5.647 53.777 9999 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.20 % Favored : 92.78 % Rotamer: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.63 (0.08), residues: 9050 helix: 0.02 (0.08), residues: 4333 sheet: -1.82 (0.18), residues: 709 loop : -2.20 (0.09), residues: 4008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 416 HIS 0.015 0.001 HIS E 253 PHE 0.042 0.002 PHE D 373 TYR 0.035 0.002 TYR G 561 ARG 0.017 0.001 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2736 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2732 time to evaluate : 8.654 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8976 (tt0) cc_final: 0.8378 (tm-30) REVERT: A 126 GLN cc_start: 0.7687 (pt0) cc_final: 0.7394 (pt0) REVERT: A 290 ASN cc_start: 0.8198 (m110) cc_final: 0.7897 (m110) REVERT: A 313 ASP cc_start: 0.7861 (t0) cc_final: 0.7186 (m-30) REVERT: A 316 ASN cc_start: 0.9385 (m110) cc_final: 0.9158 (m110) REVERT: A 326 ASP cc_start: 0.8320 (t70) cc_final: 0.8079 (t70) REVERT: A 355 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8756 (tppt) REVERT: A 649 VAL cc_start: 0.7873 (t) cc_final: 0.7425 (t) REVERT: A 777 SER cc_start: 0.8917 (t) cc_final: 0.8688 (p) REVERT: A 822 TYR cc_start: 0.5764 (m-80) cc_final: 0.5436 (m-10) REVERT: B 178 ASP cc_start: 0.8220 (t0) cc_final: 0.7894 (t0) REVERT: B 266 HIS cc_start: 0.9111 (m90) cc_final: 0.8535 (m90) REVERT: B 361 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6911 (tm-30) REVERT: B 467 GLU cc_start: 0.8057 (tt0) cc_final: 0.7625 (tt0) REVERT: B 514 MET cc_start: 0.8558 (mmp) cc_final: 0.7780 (tpp) REVERT: B 561 TYR cc_start: 0.8525 (t80) cc_final: 0.7835 (t80) REVERT: B 576 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8428 (mm-40) REVERT: B 592 CYS cc_start: 0.6608 (m) cc_final: 0.6337 (t) REVERT: B 724 MET cc_start: 0.8338 (pmm) cc_final: 0.7883 (pmm) REVERT: B 817 TYR cc_start: 0.9066 (p90) cc_final: 0.8845 (p90) REVERT: B 821 ASN cc_start: 0.7750 (m-40) cc_final: 0.7519 (m-40) REVERT: B 839 GLN cc_start: 0.6730 (mp10) cc_final: 0.6501 (mp10) REVERT: C 209 SER cc_start: 0.8746 (m) cc_final: 0.8422 (t) REVERT: C 211 THR cc_start: 0.8791 (m) cc_final: 0.8478 (m) REVERT: C 228 VAL cc_start: 0.9285 (m) cc_final: 0.8836 (p) REVERT: C 235 MET cc_start: 0.8384 (ppp) cc_final: 0.7825 (ppp) REVERT: C 261 GLU cc_start: 0.8346 (tp30) cc_final: 0.8067 (tp30) REVERT: C 289 VAL cc_start: 0.9150 (m) cc_final: 0.8759 (p) REVERT: C 354 GLN cc_start: 0.7652 (pt0) cc_final: 0.7438 (pt0) REVERT: C 355 LYS cc_start: 0.7451 (ttpt) cc_final: 0.6850 (ttpp) REVERT: C 356 MET cc_start: 0.9186 (mmm) cc_final: 0.8967 (mmm) REVERT: C 386 PHE cc_start: 0.8294 (t80) cc_final: 0.8057 (t80) REVERT: C 423 ASN cc_start: 0.8768 (m110) cc_final: 0.8345 (p0) REVERT: C 528 MET cc_start: 0.8188 (mmt) cc_final: 0.7930 (mmm) REVERT: C 626 ASN cc_start: 0.8553 (m-40) cc_final: 0.7448 (m110) REVERT: C 683 ILE cc_start: 0.9047 (mm) cc_final: 0.8736 (tp) REVERT: C 696 MET cc_start: 0.8977 (ptm) cc_final: 0.8069 (ppp) REVERT: C 697 GLU cc_start: 0.7968 (pm20) cc_final: 0.6874 (pm20) REVERT: C 721 ARG cc_start: 0.7984 (mtt90) cc_final: 0.6228 (ptt-90) REVERT: C 784 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8268 (mtpt) REVERT: C 797 ARG cc_start: 0.7876 (mpp80) cc_final: 0.7000 (mtt-85) REVERT: C 860 ASP cc_start: 0.8600 (t0) cc_final: 0.8354 (t0) REVERT: D 142 ARG cc_start: 0.7383 (ptm-80) cc_final: 0.7049 (mmt180) REVERT: D 215 CYS cc_start: 0.9034 (m) cc_final: 0.8477 (t) REVERT: D 232 ILE cc_start: 0.8887 (mt) cc_final: 0.8084 (mt) REVERT: D 270 GLU cc_start: 0.7713 (mt-10) cc_final: 0.6667 (mt-10) REVERT: D 307 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7361 (ttm-80) REVERT: D 386 PHE cc_start: 0.8410 (t80) cc_final: 0.8157 (t80) REVERT: D 393 MET cc_start: 0.8165 (mtm) cc_final: 0.7350 (mtp) REVERT: D 484 ASN cc_start: 0.8509 (m110) cc_final: 0.7937 (t0) REVERT: D 561 TYR cc_start: 0.8225 (t80) cc_final: 0.7671 (t80) REVERT: D 586 THR cc_start: 0.9159 (p) cc_final: 0.8939 (p) REVERT: D 611 TYR cc_start: 0.9364 (t80) cc_final: 0.9148 (t80) REVERT: D 701 ARG cc_start: 0.8608 (mmt180) cc_final: 0.7814 (mtt180) REVERT: D 730 ILE cc_start: 0.8983 (tt) cc_final: 0.8457 (mt) REVERT: D 879 ASP cc_start: 0.9279 (p0) cc_final: 0.8773 (p0) REVERT: E 102 ILE cc_start: 0.7208 (pt) cc_final: 0.6905 (tp) REVERT: E 154 TYR cc_start: 0.9035 (m-80) cc_final: 0.8676 (m-80) REVERT: E 160 ASP cc_start: 0.7500 (m-30) cc_final: 0.6581 (t0) REVERT: E 168 ASP cc_start: 0.9018 (m-30) cc_final: 0.8623 (m-30) REVERT: E 193 MET cc_start: 0.8439 (ptp) cc_final: 0.7749 (mtp) REVERT: E 215 CYS cc_start: 0.8819 (t) cc_final: 0.8519 (p) REVERT: E 304 ARG cc_start: 0.7105 (mmt90) cc_final: 0.6694 (mmt90) REVERT: E 454 TYR cc_start: 0.8394 (t80) cc_final: 0.8128 (t80) REVERT: E 467 GLU cc_start: 0.8460 (tt0) cc_final: 0.8005 (tt0) REVERT: E 514 MET cc_start: 0.8769 (mmp) cc_final: 0.7994 (tpt) REVERT: E 550 LEU cc_start: 0.9333 (mt) cc_final: 0.9055 (mt) REVERT: E 568 ILE cc_start: 0.8787 (mm) cc_final: 0.8439 (mm) REVERT: E 666 ASP cc_start: 0.7263 (m-30) cc_final: 0.6785 (m-30) REVERT: E 701 ARG cc_start: 0.9137 (mmt180) cc_final: 0.8812 (mmt90) REVERT: E 821 ASN cc_start: 0.8727 (m-40) cc_final: 0.7972 (t0) REVERT: E 822 TYR cc_start: 0.6748 (m-80) cc_final: 0.6010 (m-10) REVERT: E 846 MET cc_start: 0.8305 (tmm) cc_final: 0.7999 (tmm) REVERT: F 199 ASN cc_start: 0.9123 (m-40) cc_final: 0.8916 (m-40) REVERT: F 216 ASP cc_start: 0.9223 (m-30) cc_final: 0.8717 (t70) REVERT: F 231 PHE cc_start: 0.8808 (t80) cc_final: 0.8583 (t80) REVERT: F 256 ASP cc_start: 0.8066 (m-30) cc_final: 0.7779 (m-30) REVERT: F 307 ARG cc_start: 0.9011 (ttp-110) cc_final: 0.8797 (ttp80) REVERT: F 355 LYS cc_start: 0.8441 (ptmm) cc_final: 0.8031 (ttmt) REVERT: F 458 ASP cc_start: 0.8483 (t0) cc_final: 0.8101 (t0) REVERT: F 636 ASN cc_start: 0.8798 (m-40) cc_final: 0.8573 (t0) REVERT: F 687 ASP cc_start: 0.8689 (m-30) cc_final: 0.8302 (m-30) REVERT: F 696 MET cc_start: 0.8156 (ptm) cc_final: 0.7805 (ttp) REVERT: F 722 ASP cc_start: 0.8305 (t0) cc_final: 0.8096 (t70) REVERT: F 744 GLU cc_start: 0.8728 (mp0) cc_final: 0.7843 (tp30) REVERT: F 746 MET cc_start: 0.7012 (tmm) cc_final: 0.6390 (tpt) REVERT: F 816 PHE cc_start: 0.7811 (t80) cc_final: 0.7459 (t80) REVERT: F 843 ARG cc_start: 0.8556 (mtt90) cc_final: 0.7786 (tpt170) REVERT: F 874 ASN cc_start: 0.9011 (m110) cc_final: 0.8791 (t0) REVERT: G 154 TYR cc_start: 0.5344 (m-80) cc_final: 0.5121 (m-80) REVERT: G 179 GLN cc_start: 0.8412 (pt0) cc_final: 0.8000 (tm-30) REVERT: G 225 GLU cc_start: 0.7938 (pm20) cc_final: 0.7348 (pm20) REVERT: G 256 ASP cc_start: 0.8579 (m-30) cc_final: 0.8279 (m-30) REVERT: G 262 TYR cc_start: 0.7467 (t80) cc_final: 0.7246 (t80) REVERT: G 265 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8041 (tt0) REVERT: G 295 MET cc_start: 0.6933 (mmm) cc_final: 0.5569 (mmm) REVERT: G 304 ARG cc_start: 0.7452 (mpt-90) cc_final: 0.7165 (mpt-90) REVERT: G 316 ASN cc_start: 0.7842 (m-40) cc_final: 0.7468 (m-40) REVERT: G 318 HIS cc_start: 0.8164 (p-80) cc_final: 0.7750 (p-80) REVERT: G 394 LEU cc_start: 0.9263 (mt) cc_final: 0.8930 (tt) REVERT: G 396 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8659 (mm-40) REVERT: G 402 ASP cc_start: 0.8488 (m-30) cc_final: 0.8148 (m-30) REVERT: G 582 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8022 (mmtm) REVERT: G 620 ASN cc_start: 0.8291 (t0) cc_final: 0.7859 (t0) REVERT: G 621 TYR cc_start: 0.8799 (t80) cc_final: 0.8588 (t80) REVERT: G 625 ILE cc_start: 0.8921 (mt) cc_final: 0.8659 (tt) REVERT: G 687 ASP cc_start: 0.9037 (m-30) cc_final: 0.8516 (m-30) REVERT: G 694 MET cc_start: 0.7018 (mtp) cc_final: 0.6727 (mtm) REVERT: G 827 THR cc_start: 0.7452 (p) cc_final: 0.7197 (p) REVERT: H 121 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7255 (mm-30) REVERT: H 122 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8229 (tm-30) REVERT: H 152 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: H 210 GLU cc_start: 0.7904 (tt0) cc_final: 0.7614 (tt0) REVERT: H 224 THR cc_start: 0.8797 (m) cc_final: 0.8472 (t) REVERT: H 277 ILE cc_start: 0.9104 (mt) cc_final: 0.8761 (mm) REVERT: H 404 VAL cc_start: 0.8491 (t) cc_final: 0.8263 (m) REVERT: H 470 ILE cc_start: 0.8826 (mm) cc_final: 0.8617 (mt) REVERT: H 493 ASP cc_start: 0.7619 (t0) cc_final: 0.7257 (t0) REVERT: H 514 MET cc_start: 0.6241 (tmm) cc_final: 0.6014 (tmm) REVERT: H 541 LEU cc_start: 0.8306 (mt) cc_final: 0.8059 (mt) REVERT: H 759 LEU cc_start: 0.8703 (mt) cc_final: 0.8386 (tp) REVERT: H 807 TYR cc_start: 0.7721 (m-80) cc_final: 0.6903 (m-80) REVERT: H 868 ASP cc_start: 0.7366 (t70) cc_final: 0.7152 (t70) REVERT: I 130 PHE cc_start: 0.7643 (t80) cc_final: 0.7431 (t80) REVERT: I 132 ILE cc_start: 0.8575 (mm) cc_final: 0.8340 (mm) REVERT: I 305 TYR cc_start: 0.8754 (p90) cc_final: 0.8367 (p90) REVERT: I 316 ASN cc_start: 0.8898 (m110) cc_final: 0.8165 (m110) REVERT: I 322 GLU cc_start: 0.9158 (pm20) cc_final: 0.8800 (pm20) REVERT: I 423 ASN cc_start: 0.8853 (m110) cc_final: 0.8422 (t0) REVERT: I 443 ILE cc_start: 0.9346 (mm) cc_final: 0.9096 (mp) REVERT: I 521 SER cc_start: 0.8482 (m) cc_final: 0.8251 (p) REVERT: I 567 CYS cc_start: 0.8774 (m) cc_final: 0.8570 (m) REVERT: I 645 MET cc_start: 0.5198 (mpp) cc_final: 0.4868 (mpp) REVERT: I 663 ARG cc_start: 0.7553 (tpp80) cc_final: 0.7168 (tpp80) REVERT: I 717 MET cc_start: 0.5559 (mpp) cc_final: 0.5345 (mpp) REVERT: J 150 ARG cc_start: 0.8109 (ptt180) cc_final: 0.5634 (mtt180) REVERT: J 168 ASP cc_start: 0.9004 (m-30) cc_final: 0.8565 (m-30) REVERT: J 208 ASP cc_start: 0.7914 (m-30) cc_final: 0.7699 (m-30) REVERT: J 274 ASN cc_start: 0.8529 (m110) cc_final: 0.8215 (m-40) REVERT: J 305 TYR cc_start: 0.8368 (p90) cc_final: 0.7410 (p90) REVERT: J 495 VAL cc_start: 0.7634 (m) cc_final: 0.7239 (m) REVERT: J 571 ASN cc_start: 0.8872 (m-40) cc_final: 0.8442 (m-40) REVERT: J 588 VAL cc_start: 0.8918 (t) cc_final: 0.8387 (t) REVERT: J 658 ILE cc_start: 0.8777 (pt) cc_final: 0.8483 (mp) REVERT: J 696 MET cc_start: 0.7760 (ppp) cc_final: 0.7396 (ppp) REVERT: J 701 ARG cc_start: 0.9249 (mtt180) cc_final: 0.8807 (ttm170) REVERT: J 706 ILE cc_start: 0.8728 (pt) cc_final: 0.8481 (tt) REVERT: J 742 LEU cc_start: 0.9180 (tt) cc_final: 0.8963 (tt) REVERT: J 833 TYR cc_start: 0.7507 (t80) cc_final: 0.5829 (t80) REVERT: J 835 GLN cc_start: 0.7670 (mm110) cc_final: 0.6206 (mm110) REVERT: J 848 MET cc_start: 0.8004 (mmm) cc_final: 0.7742 (mmm) REVERT: P 213 MET cc_start: 0.7224 (mtm) cc_final: 0.6737 (mtm) REVERT: P 215 MET cc_start: 0.8663 (mmp) cc_final: 0.7836 (tpp) REVERT: P 257 ILE cc_start: 0.8525 (mt) cc_final: 0.8300 (mt) REVERT: P 293 ASP cc_start: 0.7332 (m-30) cc_final: 0.7068 (t0) REVERT: P 294 ASN cc_start: 0.8333 (m110) cc_final: 0.8121 (m110) REVERT: P 308 GLN cc_start: 0.8890 (tt0) cc_final: 0.8160 (tm-30) REVERT: P 363 TYR cc_start: 0.7788 (t80) cc_final: 0.7493 (t80) REVERT: P 365 MET cc_start: 0.7366 (ttt) cc_final: 0.6526 (ttt) REVERT: P 373 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7945 (mtpp) REVERT: P 374 MET cc_start: 0.8459 (mmt) cc_final: 0.8227 (mmt) REVERT: P 518 TYR cc_start: 0.7228 (p90) cc_final: 0.6923 (p90) REVERT: P 540 MET cc_start: 0.8272 (mtp) cc_final: 0.7932 (mtt) REVERT: P 646 GLN cc_start: 0.8700 (mt0) cc_final: 0.8270 (tp40) REVERT: P 653 ASN cc_start: 0.7790 (m110) cc_final: 0.6875 (t0) REVERT: P 657 GLU cc_start: 0.8092 (mp0) cc_final: 0.6962 (mp0) REVERT: P 687 ILE cc_start: 0.8670 (tp) cc_final: 0.8467 (tp) REVERT: P 756 VAL cc_start: 0.9325 (t) cc_final: 0.9046 (p) REVERT: P 763 PHE cc_start: 0.8342 (m-10) cc_final: 0.8003 (m-10) REVERT: P 863 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8020 (mmmm) REVERT: P 1051 TRP cc_start: 0.8519 (m100) cc_final: 0.7836 (m100) outliers start: 4 outliers final: 2 residues processed: 2734 average time/residue: 1.8576 time to fit residues: 8453.4979 Evaluate side-chains 2345 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2343 time to evaluate : 8.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 5.9990 chunk 786 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 513 optimal weight: 0.0570 chunk 215 optimal weight: 4.9990 chunk 874 optimal weight: 8.9990 chunk 726 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 459 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN B 622 ASN B 874 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 753 GLN C 792 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN D 584 GLN ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 HIS F 512 GLN F 519 GLN F 523 GLN ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 537 GLN ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 480 HIS I 486 GLN I 576 GLN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 75455 Z= 0.310 Angle : 0.643 7.515 102320 Z= 0.350 Chirality : 0.041 0.181 11722 Planarity : 0.005 0.111 13254 Dihedral : 5.634 55.628 9999 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.51 % Favored : 90.46 % Rotamer: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.70 (0.08), residues: 9050 helix: -0.02 (0.08), residues: 4290 sheet: -1.74 (0.18), residues: 686 loop : -2.25 (0.09), residues: 4074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 153 HIS 0.009 0.002 HIS I 847 PHE 0.030 0.002 PHE B 481 TYR 0.034 0.002 TYR E 621 ARG 0.008 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2602 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2600 time to evaluate : 8.664 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 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.9016 (tt0) cc_final: 0.7563 (pm20) REVERT: A 317 LEU cc_start: 0.9271 (mt) cc_final: 0.8979 (mt) REVERT: A 355 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8655 (tppt) REVERT: A 399 MET cc_start: 0.6307 (pmm) cc_final: 0.6106 (pmm) REVERT: A 452 MET cc_start: 0.8567 (tpt) cc_final: 0.8260 (tpt) REVERT: A 649 VAL cc_start: 0.8110 (t) cc_final: 0.7713 (t) REVERT: A 660 ASP cc_start: 0.7624 (p0) cc_final: 0.7161 (p0) REVERT: A 843 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7748 (mtm110) REVERT: B 178 ASP cc_start: 0.8220 (t0) cc_final: 0.7925 (t0) REVERT: B 261 GLU cc_start: 0.7447 (tp30) cc_final: 0.7120 (tp30) REVERT: B 266 HIS cc_start: 0.9175 (m90) cc_final: 0.8588 (m90) REVERT: B 361 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6665 (tm-30) REVERT: B 427 ILE cc_start: 0.9109 (tt) cc_final: 0.8881 (tt) REVERT: B 467 GLU cc_start: 0.8147 (tt0) cc_final: 0.7760 (tt0) REVERT: B 514 MET cc_start: 0.8493 (mmp) cc_final: 0.7596 (tpp) REVERT: B 550 LEU cc_start: 0.9534 (mt) cc_final: 0.9161 (mt) REVERT: B 561 TYR cc_start: 0.8546 (t80) cc_final: 0.7991 (t80) REVERT: B 576 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8581 (mm-40) REVERT: B 645 MET cc_start: 0.7456 (mmp) cc_final: 0.6305 (mtt) REVERT: B 688 ILE cc_start: 0.8946 (mm) cc_final: 0.8719 (mm) REVERT: B 817 TYR cc_start: 0.9080 (p90) cc_final: 0.8820 (p90) REVERT: C 164 ASP cc_start: 0.7233 (m-30) cc_final: 0.6895 (m-30) REVERT: C 209 SER cc_start: 0.8805 (m) cc_final: 0.8487 (t) REVERT: C 211 THR cc_start: 0.8877 (m) cc_final: 0.8594 (m) REVERT: C 228 VAL cc_start: 0.9346 (m) cc_final: 0.8932 (p) REVERT: C 289 VAL cc_start: 0.9216 (m) cc_final: 0.8859 (p) REVERT: C 305 TYR cc_start: 0.6737 (p90) cc_final: 0.6531 (p90) REVERT: C 354 GLN cc_start: 0.7688 (pt0) cc_final: 0.7461 (pt0) REVERT: C 355 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7015 (ttpp) REVERT: C 423 ASN cc_start: 0.8799 (m110) cc_final: 0.8359 (p0) REVERT: C 518 MET cc_start: 0.8783 (mmm) cc_final: 0.8333 (tpp) REVERT: C 683 ILE cc_start: 0.9052 (mm) cc_final: 0.8700 (tp) REVERT: C 693 LEU cc_start: 0.9093 (mt) cc_final: 0.8441 (mp) REVERT: C 696 MET cc_start: 0.8962 (ptm) cc_final: 0.8184 (ppp) REVERT: C 697 GLU cc_start: 0.8030 (pm20) cc_final: 0.7188 (pm20) REVERT: C 721 ARG cc_start: 0.8030 (mtt90) cc_final: 0.6514 (ptt-90) REVERT: C 784 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8295 (mtpt) REVERT: C 797 ARG cc_start: 0.7783 (mpp80) cc_final: 0.6972 (mtt-85) REVERT: C 860 ASP cc_start: 0.8684 (t0) cc_final: 0.8444 (t0) REVERT: C 862 LEU cc_start: 0.8983 (mt) cc_final: 0.8746 (mp) REVERT: D 131 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7647 (ttm170) REVERT: D 142 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.7020 (mmt180) REVERT: D 210 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 215 CYS cc_start: 0.9072 (m) cc_final: 0.8748 (t) REVERT: D 232 ILE cc_start: 0.9019 (mt) cc_final: 0.8295 (mt) REVERT: D 307 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7380 (ttm-80) REVERT: D 393 MET cc_start: 0.8191 (mtm) cc_final: 0.7463 (mtp) REVERT: D 484 ASN cc_start: 0.8498 (m110) cc_final: 0.8022 (t0) REVERT: D 561 TYR cc_start: 0.8190 (t80) cc_final: 0.7748 (t80) REVERT: D 701 ARG cc_start: 0.8743 (mmt180) cc_final: 0.8044 (mtt-85) REVERT: D 730 ILE cc_start: 0.9122 (tt) cc_final: 0.8627 (mt) REVERT: D 881 MET cc_start: 0.8074 (mmp) cc_final: 0.7511 (mmm) REVERT: E 102 ILE cc_start: 0.7231 (pt) cc_final: 0.6873 (tp) REVERT: E 154 TYR cc_start: 0.9059 (m-80) cc_final: 0.8648 (m-80) REVERT: E 160 ASP cc_start: 0.7589 (m-30) cc_final: 0.6730 (t0) REVERT: E 168 ASP cc_start: 0.8983 (m-30) cc_final: 0.8546 (m-30) REVERT: E 193 MET cc_start: 0.8365 (ptp) cc_final: 0.7814 (mtp) REVERT: E 244 ASN cc_start: 0.7814 (m-40) cc_final: 0.7515 (m-40) REVERT: E 248 TYR cc_start: 0.7258 (m-80) cc_final: 0.6817 (m-10) REVERT: E 261 GLU cc_start: 0.8503 (tp30) cc_final: 0.8091 (tm-30) REVERT: E 287 ASN cc_start: 0.8382 (m-40) cc_final: 0.7638 (m110) REVERT: E 295 MET cc_start: 0.7086 (pmm) cc_final: 0.6699 (pmm) REVERT: E 362 LEU cc_start: 0.7953 (mt) cc_final: 0.7570 (pp) REVERT: E 409 MET cc_start: 0.9032 (tpp) cc_final: 0.8825 (tpp) REVERT: E 514 MET cc_start: 0.8812 (mmp) cc_final: 0.8248 (tpt) REVERT: E 550 LEU cc_start: 0.9389 (mt) cc_final: 0.9151 (mt) REVERT: E 582 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7569 (mmmt) REVERT: E 666 ASP cc_start: 0.7377 (m-30) cc_final: 0.6969 (m-30) REVERT: E 669 MET cc_start: 0.8623 (mmm) cc_final: 0.8393 (tpp) REVERT: E 701 ARG cc_start: 0.9213 (mmt180) cc_final: 0.8447 (mmm-85) REVERT: E 821 ASN cc_start: 0.8779 (m-40) cc_final: 0.8351 (t0) REVERT: E 822 TYR cc_start: 0.6654 (m-80) cc_final: 0.5838 (m-10) REVERT: E 846 MET cc_start: 0.8329 (tmm) cc_final: 0.7785 (tmm) REVERT: F 99 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8017 (tm-30) REVERT: F 199 ASN cc_start: 0.9025 (m-40) cc_final: 0.8797 (m-40) REVERT: F 216 ASP cc_start: 0.9097 (m-30) cc_final: 0.8672 (m-30) REVERT: F 256 ASP cc_start: 0.8014 (m-30) cc_final: 0.7727 (m-30) REVERT: F 307 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8841 (ttp80) REVERT: F 312 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8289 (pp30) REVERT: F 355 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8000 (ttmt) REVERT: F 356 MET cc_start: 0.8486 (mmt) cc_final: 0.8215 (mmt) REVERT: F 415 MET cc_start: 0.8416 (ptp) cc_final: 0.8181 (ptp) REVERT: F 687 ASP cc_start: 0.8705 (m-30) cc_final: 0.8317 (m-30) REVERT: F 696 MET cc_start: 0.8182 (ptm) cc_final: 0.7886 (ttp) REVERT: F 744 GLU cc_start: 0.8981 (mp0) cc_final: 0.7880 (tp30) REVERT: F 745 LEU cc_start: 0.8102 (tp) cc_final: 0.7831 (tp) REVERT: F 746 MET cc_start: 0.7438 (tmm) cc_final: 0.6827 (tmm) REVERT: F 843 ARG cc_start: 0.8633 (mtt90) cc_final: 0.7905 (tpt170) REVERT: F 874 ASN cc_start: 0.9066 (m110) cc_final: 0.8784 (t0) REVERT: G 256 ASP cc_start: 0.8609 (m-30) cc_final: 0.8341 (m-30) REVERT: G 265 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8260 (tt0) REVERT: G 295 MET cc_start: 0.7089 (mmm) cc_final: 0.5805 (mmm) REVERT: G 318 HIS cc_start: 0.8175 (p-80) cc_final: 0.7770 (p-80) REVERT: G 394 LEU cc_start: 0.9379 (mt) cc_final: 0.8972 (tt) REVERT: G 396 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8591 (mm-40) REVERT: G 418 LEU cc_start: 0.9093 (mm) cc_final: 0.8887 (mm) REVERT: G 565 MET cc_start: 0.9024 (mtt) cc_final: 0.8783 (mtt) REVERT: G 582 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8081 (mmtm) REVERT: G 620 ASN cc_start: 0.8346 (t0) cc_final: 0.8139 (t0) REVERT: G 621 TYR cc_start: 0.8896 (t80) cc_final: 0.8650 (t80) REVERT: G 625 ILE cc_start: 0.8982 (mt) cc_final: 0.8687 (tt) REVERT: G 687 ASP cc_start: 0.9100 (m-30) cc_final: 0.8663 (m-30) REVERT: G 694 MET cc_start: 0.7102 (mtp) cc_final: 0.6729 (mtm) REVERT: G 721 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7555 (mtp180) REVERT: G 827 THR cc_start: 0.7499 (p) cc_final: 0.7248 (p) REVERT: H 121 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7319 (mm-30) REVERT: H 122 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8286 (tm-30) REVERT: H 148 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7325 (mt-10) REVERT: H 152 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7940 (ttm-80) REVERT: H 182 THR cc_start: 0.7476 (m) cc_final: 0.7262 (m) REVERT: H 210 GLU cc_start: 0.7981 (tt0) cc_final: 0.7683 (tt0) REVERT: H 221 ASP cc_start: 0.7519 (t0) cc_final: 0.7200 (t0) REVERT: H 242 ASP cc_start: 0.7605 (p0) cc_final: 0.7253 (p0) REVERT: H 277 ILE cc_start: 0.9068 (mt) cc_final: 0.8753 (mm) REVERT: H 404 VAL cc_start: 0.8592 (t) cc_final: 0.8360 (m) REVERT: H 470 ILE cc_start: 0.8861 (mm) cc_final: 0.8657 (mt) REVERT: H 493 ASP cc_start: 0.7605 (t0) cc_final: 0.7222 (t0) REVERT: H 515 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7254 (mt-10) REVERT: H 541 LEU cc_start: 0.8176 (mt) cc_final: 0.7942 (mt) REVERT: H 593 MET cc_start: 0.8148 (mmm) cc_final: 0.7706 (mmm) REVERT: H 690 ASN cc_start: 0.8190 (m110) cc_final: 0.7973 (m110) REVERT: H 715 ARG cc_start: 0.8550 (ptp-110) cc_final: 0.8156 (mtm-85) REVERT: H 724 MET cc_start: 0.7551 (ttt) cc_final: 0.7258 (tpp) REVERT: H 759 LEU cc_start: 0.8645 (mt) cc_final: 0.8350 (tp) REVERT: H 807 TYR cc_start: 0.7916 (m-80) cc_final: 0.7115 (m-80) REVERT: I 316 ASN cc_start: 0.8542 (m110) cc_final: 0.8294 (m110) REVERT: I 394 LEU cc_start: 0.8697 (mt) cc_final: 0.8249 (mt) REVERT: I 407 ASN cc_start: 0.8176 (t0) cc_final: 0.7904 (t0) REVERT: I 423 ASN cc_start: 0.8902 (m110) cc_final: 0.8506 (t0) REVERT: I 440 ASN cc_start: 0.8918 (m-40) cc_final: 0.8281 (p0) REVERT: I 443 ILE cc_start: 0.9289 (mm) cc_final: 0.9003 (mp) REVERT: I 521 SER cc_start: 0.8547 (m) cc_final: 0.8296 (p) REVERT: I 637 ARG cc_start: 0.8712 (mtt180) cc_final: 0.6869 (tpm170) REVERT: I 714 TYR cc_start: 0.8187 (m-80) cc_final: 0.7617 (m-80) REVERT: I 717 MET cc_start: 0.5780 (mpp) cc_final: 0.5579 (mpp) REVERT: I 880 ASN cc_start: 0.8238 (t0) cc_final: 0.8005 (t0) REVERT: J 168 ASP cc_start: 0.9003 (m-30) cc_final: 0.8672 (m-30) REVERT: J 199 ASN cc_start: 0.7009 (m110) cc_final: 0.6672 (m-40) REVERT: J 274 ASN cc_start: 0.8632 (m110) cc_final: 0.8340 (m-40) REVERT: J 305 TYR cc_start: 0.8548 (p90) cc_final: 0.8271 (p90) REVERT: J 588 VAL cc_start: 0.9079 (t) cc_final: 0.8593 (t) REVERT: J 658 ILE cc_start: 0.8832 (pt) cc_final: 0.8632 (mp) REVERT: J 659 PHE cc_start: 0.8777 (m-10) cc_final: 0.8548 (m-10) REVERT: J 742 LEU cc_start: 0.9263 (tt) cc_final: 0.8997 (tt) REVERT: J 833 TYR cc_start: 0.7589 (t80) cc_final: 0.5836 (t80) REVERT: J 835 GLN cc_start: 0.7590 (mm110) cc_final: 0.6582 (mm110) REVERT: P 215 MET cc_start: 0.8654 (mmp) cc_final: 0.7865 (tpp) REVERT: P 257 ILE cc_start: 0.8591 (mt) cc_final: 0.8312 (mt) REVERT: P 258 ASN cc_start: 0.6613 (t0) cc_final: 0.5810 (p0) REVERT: P 293 ASP cc_start: 0.7393 (m-30) cc_final: 0.7098 (t0) REVERT: P 294 ASN cc_start: 0.8410 (m110) cc_final: 0.8113 (m110) REVERT: P 308 GLN cc_start: 0.8960 (tt0) cc_final: 0.8180 (tm-30) REVERT: P 363 TYR cc_start: 0.7931 (t80) cc_final: 0.7708 (t80) REVERT: P 365 MET cc_start: 0.7505 (ttt) cc_final: 0.6656 (ttt) REVERT: P 374 MET cc_start: 0.8642 (mmt) cc_final: 0.8290 (mmt) REVERT: P 518 TYR cc_start: 0.7357 (p90) cc_final: 0.7138 (p90) REVERT: P 540 MET cc_start: 0.8335 (mtp) cc_final: 0.7957 (mtt) REVERT: P 548 MET cc_start: 0.7738 (ttp) cc_final: 0.7335 (tmm) REVERT: P 561 TYR cc_start: 0.7711 (t80) cc_final: 0.7439 (t80) REVERT: P 646 GLN cc_start: 0.8741 (mt0) cc_final: 0.8274 (tp40) REVERT: P 653 ASN cc_start: 0.7874 (m110) cc_final: 0.7307 (t0) REVERT: P 657 GLU cc_start: 0.8269 (mp0) cc_final: 0.7548 (mp0) REVERT: P 756 VAL cc_start: 0.9297 (t) cc_final: 0.9016 (p) REVERT: P 763 PHE cc_start: 0.8470 (m-10) cc_final: 0.8126 (m-10) REVERT: P 863 LYS cc_start: 0.8297 (mmmt) cc_final: 0.8010 (mmmm) REVERT: P 1051 TRP cc_start: 0.8529 (m100) cc_final: 0.7930 (m100) outliers start: 2 outliers final: 0 residues processed: 2601 average time/residue: 1.7797 time to fit residues: 7614.1061 Evaluate side-chains 2287 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2287 time to evaluate : 8.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 498 optimal weight: 5.9990 chunk 638 optimal weight: 0.9980 chunk 494 optimal weight: 4.9990 chunk 736 optimal weight: 6.9990 chunk 488 optimal weight: 0.8980 chunk 871 optimal weight: 1.9990 chunk 545 optimal weight: 4.9990 chunk 531 optimal weight: 4.9990 chunk 402 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 199 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 668 GLN ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN B 874 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN C 614 ASN C 792 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 HIS G 267 GLN G 523 GLN ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN I 240 GLN I 480 HIS I 486 GLN I 576 GLN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 75455 Z= 0.195 Angle : 0.564 6.344 102320 Z= 0.304 Chirality : 0.040 0.164 11722 Planarity : 0.005 0.110 13254 Dihedral : 5.394 55.263 9999 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.36 % Favored : 92.62 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.32 (0.09), residues: 9050 helix: 0.34 (0.08), residues: 4303 sheet: -1.63 (0.18), residues: 704 loop : -2.11 (0.09), residues: 4043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 153 HIS 0.008 0.001 HIS E 253 PHE 0.037 0.001 PHE B 481 TYR 0.039 0.002 TYR I 532 ARG 0.009 0.001 ARG H 882 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2649 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2645 time to evaluate : 8.724 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8095 (m110) cc_final: 0.7800 (m110) REVERT: A 326 ASP cc_start: 0.8248 (t70) cc_final: 0.7989 (t70) REVERT: A 355 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8736 (tppt) REVERT: A 443 ILE cc_start: 0.9441 (mp) cc_final: 0.9232 (mm) REVERT: A 570 MET cc_start: 0.8722 (ptp) cc_final: 0.8406 (ptt) REVERT: B 178 ASP cc_start: 0.8294 (t0) cc_final: 0.7951 (t0) REVERT: B 261 GLU cc_start: 0.7476 (tp30) cc_final: 0.7060 (tp30) REVERT: B 320 ASN cc_start: 0.8655 (t0) cc_final: 0.8198 (t0) REVERT: B 427 ILE cc_start: 0.9122 (tt) cc_final: 0.8913 (tt) REVERT: B 467 GLU cc_start: 0.8257 (tt0) cc_final: 0.7554 (tt0) REVERT: B 514 MET cc_start: 0.8554 (mmp) cc_final: 0.7619 (tpp) REVERT: B 561 TYR cc_start: 0.8445 (t80) cc_final: 0.7808 (t80) REVERT: B 704 ASP cc_start: 0.7647 (m-30) cc_final: 0.7125 (p0) REVERT: C 164 ASP cc_start: 0.7259 (m-30) cc_final: 0.6940 (m-30) REVERT: C 209 SER cc_start: 0.8783 (m) cc_final: 0.8421 (t) REVERT: C 211 THR cc_start: 0.8850 (m) cc_final: 0.8562 (m) REVERT: C 228 VAL cc_start: 0.9352 (m) cc_final: 0.8955 (p) REVERT: C 289 VAL cc_start: 0.9179 (m) cc_final: 0.8787 (p) REVERT: C 354 GLN cc_start: 0.7724 (pt0) cc_final: 0.7522 (pt0) REVERT: C 355 LYS cc_start: 0.7567 (ttpt) cc_final: 0.7018 (ttpp) REVERT: C 423 ASN cc_start: 0.8824 (m110) cc_final: 0.8283 (p0) REVERT: C 518 MET cc_start: 0.8619 (mmm) cc_final: 0.8040 (tpp) REVERT: C 531 ASP cc_start: 0.7665 (p0) cc_final: 0.7387 (p0) REVERT: C 683 ILE cc_start: 0.9090 (mm) cc_final: 0.8797 (tp) REVERT: C 685 ARG cc_start: 0.8894 (mtt-85) cc_final: 0.8049 (mtt90) REVERT: C 693 LEU cc_start: 0.8949 (mt) cc_final: 0.8393 (mp) REVERT: C 696 MET cc_start: 0.8898 (ptm) cc_final: 0.8144 (ppp) REVERT: C 697 GLU cc_start: 0.8060 (pm20) cc_final: 0.6939 (pm20) REVERT: C 704 ASP cc_start: 0.8526 (m-30) cc_final: 0.8187 (m-30) REVERT: C 721 ARG cc_start: 0.7936 (mtt90) cc_final: 0.6450 (ptt-90) REVERT: C 784 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8234 (mtpt) REVERT: C 797 ARG cc_start: 0.7838 (mpp80) cc_final: 0.6913 (mtt-85) REVERT: C 860 ASP cc_start: 0.8633 (t0) cc_final: 0.8349 (t0) REVERT: D 92 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7352 (tp30) REVERT: D 131 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7601 (ttm170) REVERT: D 142 ARG cc_start: 0.7334 (ptm-80) cc_final: 0.6947 (mmt180) REVERT: D 173 PHE cc_start: 0.8469 (m-80) cc_final: 0.8021 (m-10) REVERT: D 186 ASP cc_start: 0.6649 (m-30) cc_final: 0.6128 (m-30) REVERT: D 210 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8074 (mt-10) REVERT: D 215 CYS cc_start: 0.9060 (m) cc_final: 0.8621 (t) REVERT: D 232 ILE cc_start: 0.9081 (mt) cc_final: 0.8218 (mt) REVERT: D 270 GLU cc_start: 0.7822 (mt-10) cc_final: 0.6712 (mt-10) REVERT: D 307 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7401 (ttm-80) REVERT: D 393 MET cc_start: 0.8102 (mtm) cc_final: 0.7321 (mtp) REVERT: D 471 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7866 (mm110) REVERT: D 484 ASN cc_start: 0.8570 (m110) cc_final: 0.8060 (t0) REVERT: D 510 VAL cc_start: 0.9221 (m) cc_final: 0.8984 (p) REVERT: D 561 TYR cc_start: 0.8184 (t80) cc_final: 0.7693 (t80) REVERT: D 586 THR cc_start: 0.9150 (p) cc_final: 0.8837 (p) REVERT: D 701 ARG cc_start: 0.8602 (mmt180) cc_final: 0.7913 (mtt180) REVERT: D 730 ILE cc_start: 0.9153 (tt) cc_final: 0.8592 (mt) REVERT: D 879 ASP cc_start: 0.9277 (p0) cc_final: 0.8871 (p0) REVERT: E 102 ILE cc_start: 0.7296 (pt) cc_final: 0.6932 (tp) REVERT: E 160 ASP cc_start: 0.7566 (m-30) cc_final: 0.6559 (t0) REVERT: E 193 MET cc_start: 0.8308 (ptp) cc_final: 0.7680 (mtp) REVERT: E 244 ASN cc_start: 0.7729 (m-40) cc_final: 0.7455 (m-40) REVERT: E 319 ASP cc_start: 0.8572 (t0) cc_final: 0.8321 (t0) REVERT: E 333 TYR cc_start: 0.8857 (t80) cc_final: 0.8583 (t80) REVERT: E 362 LEU cc_start: 0.7702 (mt) cc_final: 0.7394 (pp) REVERT: E 393 MET cc_start: 0.9258 (mtp) cc_final: 0.9053 (mtp) REVERT: E 409 MET cc_start: 0.9004 (tpp) cc_final: 0.8719 (tpp) REVERT: E 452 MET cc_start: 0.8579 (tpp) cc_final: 0.7964 (tpp) REVERT: E 467 GLU cc_start: 0.8421 (tt0) cc_final: 0.8007 (tt0) REVERT: E 514 MET cc_start: 0.8720 (mmp) cc_final: 0.8148 (tpt) REVERT: E 550 LEU cc_start: 0.9349 (mt) cc_final: 0.9084 (mt) REVERT: E 582 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7635 (mmmt) REVERT: E 593 MET cc_start: 0.8814 (tpp) cc_final: 0.8577 (tpp) REVERT: E 666 ASP cc_start: 0.7655 (m-30) cc_final: 0.6996 (m-30) REVERT: E 669 MET cc_start: 0.8468 (mtp) cc_final: 0.7802 (ttm) REVERT: E 701 ARG cc_start: 0.9237 (mmt180) cc_final: 0.8564 (mmm-85) REVERT: E 821 ASN cc_start: 0.8773 (m-40) cc_final: 0.8218 (t0) REVERT: E 831 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8056 (mtmt) REVERT: F 99 GLN cc_start: 0.8475 (tp-100) cc_final: 0.7563 (tm-30) REVERT: F 168 ASP cc_start: 0.8488 (m-30) cc_final: 0.8265 (m-30) REVERT: F 216 ASP cc_start: 0.9097 (m-30) cc_final: 0.8771 (t70) REVERT: F 243 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8412 (mtm110) REVERT: F 256 ASP cc_start: 0.8038 (m-30) cc_final: 0.7705 (m-30) REVERT: F 268 LEU cc_start: 0.8351 (mm) cc_final: 0.8025 (mm) REVERT: F 312 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8285 (pp30) REVERT: F 355 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8291 (ttmt) REVERT: F 356 MET cc_start: 0.8535 (mmt) cc_final: 0.8273 (mmt) REVERT: F 643 LYS cc_start: 0.9278 (ttmt) cc_final: 0.8943 (ttmm) REVERT: F 687 ASP cc_start: 0.8607 (m-30) cc_final: 0.8246 (m-30) REVERT: F 696 MET cc_start: 0.8097 (ptm) cc_final: 0.7780 (ttp) REVERT: F 722 ASP cc_start: 0.8435 (t0) cc_final: 0.8161 (t70) REVERT: F 725 TYR cc_start: 0.7253 (m-80) cc_final: 0.7023 (m-80) REVERT: F 744 GLU cc_start: 0.8989 (mp0) cc_final: 0.8001 (tp30) REVERT: F 745 LEU cc_start: 0.8054 (tp) cc_final: 0.7770 (tp) REVERT: F 746 MET cc_start: 0.7412 (tmm) cc_final: 0.6865 (tmm) REVERT: F 816 PHE cc_start: 0.7898 (t80) cc_final: 0.7540 (t80) REVERT: F 843 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8238 (mmm160) REVERT: F 874 ASN cc_start: 0.8982 (m110) cc_final: 0.8776 (t0) REVERT: G 154 TYR cc_start: 0.5679 (m-80) cc_final: 0.4428 (m-80) REVERT: G 235 MET cc_start: 0.8162 (mtp) cc_final: 0.7828 (mtp) REVERT: G 256 ASP cc_start: 0.8637 (m-30) cc_final: 0.8381 (m-30) REVERT: G 265 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7889 (tt0) REVERT: G 295 MET cc_start: 0.7046 (mmm) cc_final: 0.5706 (mmm) REVERT: G 318 HIS cc_start: 0.8161 (p-80) cc_final: 0.7808 (p-80) REVERT: G 393 MET cc_start: 0.9505 (mmp) cc_final: 0.8937 (mmp) REVERT: G 394 LEU cc_start: 0.9196 (mt) cc_final: 0.8968 (tt) REVERT: G 396 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8611 (mm-40) REVERT: G 418 LEU cc_start: 0.9101 (mm) cc_final: 0.8828 (mm) REVERT: G 565 MET cc_start: 0.9052 (mtt) cc_final: 0.8835 (mtm) REVERT: G 582 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8040 (mmtm) REVERT: G 583 LEU cc_start: 0.9323 (tt) cc_final: 0.9059 (tt) REVERT: G 620 ASN cc_start: 0.8271 (t0) cc_final: 0.8070 (t0) REVERT: G 621 TYR cc_start: 0.8816 (t80) cc_final: 0.8588 (t80) REVERT: G 687 ASP cc_start: 0.9002 (m-30) cc_final: 0.8509 (m-30) REVERT: G 694 MET cc_start: 0.7050 (mtp) cc_final: 0.6666 (mtm) REVERT: G 746 MET cc_start: 0.8188 (tmm) cc_final: 0.7806 (tmm) REVERT: H 121 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7301 (mm-30) REVERT: H 122 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8039 (tm-30) REVERT: H 148 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7063 (mt-10) REVERT: H 152 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: H 170 ARG cc_start: 0.9187 (mtm180) cc_final: 0.8948 (mtm180) REVERT: H 182 THR cc_start: 0.7354 (m) cc_final: 0.7148 (m) REVERT: H 210 GLU cc_start: 0.7888 (tt0) cc_final: 0.7574 (tt0) REVERT: H 221 ASP cc_start: 0.7419 (t0) cc_final: 0.7066 (t0) REVERT: H 277 ILE cc_start: 0.9064 (mt) cc_final: 0.8715 (mm) REVERT: H 291 TYR cc_start: 0.8439 (m-80) cc_final: 0.8200 (m-80) REVERT: H 404 VAL cc_start: 0.8538 (t) cc_final: 0.8337 (m) REVERT: H 493 ASP cc_start: 0.7890 (t0) cc_final: 0.7528 (t0) REVERT: H 541 LEU cc_start: 0.8385 (mt) cc_final: 0.8168 (mt) REVERT: H 715 ARG cc_start: 0.8465 (ptp-110) cc_final: 0.8093 (mtm-85) REVERT: H 723 GLU cc_start: 0.7627 (tm-30) cc_final: 0.6453 (tm-30) REVERT: H 724 MET cc_start: 0.7674 (ttt) cc_final: 0.7030 (tpp) REVERT: H 759 LEU cc_start: 0.8648 (mt) cc_final: 0.8351 (tp) REVERT: H 807 TYR cc_start: 0.7989 (m-80) cc_final: 0.7241 (m-80) REVERT: I 316 ASN cc_start: 0.8346 (m110) cc_final: 0.8093 (m110) REVERT: I 322 GLU cc_start: 0.8989 (pm20) cc_final: 0.8789 (pm20) REVERT: I 407 ASN cc_start: 0.8192 (t0) cc_final: 0.7941 (t0) REVERT: I 423 ASN cc_start: 0.8836 (m110) cc_final: 0.8401 (t0) REVERT: I 428 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8650 (mmm-85) REVERT: I 440 ASN cc_start: 0.8942 (m-40) cc_final: 0.8309 (p0) REVERT: I 443 ILE cc_start: 0.9322 (mm) cc_final: 0.9019 (mp) REVERT: I 451 ARG cc_start: 0.7317 (mmm-85) cc_final: 0.7065 (mmm-85) REVERT: I 468 GLN cc_start: 0.9321 (tp40) cc_final: 0.8559 (tp40) REVERT: J 150 ARG cc_start: 0.8107 (ptt180) cc_final: 0.5556 (mtt180) REVERT: J 199 ASN cc_start: 0.6946 (m110) cc_final: 0.6667 (m-40) REVERT: J 305 TYR cc_start: 0.8409 (p90) cc_final: 0.8150 (p90) REVERT: J 514 MET cc_start: 0.8482 (tpp) cc_final: 0.7969 (mmt) REVERT: J 588 VAL cc_start: 0.9012 (t) cc_final: 0.8486 (t) REVERT: J 658 ILE cc_start: 0.8814 (pt) cc_final: 0.8608 (mp) REVERT: J 659 PHE cc_start: 0.8767 (m-10) cc_final: 0.8551 (m-10) REVERT: J 827 THR cc_start: 0.8083 (p) cc_final: 0.7744 (t) REVERT: J 833 TYR cc_start: 0.7541 (t80) cc_final: 0.5932 (t80) REVERT: P 143 ASN cc_start: 0.7801 (t0) cc_final: 0.7488 (t0) REVERT: P 248 MET cc_start: 0.8993 (ttt) cc_final: 0.8764 (ttt) REVERT: P 257 ILE cc_start: 0.8526 (mt) cc_final: 0.8243 (mt) REVERT: P 258 ASN cc_start: 0.6625 (t0) cc_final: 0.5892 (p0) REVERT: P 294 ASN cc_start: 0.8218 (m110) cc_final: 0.7898 (m110) REVERT: P 308 GLN cc_start: 0.8881 (tt0) cc_final: 0.8124 (tm-30) REVERT: P 359 MET cc_start: 0.7963 (mmt) cc_final: 0.7683 (mpp) REVERT: P 365 MET cc_start: 0.7493 (ttt) cc_final: 0.6701 (ttt) REVERT: P 374 MET cc_start: 0.8576 (mmt) cc_final: 0.8336 (mmt) REVERT: P 430 ASN cc_start: 0.8717 (m110) cc_final: 0.8336 (m110) REVERT: P 540 MET cc_start: 0.8082 (mtp) cc_final: 0.7662 (mtt) REVERT: P 561 TYR cc_start: 0.7469 (t80) cc_final: 0.7211 (t80) REVERT: P 608 ILE cc_start: 0.8420 (mm) cc_final: 0.8018 (tt) REVERT: P 646 GLN cc_start: 0.8773 (mt0) cc_final: 0.8229 (tp40) REVERT: P 653 ASN cc_start: 0.7799 (m110) cc_final: 0.7538 (t0) REVERT: P 657 GLU cc_start: 0.8261 (mp0) cc_final: 0.7770 (mp0) REVERT: P 756 VAL cc_start: 0.9297 (t) cc_final: 0.9045 (p) REVERT: P 763 PHE cc_start: 0.8424 (m-10) cc_final: 0.7988 (m-10) REVERT: P 854 ILE cc_start: 0.8980 (mm) cc_final: 0.8763 (mm) REVERT: P 863 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7881 (mmmm) REVERT: P 1051 TRP cc_start: 0.8548 (m100) cc_final: 0.7891 (m100) outliers start: 4 outliers final: 0 residues processed: 2648 average time/residue: 1.7722 time to fit residues: 7796.7603 Evaluate side-chains 2318 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2318 time to evaluate : 8.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 1.9990 chunk 347 optimal weight: 0.4980 chunk 520 optimal weight: 0.7980 chunk 262 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 553 optimal weight: 5.9990 chunk 593 optimal weight: 7.9990 chunk 430 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 684 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 312 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 792 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN D 614 ASN ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 ASN ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 GLN I 486 GLN I 576 GLN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 75455 Z= 0.172 Angle : 0.541 7.073 102320 Z= 0.290 Chirality : 0.040 0.163 11722 Planarity : 0.005 0.125 13254 Dihedral : 5.193 57.365 9999 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.57 % Favored : 92.42 % Rotamer: Outliers : 0.01 % Allowed : 0.68 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.03 (0.09), residues: 9050 helix: 0.60 (0.08), residues: 4290 sheet: -1.50 (0.18), residues: 711 loop : -1.96 (0.10), residues: 4049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 155 HIS 0.007 0.001 HIS A 266 PHE 0.027 0.001 PHE B 481 TYR 0.030 0.001 TYR I 621 ARG 0.011 0.000 ARG B 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2623 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2622 time to evaluate : 8.805 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 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8262 (mm-30) cc_final: 0.6654 (mm-30) REVERT: A 122 GLN cc_start: 0.8944 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 196 GLU cc_start: 0.7090 (tp30) cc_final: 0.6658 (pm20) REVERT: A 290 ASN cc_start: 0.8023 (m110) cc_final: 0.7719 (m110) REVERT: A 326 ASP cc_start: 0.8264 (t70) cc_final: 0.8060 (t70) REVERT: A 355 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8731 (tppt) REVERT: A 425 MET cc_start: 0.8015 (tpp) cc_final: 0.7477 (tpt) REVERT: A 443 ILE cc_start: 0.9424 (mp) cc_final: 0.9189 (mm) REVERT: A 487 PHE cc_start: 0.8800 (m-80) cc_final: 0.7713 (m-80) REVERT: A 570 MET cc_start: 0.8744 (ptp) cc_final: 0.8398 (ptt) REVERT: A 649 VAL cc_start: 0.8006 (t) cc_final: 0.7502 (t) REVERT: B 178 ASP cc_start: 0.8281 (t0) cc_final: 0.7934 (t0) REVERT: B 261 GLU cc_start: 0.7478 (tp30) cc_final: 0.7052 (tp30) REVERT: B 296 ASP cc_start: 0.8418 (p0) cc_final: 0.8214 (p0) REVERT: B 320 ASN cc_start: 0.8632 (t0) cc_final: 0.8227 (t0) REVERT: B 427 ILE cc_start: 0.9125 (tt) cc_final: 0.8870 (tt) REVERT: B 467 GLU cc_start: 0.8015 (tt0) cc_final: 0.7535 (tt0) REVERT: B 514 MET cc_start: 0.8492 (mmp) cc_final: 0.7601 (tpp) REVERT: B 561 TYR cc_start: 0.8396 (t80) cc_final: 0.7888 (t80) REVERT: B 645 MET cc_start: 0.7334 (mmp) cc_final: 0.6198 (mtt) REVERT: C 164 ASP cc_start: 0.7231 (m-30) cc_final: 0.6899 (m-30) REVERT: C 189 LEU cc_start: 0.7756 (mm) cc_final: 0.7211 (mm) REVERT: C 211 THR cc_start: 0.8827 (m) cc_final: 0.8557 (m) REVERT: C 228 VAL cc_start: 0.9325 (m) cc_final: 0.8943 (p) REVERT: C 289 VAL cc_start: 0.9156 (m) cc_final: 0.8759 (p) REVERT: C 355 LYS cc_start: 0.7515 (ttpt) cc_final: 0.7060 (ttpp) REVERT: C 423 ASN cc_start: 0.8828 (m110) cc_final: 0.8347 (p0) REVERT: C 435 GLN cc_start: 0.8539 (mt0) cc_final: 0.8307 (mt0) REVERT: C 491 VAL cc_start: 0.8249 (p) cc_final: 0.8048 (p) REVERT: C 500 LEU cc_start: 0.8983 (mp) cc_final: 0.8769 (mp) REVERT: C 518 MET cc_start: 0.8468 (mmm) cc_final: 0.7873 (tpp) REVERT: C 531 ASP cc_start: 0.7663 (p0) cc_final: 0.7367 (p0) REVERT: C 561 TYR cc_start: 0.8272 (t80) cc_final: 0.7601 (t80) REVERT: C 683 ILE cc_start: 0.9096 (mm) cc_final: 0.8771 (tp) REVERT: C 685 ARG cc_start: 0.8850 (mtt-85) cc_final: 0.8043 (mtt90) REVERT: C 693 LEU cc_start: 0.8971 (mt) cc_final: 0.8439 (mp) REVERT: C 696 MET cc_start: 0.8909 (ptm) cc_final: 0.8207 (ppp) REVERT: C 697 GLU cc_start: 0.8010 (pm20) cc_final: 0.7122 (pm20) REVERT: C 704 ASP cc_start: 0.8547 (m-30) cc_final: 0.8196 (m-30) REVERT: C 721 ARG cc_start: 0.7925 (mtt90) cc_final: 0.6459 (ptt-90) REVERT: C 784 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8236 (mtpt) REVERT: C 797 ARG cc_start: 0.7772 (mpp80) cc_final: 0.6896 (mtt-85) REVERT: C 860 ASP cc_start: 0.8626 (t0) cc_final: 0.8347 (t0) REVERT: D 92 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7314 (tp30) REVERT: D 131 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7520 (ttm170) REVERT: D 142 ARG cc_start: 0.7378 (ptm-80) cc_final: 0.6975 (mmt180) REVERT: D 173 PHE cc_start: 0.8430 (m-80) cc_final: 0.8115 (m-10) REVERT: D 175 ASN cc_start: 0.8290 (m-40) cc_final: 0.8012 (m-40) REVERT: D 210 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 215 CYS cc_start: 0.9033 (m) cc_final: 0.8640 (t) REVERT: D 232 ILE cc_start: 0.9079 (mt) cc_final: 0.8261 (mt) REVERT: D 270 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6848 (mt-10) REVERT: D 307 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7385 (ttm-80) REVERT: D 393 MET cc_start: 0.8128 (mtm) cc_final: 0.7434 (mtp) REVERT: D 471 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7822 (mm110) REVERT: D 484 ASN cc_start: 0.8510 (m110) cc_final: 0.8054 (t0) REVERT: D 510 VAL cc_start: 0.9329 (m) cc_final: 0.9113 (p) REVERT: D 561 TYR cc_start: 0.8173 (t80) cc_final: 0.7663 (t80) REVERT: D 586 THR cc_start: 0.9107 (p) cc_final: 0.8771 (p) REVERT: D 701 ARG cc_start: 0.8609 (mmt180) cc_final: 0.7936 (mtt180) REVERT: D 730 ILE cc_start: 0.9177 (tt) cc_final: 0.8646 (mt) REVERT: D 744 GLU cc_start: 0.7964 (tt0) cc_final: 0.7700 (tt0) REVERT: D 879 ASP cc_start: 0.9246 (p0) cc_final: 0.8803 (p0) REVERT: E 102 ILE cc_start: 0.7314 (pt) cc_final: 0.6977 (tp) REVERT: E 160 ASP cc_start: 0.7565 (m-30) cc_final: 0.6567 (t0) REVERT: E 193 MET cc_start: 0.8427 (ptp) cc_final: 0.7622 (mtp) REVERT: E 244 ASN cc_start: 0.7670 (m-40) cc_final: 0.7391 (m-40) REVERT: E 261 GLU cc_start: 0.8325 (tp30) cc_final: 0.7973 (tm-30) REVERT: E 333 TYR cc_start: 0.8872 (t80) cc_final: 0.8555 (t80) REVERT: E 362 LEU cc_start: 0.7735 (mt) cc_final: 0.7398 (pp) REVERT: E 393 MET cc_start: 0.9263 (mtp) cc_final: 0.9001 (mtp) REVERT: E 409 MET cc_start: 0.8947 (tpp) cc_final: 0.8504 (tpp) REVERT: E 454 TYR cc_start: 0.8402 (t80) cc_final: 0.8198 (t80) REVERT: E 467 GLU cc_start: 0.8414 (tt0) cc_final: 0.8004 (tt0) REVERT: E 514 MET cc_start: 0.8689 (mmp) cc_final: 0.8151 (tpt) REVERT: E 550 LEU cc_start: 0.9307 (mt) cc_final: 0.9053 (mt) REVERT: E 568 ILE cc_start: 0.8945 (mm) cc_final: 0.8689 (mm) REVERT: E 582 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7667 (mmmt) REVERT: E 666 ASP cc_start: 0.7619 (m-30) cc_final: 0.6892 (m-30) REVERT: E 677 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8293 (mtt180) REVERT: E 701 ARG cc_start: 0.9246 (mmt180) cc_final: 0.8519 (mmm-85) REVERT: E 821 ASN cc_start: 0.8745 (m-40) cc_final: 0.8117 (t0) REVERT: E 822 TYR cc_start: 0.6822 (m-80) cc_final: 0.5974 (m-80) REVERT: E 831 LYS cc_start: 0.8354 (mtpp) cc_final: 0.8016 (mtmt) REVERT: F 99 GLN cc_start: 0.8505 (tp-100) cc_final: 0.7574 (tm-30) REVERT: F 168 ASP cc_start: 0.8384 (m-30) cc_final: 0.8159 (m-30) REVERT: F 187 TYR cc_start: 0.8668 (p90) cc_final: 0.8287 (p90) REVERT: F 216 ASP cc_start: 0.9066 (m-30) cc_final: 0.8778 (m-30) REVERT: F 256 ASP cc_start: 0.8018 (m-30) cc_final: 0.7684 (m-30) REVERT: F 355 LYS cc_start: 0.8590 (ptmm) cc_final: 0.8276 (ttmt) REVERT: F 356 MET cc_start: 0.8526 (mmt) cc_final: 0.8300 (mmt) REVERT: F 497 ASN cc_start: 0.8623 (m110) cc_final: 0.8066 (m110) REVERT: F 687 ASP cc_start: 0.8585 (m-30) cc_final: 0.8215 (m-30) REVERT: F 696 MET cc_start: 0.8152 (ptm) cc_final: 0.7723 (ttp) REVERT: F 722 ASP cc_start: 0.8433 (t0) cc_final: 0.8186 (t70) REVERT: F 727 TYR cc_start: 0.7936 (m-80) cc_final: 0.7335 (m-80) REVERT: F 744 GLU cc_start: 0.8919 (mp0) cc_final: 0.7970 (tp30) REVERT: F 745 LEU cc_start: 0.8025 (tp) cc_final: 0.7740 (tp) REVERT: F 746 MET cc_start: 0.7404 (tmm) cc_final: 0.6871 (tmm) REVERT: F 816 PHE cc_start: 0.7881 (t80) cc_final: 0.7474 (t80) REVERT: F 819 VAL cc_start: 0.8884 (t) cc_final: 0.8678 (t) REVERT: F 843 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7867 (tpt170) REVERT: F 874 ASN cc_start: 0.9015 (m110) cc_final: 0.8755 (t0) REVERT: G 235 MET cc_start: 0.8187 (mtp) cc_final: 0.7670 (mtp) REVERT: G 256 ASP cc_start: 0.8615 (m-30) cc_final: 0.8295 (m-30) REVERT: G 262 TYR cc_start: 0.7445 (t80) cc_final: 0.7153 (t80) REVERT: G 265 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8063 (tt0) REVERT: G 295 MET cc_start: 0.7020 (mmm) cc_final: 0.5646 (mmm) REVERT: G 393 MET cc_start: 0.9424 (mmp) cc_final: 0.8868 (mmp) REVERT: G 394 LEU cc_start: 0.9311 (mt) cc_final: 0.8910 (tt) REVERT: G 396 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8407 (mm-40) REVERT: G 418 LEU cc_start: 0.9090 (mm) cc_final: 0.8808 (mm) REVERT: G 582 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7812 (mmtm) REVERT: G 621 TYR cc_start: 0.8816 (t80) cc_final: 0.8610 (t80) REVERT: G 687 ASP cc_start: 0.9002 (m-30) cc_final: 0.8488 (m-30) REVERT: G 694 MET cc_start: 0.6936 (mtp) cc_final: 0.6558 (mtm) REVERT: G 746 MET cc_start: 0.8144 (tmm) cc_final: 0.7756 (tmm) REVERT: H 121 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7258 (mm-30) REVERT: H 122 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7994 (tm-30) REVERT: H 140 VAL cc_start: 0.7800 (m) cc_final: 0.6190 (m) REVERT: H 148 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6772 (mt-10) REVERT: H 152 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8132 (ttm-80) REVERT: H 277 ILE cc_start: 0.9036 (mt) cc_final: 0.8688 (mm) REVERT: H 404 VAL cc_start: 0.8554 (t) cc_final: 0.8354 (m) REVERT: H 493 ASP cc_start: 0.7902 (t0) cc_final: 0.7611 (t70) REVERT: H 541 LEU cc_start: 0.8279 (mt) cc_final: 0.8052 (mt) REVERT: H 593 MET cc_start: 0.8203 (mmm) cc_final: 0.7893 (mmp) REVERT: H 724 MET cc_start: 0.7549 (ttt) cc_final: 0.7128 (tpp) REVERT: H 759 LEU cc_start: 0.8620 (mt) cc_final: 0.8330 (tp) REVERT: I 316 ASN cc_start: 0.8282 (m110) cc_final: 0.8075 (m110) REVERT: I 342 ASP cc_start: 0.6873 (m-30) cc_final: 0.6581 (m-30) REVERT: I 356 MET cc_start: 0.7744 (mmp) cc_final: 0.7323 (mmp) REVERT: I 407 ASN cc_start: 0.8151 (t0) cc_final: 0.7861 (t0) REVERT: I 423 ASN cc_start: 0.8793 (m110) cc_final: 0.8360 (t0) REVERT: I 440 ASN cc_start: 0.9051 (m-40) cc_final: 0.8344 (p0) REVERT: I 443 ILE cc_start: 0.9292 (mm) cc_final: 0.9034 (mp) REVERT: I 451 ARG cc_start: 0.7232 (mmm-85) cc_final: 0.6982 (mmm-85) REVERT: I 468 GLN cc_start: 0.9317 (tp40) cc_final: 0.8575 (tp40) REVERT: I 830 THR cc_start: 0.8361 (m) cc_final: 0.7978 (m) REVERT: J 150 ARG cc_start: 0.8075 (ptt180) cc_final: 0.5612 (mtt180) REVERT: J 199 ASN cc_start: 0.6846 (m110) cc_final: 0.6574 (m-40) REVERT: J 274 ASN cc_start: 0.8524 (m110) cc_final: 0.8314 (m110) REVERT: J 454 TYR cc_start: 0.8477 (t80) cc_final: 0.8182 (t80) REVERT: J 514 MET cc_start: 0.8545 (tpp) cc_final: 0.7996 (mmt) REVERT: J 549 GLN cc_start: 0.8433 (mp10) cc_final: 0.7999 (mp10) REVERT: J 574 HIS cc_start: 0.6751 (m-70) cc_final: 0.6498 (m-70) REVERT: J 588 VAL cc_start: 0.8979 (t) cc_final: 0.8413 (t) REVERT: J 658 ILE cc_start: 0.8757 (pt) cc_final: 0.8526 (mp) REVERT: J 827 THR cc_start: 0.7976 (p) cc_final: 0.7664 (t) REVERT: J 833 TYR cc_start: 0.7400 (t80) cc_final: 0.5908 (t80) REVERT: P 141 ASN cc_start: 0.8641 (m110) cc_final: 0.8349 (m110) REVERT: P 143 ASN cc_start: 0.7838 (t0) cc_final: 0.7425 (t0) REVERT: P 210 SER cc_start: 0.8370 (m) cc_final: 0.8028 (p) REVERT: P 248 MET cc_start: 0.8818 (ttt) cc_final: 0.8613 (ttt) REVERT: P 257 ILE cc_start: 0.8574 (mt) cc_final: 0.8325 (mt) REVERT: P 308 GLN cc_start: 0.8848 (tt0) cc_final: 0.8114 (tm-30) REVERT: P 365 MET cc_start: 0.7453 (ttt) cc_final: 0.6673 (ttt) REVERT: P 374 MET cc_start: 0.8581 (mmt) cc_final: 0.8288 (mmt) REVERT: P 540 MET cc_start: 0.7982 (mtp) cc_final: 0.7579 (mtt) REVERT: P 561 TYR cc_start: 0.7436 (t80) cc_final: 0.7159 (t80) REVERT: P 608 ILE cc_start: 0.8389 (mm) cc_final: 0.8154 (tt) REVERT: P 646 GLN cc_start: 0.8743 (mt0) cc_final: 0.8240 (tp40) REVERT: P 657 GLU cc_start: 0.8142 (mp0) cc_final: 0.7701 (mp0) REVERT: P 737 MET cc_start: 0.9026 (ptp) cc_final: 0.8769 (ptp) REVERT: P 756 VAL cc_start: 0.9299 (t) cc_final: 0.9078 (p) REVERT: P 763 PHE cc_start: 0.8383 (m-10) cc_final: 0.7973 (m-10) REVERT: P 863 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7870 (mmmm) REVERT: P 1051 TRP cc_start: 0.8576 (m100) cc_final: 0.7905 (m100) outliers start: 1 outliers final: 1 residues processed: 2623 average time/residue: 1.8446 time to fit residues: 8075.6965 Evaluate side-chains 2337 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2336 time to evaluate : 8.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 7.9990 chunk 834 optimal weight: 10.0000 chunk 761 optimal weight: 6.9990 chunk 811 optimal weight: 5.9990 chunk 488 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 chunk 637 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 733 optimal weight: 2.9990 chunk 767 optimal weight: 0.8980 chunk 809 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 199 ASN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN G 267 GLN ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN I 480 HIS I 486 GLN ** I 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 733 ASN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 75455 Z= 0.262 Angle : 0.590 8.890 102320 Z= 0.321 Chirality : 0.040 0.157 11722 Planarity : 0.005 0.109 13254 Dihedral : 5.258 55.110 9999 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.14 % Favored : 90.85 % Rotamer: Outliers : 0.01 % Allowed : 0.60 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.21 (0.09), residues: 9050 helix: 0.44 (0.08), residues: 4295 sheet: -1.58 (0.17), residues: 773 loop : -2.05 (0.10), residues: 3982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 325 HIS 0.008 0.001 HIS A 847 PHE 0.046 0.002 PHE A 263 TYR 0.029 0.002 TYR I 621 ARG 0.009 0.001 ARG E 637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2569 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2568 time to evaluate : 8.685 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8960 (tt0) cc_final: 0.7529 (pm20) REVERT: A 196 GLU cc_start: 0.7287 (tp30) cc_final: 0.6779 (pm20) REVERT: A 266 HIS cc_start: 0.7662 (t-170) cc_final: 0.7263 (t-170) REVERT: A 570 MET cc_start: 0.8735 (ptp) cc_final: 0.8391 (ptt) REVERT: B 178 ASP cc_start: 0.8204 (t0) cc_final: 0.7907 (t0) REVERT: B 261 GLU cc_start: 0.7410 (tp30) cc_final: 0.7010 (tp30) REVERT: B 273 ASN cc_start: 0.8504 (p0) cc_final: 0.8214 (p0) REVERT: B 320 ASN cc_start: 0.8577 (t0) cc_final: 0.8110 (t0) REVERT: B 363 GLU cc_start: 0.7260 (mp0) cc_final: 0.6991 (mp0) REVERT: B 407 ASN cc_start: 0.8992 (t0) cc_final: 0.8791 (t0) REVERT: B 424 ASP cc_start: 0.8101 (t0) cc_final: 0.7666 (t0) REVERT: B 427 ILE cc_start: 0.9166 (tt) cc_final: 0.8895 (tt) REVERT: B 514 MET cc_start: 0.8564 (mmp) cc_final: 0.7520 (tpp) REVERT: B 561 TYR cc_start: 0.8431 (t80) cc_final: 0.7928 (t80) REVERT: B 645 MET cc_start: 0.7471 (mmp) cc_final: 0.6294 (mtt) REVERT: B 688 ILE cc_start: 0.8892 (mm) cc_final: 0.8663 (mm) REVERT: B 717 MET cc_start: 0.7732 (mmm) cc_final: 0.6741 (mmm) REVERT: B 746 MET cc_start: 0.7815 (mmp) cc_final: 0.7565 (tpt) REVERT: C 164 ASP cc_start: 0.7224 (m-30) cc_final: 0.6874 (m-30) REVERT: C 189 LEU cc_start: 0.8022 (mm) cc_final: 0.7491 (mm) REVERT: C 209 SER cc_start: 0.8796 (m) cc_final: 0.8469 (t) REVERT: C 211 THR cc_start: 0.8906 (m) cc_final: 0.8637 (m) REVERT: C 228 VAL cc_start: 0.9368 (m) cc_final: 0.9007 (p) REVERT: C 289 VAL cc_start: 0.9219 (m) cc_final: 0.8835 (p) REVERT: C 355 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7075 (ttpp) REVERT: C 356 MET cc_start: 0.9144 (mmm) cc_final: 0.8939 (tpt) REVERT: C 386 PHE cc_start: 0.8379 (t80) cc_final: 0.8099 (t80) REVERT: C 435 GLN cc_start: 0.8517 (mt0) cc_final: 0.8263 (mt0) REVERT: C 444 TYR cc_start: 0.7794 (m-10) cc_final: 0.7585 (m-10) REVERT: C 452 MET cc_start: 0.8337 (mmm) cc_final: 0.7609 (tpp) REVERT: C 518 MET cc_start: 0.8447 (mmm) cc_final: 0.7843 (tpp) REVERT: C 531 ASP cc_start: 0.7745 (p0) cc_final: 0.7497 (p0) REVERT: C 569 THR cc_start: 0.8546 (p) cc_final: 0.8043 (t) REVERT: C 683 ILE cc_start: 0.9124 (mm) cc_final: 0.8819 (tp) REVERT: C 693 LEU cc_start: 0.8980 (mt) cc_final: 0.8457 (mp) REVERT: C 696 MET cc_start: 0.8936 (ptm) cc_final: 0.8210 (ppp) REVERT: C 697 GLU cc_start: 0.8135 (pm20) cc_final: 0.7244 (pm20) REVERT: C 704 ASP cc_start: 0.8528 (m-30) cc_final: 0.8178 (m-30) REVERT: C 721 ARG cc_start: 0.7949 (mtt90) cc_final: 0.6488 (ptt-90) REVERT: C 784 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8278 (mtpt) REVERT: C 797 ARG cc_start: 0.7699 (mpp80) cc_final: 0.7023 (ptp-110) REVERT: C 803 LYS cc_start: 0.9066 (mttt) cc_final: 0.8801 (mtmm) REVERT: C 860 ASP cc_start: 0.8662 (t0) cc_final: 0.8394 (t0) REVERT: D 92 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7270 (tp30) REVERT: D 106 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6890 (tm-30) REVERT: D 142 ARG cc_start: 0.7473 (ptm-80) cc_final: 0.6997 (mmt180) REVERT: D 164 ASP cc_start: 0.7520 (t0) cc_final: 0.7293 (t70) REVERT: D 175 ASN cc_start: 0.8387 (m-40) cc_final: 0.8116 (m-40) REVERT: D 393 MET cc_start: 0.8166 (mtm) cc_final: 0.7495 (mtp) REVERT: D 471 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7836 (mm110) REVERT: D 484 ASN cc_start: 0.8648 (m110) cc_final: 0.8103 (t0) REVERT: D 510 VAL cc_start: 0.9262 (m) cc_final: 0.9043 (p) REVERT: D 561 TYR cc_start: 0.8185 (t80) cc_final: 0.7726 (t80) REVERT: D 586 THR cc_start: 0.9166 (p) cc_final: 0.8862 (p) REVERT: D 701 ARG cc_start: 0.8643 (mmt180) cc_final: 0.8007 (mtt180) REVERT: D 730 ILE cc_start: 0.9188 (tt) cc_final: 0.8605 (mt) REVERT: D 879 ASP cc_start: 0.9311 (p0) cc_final: 0.9013 (p0) REVERT: D 881 MET cc_start: 0.8188 (mmp) cc_final: 0.7695 (mmm) REVERT: E 102 ILE cc_start: 0.7292 (pt) cc_final: 0.6923 (tp) REVERT: E 160 ASP cc_start: 0.7575 (m-30) cc_final: 0.6293 (t0) REVERT: E 193 MET cc_start: 0.8489 (ptp) cc_final: 0.7775 (mtp) REVERT: E 244 ASN cc_start: 0.7779 (m-40) cc_final: 0.7516 (m-40) REVERT: E 248 TYR cc_start: 0.7205 (m-80) cc_final: 0.6765 (m-10) REVERT: E 261 GLU cc_start: 0.8354 (tp30) cc_final: 0.7998 (tm-30) REVERT: E 287 ASN cc_start: 0.8311 (m-40) cc_final: 0.7977 (m110) REVERT: E 333 TYR cc_start: 0.8881 (t80) cc_final: 0.8555 (t80) REVERT: E 362 LEU cc_start: 0.7650 (mt) cc_final: 0.7261 (pp) REVERT: E 393 MET cc_start: 0.9209 (mtp) cc_final: 0.8866 (mtp) REVERT: E 409 MET cc_start: 0.9021 (tpp) cc_final: 0.8633 (tpp) REVERT: E 452 MET cc_start: 0.8608 (tpp) cc_final: 0.8002 (tpp) REVERT: E 454 TYR cc_start: 0.8463 (t80) cc_final: 0.8226 (t80) REVERT: E 467 GLU cc_start: 0.8516 (tt0) cc_final: 0.8105 (tt0) REVERT: E 514 MET cc_start: 0.8741 (mmp) cc_final: 0.8132 (tpt) REVERT: E 550 LEU cc_start: 0.9373 (mt) cc_final: 0.9121 (mt) REVERT: E 577 THR cc_start: 0.8840 (p) cc_final: 0.8433 (p) REVERT: E 582 LYS cc_start: 0.8528 (mmmt) cc_final: 0.7763 (mmmt) REVERT: E 621 TYR cc_start: 0.8269 (t80) cc_final: 0.7942 (t80) REVERT: E 625 ILE cc_start: 0.8870 (mt) cc_final: 0.8621 (mt) REVERT: E 666 ASP cc_start: 0.7761 (m-30) cc_final: 0.7093 (m-30) REVERT: E 669 MET cc_start: 0.8554 (mmm) cc_final: 0.8333 (tpp) REVERT: E 695 ASN cc_start: 0.9323 (m110) cc_final: 0.8989 (m110) REVERT: E 701 ARG cc_start: 0.9243 (mmt180) cc_final: 0.8499 (mmm-85) REVERT: E 807 TYR cc_start: 0.7679 (m-80) cc_final: 0.7242 (m-10) REVERT: E 821 ASN cc_start: 0.8773 (m-40) cc_final: 0.8153 (t0) REVERT: E 822 TYR cc_start: 0.6883 (m-80) cc_final: 0.6043 (m-80) REVERT: F 89 HIS cc_start: 0.6747 (m170) cc_final: 0.6356 (m170) REVERT: F 99 GLN cc_start: 0.8559 (tp-100) cc_final: 0.7653 (tm-30) REVERT: F 123 VAL cc_start: 0.7883 (p) cc_final: 0.7602 (p) REVERT: F 168 ASP cc_start: 0.8426 (m-30) cc_final: 0.8210 (m-30) REVERT: F 312 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8274 (pp30) REVERT: F 325 TRP cc_start: 0.8861 (t-100) cc_final: 0.8444 (t-100) REVERT: F 355 LYS cc_start: 0.8617 (ptmm) cc_final: 0.8296 (ttmt) REVERT: F 356 MET cc_start: 0.8477 (mmt) cc_final: 0.8243 (mmt) REVERT: F 643 LYS cc_start: 0.9306 (ttmt) cc_final: 0.8978 (ttmm) REVERT: F 687 ASP cc_start: 0.8695 (m-30) cc_final: 0.8279 (m-30) REVERT: F 696 MET cc_start: 0.8148 (ptm) cc_final: 0.7844 (ttp) REVERT: F 722 ASP cc_start: 0.8456 (t0) cc_final: 0.8256 (t70) REVERT: F 727 TYR cc_start: 0.8081 (m-80) cc_final: 0.7399 (m-80) REVERT: F 744 GLU cc_start: 0.9084 (mp0) cc_final: 0.7979 (tp30) REVERT: F 745 LEU cc_start: 0.8128 (tp) cc_final: 0.7813 (tp) REVERT: F 816 PHE cc_start: 0.8004 (t80) cc_final: 0.7619 (t80) REVERT: F 874 ASN cc_start: 0.9065 (m110) cc_final: 0.8760 (t0) REVERT: G 256 ASP cc_start: 0.8634 (m-30) cc_final: 0.8387 (m-30) REVERT: G 265 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8119 (tt0) REVERT: G 295 MET cc_start: 0.7114 (mmm) cc_final: 0.5809 (mmm) REVERT: G 393 MET cc_start: 0.9386 (mmp) cc_final: 0.9037 (mmp) REVERT: G 394 LEU cc_start: 0.9216 (mt) cc_final: 0.8982 (tt) REVERT: G 396 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8459 (mm-40) REVERT: G 418 LEU cc_start: 0.9071 (mm) cc_final: 0.8845 (mm) REVERT: G 582 LYS cc_start: 0.8486 (mmtt) cc_final: 0.7851 (mmtm) REVERT: G 583 LEU cc_start: 0.9299 (tt) cc_final: 0.8907 (tt) REVERT: G 621 TYR cc_start: 0.8868 (t80) cc_final: 0.8654 (t80) REVERT: G 687 ASP cc_start: 0.9060 (m-30) cc_final: 0.8574 (m-30) REVERT: G 694 MET cc_start: 0.7066 (mtp) cc_final: 0.6677 (mtm) REVERT: G 746 MET cc_start: 0.8256 (tmm) cc_final: 0.7850 (tmm) REVERT: H 121 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7308 (mm-30) REVERT: H 122 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8041 (tm-30) REVERT: H 170 ARG cc_start: 0.9192 (mtm180) cc_final: 0.8898 (mtm180) REVERT: H 277 ILE cc_start: 0.8993 (mt) cc_final: 0.8654 (mm) REVERT: H 404 VAL cc_start: 0.8612 (t) cc_final: 0.8406 (m) REVERT: H 493 ASP cc_start: 0.7923 (t0) cc_final: 0.7627 (t70) REVERT: H 541 LEU cc_start: 0.8330 (mt) cc_final: 0.8108 (mt) REVERT: H 593 MET cc_start: 0.8251 (mmm) cc_final: 0.8048 (mmp) REVERT: H 723 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6345 (tm-30) REVERT: H 724 MET cc_start: 0.7629 (ttt) cc_final: 0.6945 (tpp) REVERT: H 759 LEU cc_start: 0.8657 (mt) cc_final: 0.8372 (tp) REVERT: H 807 TYR cc_start: 0.8036 (m-80) cc_final: 0.7028 (m-80) REVERT: H 868 ASP cc_start: 0.7383 (t70) cc_final: 0.7167 (t70) REVERT: I 234 GLU cc_start: 0.8243 (mp0) cc_final: 0.7979 (mp0) REVERT: I 342 ASP cc_start: 0.7341 (m-30) cc_final: 0.6795 (m-30) REVERT: I 356 MET cc_start: 0.7682 (mmp) cc_final: 0.7286 (mmp) REVERT: I 394 LEU cc_start: 0.8555 (mt) cc_final: 0.8107 (mt) REVERT: I 407 ASN cc_start: 0.8128 (t0) cc_final: 0.7821 (t0) REVERT: I 423 ASN cc_start: 0.8877 (m110) cc_final: 0.8434 (t0) REVERT: I 440 ASN cc_start: 0.8944 (m-40) cc_final: 0.8319 (p0) REVERT: I 443 ILE cc_start: 0.9290 (mm) cc_final: 0.9021 (mp) REVERT: I 468 GLN cc_start: 0.9293 (tp40) cc_final: 0.8645 (tp40) REVERT: I 479 LEU cc_start: 0.8589 (tp) cc_final: 0.8291 (tp) REVERT: I 480 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7273 (t-90) REVERT: I 830 THR cc_start: 0.8430 (m) cc_final: 0.8065 (m) REVERT: J 150 ARG cc_start: 0.8117 (ptt180) cc_final: 0.5556 (mtt180) REVERT: J 274 ASN cc_start: 0.8681 (m110) cc_final: 0.8418 (m-40) REVERT: J 356 MET cc_start: 0.9106 (mmp) cc_final: 0.8872 (mmp) REVERT: J 496 LEU cc_start: 0.8008 (tp) cc_final: 0.7784 (tp) REVERT: J 541 LEU cc_start: 0.8460 (mt) cc_final: 0.8210 (mt) REVERT: J 574 HIS cc_start: 0.6822 (m-70) cc_final: 0.6562 (m-70) REVERT: J 588 VAL cc_start: 0.8973 (t) cc_final: 0.8448 (t) REVERT: J 607 LEU cc_start: 0.9328 (tp) cc_final: 0.9059 (tp) REVERT: J 658 ILE cc_start: 0.8831 (pt) cc_final: 0.8556 (mp) REVERT: J 659 PHE cc_start: 0.8819 (m-10) cc_final: 0.8571 (m-10) REVERT: J 690 ASN cc_start: 0.8415 (m-40) cc_final: 0.7944 (p0) REVERT: J 742 LEU cc_start: 0.9172 (tt) cc_final: 0.8964 (tt) REVERT: J 827 THR cc_start: 0.8037 (p) cc_final: 0.7696 (t) REVERT: J 833 TYR cc_start: 0.7481 (t80) cc_final: 0.5920 (t80) REVERT: P 143 ASN cc_start: 0.7808 (t0) cc_final: 0.7397 (t0) REVERT: P 210 SER cc_start: 0.8515 (m) cc_final: 0.8109 (p) REVERT: P 215 MET cc_start: 0.8456 (mmp) cc_final: 0.8154 (mmp) REVERT: P 248 MET cc_start: 0.8875 (ttt) cc_final: 0.8659 (ttt) REVERT: P 257 ILE cc_start: 0.8627 (mt) cc_final: 0.8333 (mt) REVERT: P 258 ASN cc_start: 0.6456 (t0) cc_final: 0.5616 (p0) REVERT: P 308 GLN cc_start: 0.8898 (tt0) cc_final: 0.8136 (tm-30) REVERT: P 365 MET cc_start: 0.7466 (ttt) cc_final: 0.6645 (ttt) REVERT: P 374 MET cc_start: 0.8623 (mmt) cc_final: 0.8237 (mmt) REVERT: P 521 VAL cc_start: 0.8105 (m) cc_final: 0.7898 (m) REVERT: P 540 MET cc_start: 0.8019 (mtp) cc_final: 0.7656 (mtt) REVERT: P 548 MET cc_start: 0.7622 (ttp) cc_final: 0.7085 (tmm) REVERT: P 561 TYR cc_start: 0.7621 (t80) cc_final: 0.7312 (t80) REVERT: P 646 GLN cc_start: 0.8813 (mt0) cc_final: 0.8251 (tp40) REVERT: P 737 MET cc_start: 0.9049 (ptp) cc_final: 0.8796 (ptp) REVERT: P 756 VAL cc_start: 0.9243 (t) cc_final: 0.9028 (p) REVERT: P 763 PHE cc_start: 0.8501 (m-10) cc_final: 0.8076 (m-10) REVERT: P 863 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7911 (mmmm) REVERT: P 1051 TRP cc_start: 0.8600 (m100) cc_final: 0.7930 (m100) outliers start: 1 outliers final: 0 residues processed: 2568 average time/residue: 1.7770 time to fit residues: 7576.1254 Evaluate side-chains 2303 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2302 time to evaluate : 9.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 4.9990 chunk 858 optimal weight: 6.9990 chunk 524 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 596 optimal weight: 7.9990 chunk 900 optimal weight: 3.9990 chunk 828 optimal weight: 8.9990 chunk 717 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 553 optimal weight: 6.9990 chunk 439 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN B 622 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 792 GLN C 821 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 GLN ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 874 ASN ** F 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN G 523 GLN ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN I 486 GLN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 ASN P 111 ASN ** P 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 75455 Z= 0.375 Angle : 0.693 8.449 102320 Z= 0.380 Chirality : 0.042 0.182 11722 Planarity : 0.006 0.132 13254 Dihedral : 5.675 55.850 9999 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.80 % Favored : 89.19 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.77 (0.08), residues: 9050 helix: -0.11 (0.08), residues: 4311 sheet: -1.79 (0.17), residues: 794 loop : -2.26 (0.09), residues: 3945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P1067 HIS 0.009 0.002 HIS P 384 PHE 0.028 0.002 PHE I 219 TYR 0.029 0.002 TYR I 621 ARG 0.012 0.001 ARG B 522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2540 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2538 time to evaluate : 8.540 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8979 (tt0) cc_final: 0.7601 (pm20) REVERT: A 196 GLU cc_start: 0.7517 (tp30) cc_final: 0.6922 (pm20) REVERT: A 266 HIS cc_start: 0.7729 (t-170) cc_final: 0.7381 (t-170) REVERT: A 269 VAL cc_start: 0.9446 (m) cc_final: 0.9208 (m) REVERT: A 570 MET cc_start: 0.8767 (ptp) cc_final: 0.8405 (ptt) REVERT: A 670 TYR cc_start: 0.8218 (m-80) cc_final: 0.7706 (m-80) REVERT: A 700 GLU cc_start: 0.7533 (tt0) cc_final: 0.7295 (tt0) REVERT: A 873 ILE cc_start: 0.7800 (mt) cc_final: 0.7053 (tp) REVERT: B 261 GLU cc_start: 0.7301 (tp30) cc_final: 0.6982 (tp30) REVERT: B 273 ASN cc_start: 0.8516 (p0) cc_final: 0.8254 (p0) REVERT: B 320 ASN cc_start: 0.8456 (t0) cc_final: 0.7901 (t0) REVERT: B 363 GLU cc_start: 0.6902 (mp0) cc_final: 0.6694 (mp0) REVERT: B 399 MET cc_start: 0.8214 (pmm) cc_final: 0.7849 (pmm) REVERT: B 407 ASN cc_start: 0.9015 (t0) cc_final: 0.8733 (t0) REVERT: B 427 ILE cc_start: 0.9176 (tt) cc_final: 0.8901 (tt) REVERT: B 514 MET cc_start: 0.8500 (mmp) cc_final: 0.7243 (tpp) REVERT: B 561 TYR cc_start: 0.8492 (t80) cc_final: 0.7935 (t80) REVERT: B 645 MET cc_start: 0.7545 (mmp) cc_final: 0.6466 (mtt) REVERT: B 688 ILE cc_start: 0.8975 (mm) cc_final: 0.8769 (mm) REVERT: B 717 MET cc_start: 0.7874 (mmm) cc_final: 0.7010 (mmm) REVERT: B 746 MET cc_start: 0.7922 (mmp) cc_final: 0.7644 (tpt) REVERT: B 874 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8365 (t0) REVERT: C 164 ASP cc_start: 0.7329 (m-30) cc_final: 0.7063 (m-30) REVERT: C 179 GLN cc_start: 0.8290 (mt0) cc_final: 0.8033 (mt0) REVERT: C 209 SER cc_start: 0.8839 (m) cc_final: 0.8506 (t) REVERT: C 211 THR cc_start: 0.8951 (m) cc_final: 0.8698 (m) REVERT: C 228 VAL cc_start: 0.9395 (m) cc_final: 0.9054 (p) REVERT: C 289 VAL cc_start: 0.9292 (m) cc_final: 0.8909 (p) REVERT: C 305 TYR cc_start: 0.6259 (p90) cc_final: 0.5810 (p90) REVERT: C 386 PHE cc_start: 0.8462 (t80) cc_final: 0.8169 (t80) REVERT: C 423 ASN cc_start: 0.8770 (m110) cc_final: 0.8339 (p0) REVERT: C 435 GLN cc_start: 0.8651 (mt0) cc_final: 0.8411 (mt0) REVERT: C 518 MET cc_start: 0.8487 (mmm) cc_final: 0.7982 (tpp) REVERT: C 569 THR cc_start: 0.8618 (p) cc_final: 0.8067 (t) REVERT: C 614 ASN cc_start: 0.9322 (m-40) cc_final: 0.9095 (m110) REVERT: C 683 ILE cc_start: 0.9138 (mm) cc_final: 0.8827 (tp) REVERT: C 693 LEU cc_start: 0.9009 (mt) cc_final: 0.8411 (mt) REVERT: C 696 MET cc_start: 0.8994 (ptm) cc_final: 0.8243 (ppp) REVERT: C 697 GLU cc_start: 0.8197 (pm20) cc_final: 0.7328 (pm20) REVERT: C 704 ASP cc_start: 0.8514 (m-30) cc_final: 0.8211 (m-30) REVERT: C 720 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 721 ARG cc_start: 0.8016 (mtt90) cc_final: 0.6584 (ptt-90) REVERT: C 722 ASP cc_start: 0.6967 (m-30) cc_final: 0.6102 (m-30) REVERT: C 784 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8309 (mtpt) REVERT: C 797 ARG cc_start: 0.7673 (mpp80) cc_final: 0.7217 (ptp-110) REVERT: C 860 ASP cc_start: 0.8684 (t0) cc_final: 0.8452 (t0) REVERT: D 142 ARG cc_start: 0.7594 (ptm-80) cc_final: 0.6942 (mmt180) REVERT: D 164 ASP cc_start: 0.7290 (t0) cc_final: 0.6935 (t70) REVERT: D 232 ILE cc_start: 0.9004 (mt) cc_final: 0.8466 (mt) REVERT: D 305 TYR cc_start: 0.8512 (p90) cc_final: 0.8175 (p90) REVERT: D 393 MET cc_start: 0.8217 (mtm) cc_final: 0.7308 (mtp) REVERT: D 471 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7831 (mm110) REVERT: D 484 ASN cc_start: 0.8675 (m110) cc_final: 0.8097 (t0) REVERT: D 542 LEU cc_start: 0.9290 (mt) cc_final: 0.8885 (mt) REVERT: D 561 TYR cc_start: 0.8244 (t80) cc_final: 0.7812 (t80) REVERT: D 572 MET cc_start: 0.8531 (ttp) cc_final: 0.8306 (ttp) REVERT: D 701 ARG cc_start: 0.8708 (mmt180) cc_final: 0.8095 (mtt-85) REVERT: D 720 GLU cc_start: 0.8342 (tp30) cc_final: 0.8128 (mm-30) REVERT: D 730 ILE cc_start: 0.9252 (tt) cc_final: 0.8626 (mt) REVERT: D 744 GLU cc_start: 0.8047 (tt0) cc_final: 0.7808 (tt0) REVERT: D 881 MET cc_start: 0.8146 (mmp) cc_final: 0.7642 (mmm) REVERT: E 102 ILE cc_start: 0.7335 (pt) cc_final: 0.6881 (tp) REVERT: E 160 ASP cc_start: 0.7571 (m-30) cc_final: 0.6379 (t0) REVERT: E 168 ASP cc_start: 0.8877 (m-30) cc_final: 0.8476 (m-30) REVERT: E 193 MET cc_start: 0.8553 (ptp) cc_final: 0.7987 (mtp) REVERT: E 261 GLU cc_start: 0.8492 (tp30) cc_final: 0.8080 (tm-30) REVERT: E 333 TYR cc_start: 0.8975 (t80) cc_final: 0.8614 (t80) REVERT: E 393 MET cc_start: 0.9168 (mtp) cc_final: 0.8873 (mtp) REVERT: E 409 MET cc_start: 0.9042 (tpp) cc_final: 0.8662 (tpp) REVERT: E 452 MET cc_start: 0.8755 (tpp) cc_final: 0.8169 (tpp) REVERT: E 514 MET cc_start: 0.8584 (mmp) cc_final: 0.8124 (tpt) REVERT: E 550 LEU cc_start: 0.9466 (mt) cc_final: 0.9239 (mt) REVERT: E 567 CYS cc_start: 0.8903 (m) cc_final: 0.8677 (m) REVERT: E 577 THR cc_start: 0.8875 (p) cc_final: 0.8670 (p) REVERT: E 621 TYR cc_start: 0.8402 (t80) cc_final: 0.8034 (t80) REVERT: E 625 ILE cc_start: 0.8930 (mt) cc_final: 0.8694 (mt) REVERT: E 666 ASP cc_start: 0.7903 (m-30) cc_final: 0.7296 (m-30) REVERT: E 701 ARG cc_start: 0.9284 (mmt180) cc_final: 0.8577 (mmm-85) REVERT: E 795 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7117 (mttm) REVERT: E 807 TYR cc_start: 0.7929 (m-80) cc_final: 0.7121 (m-80) REVERT: E 821 ASN cc_start: 0.8839 (m-40) cc_final: 0.8414 (t0) REVERT: E 822 TYR cc_start: 0.6960 (m-80) cc_final: 0.6203 (m-80) REVERT: E 831 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8202 (mtmm) REVERT: E 848 MET cc_start: 0.8222 (mmm) cc_final: 0.7843 (mmm) REVERT: F 355 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8305 (ttmt) REVERT: F 356 MET cc_start: 0.8484 (mmt) cc_final: 0.8252 (mmt) REVERT: F 403 PHE cc_start: 0.8176 (p90) cc_final: 0.7906 (p90) REVERT: F 415 MET cc_start: 0.8460 (ptp) cc_final: 0.8173 (ptp) REVERT: F 643 LYS cc_start: 0.9316 (ttmt) cc_final: 0.8977 (ttmm) REVERT: F 687 ASP cc_start: 0.8714 (m-30) cc_final: 0.8349 (m-30) REVERT: F 696 MET cc_start: 0.8267 (ptm) cc_final: 0.7922 (ttp) REVERT: F 700 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8406 (tm-30) REVERT: F 727 TYR cc_start: 0.8099 (m-80) cc_final: 0.7395 (m-80) REVERT: F 744 GLU cc_start: 0.9107 (mp0) cc_final: 0.7738 (tp30) REVERT: F 745 LEU cc_start: 0.8184 (tp) cc_final: 0.7887 (tp) REVERT: F 816 PHE cc_start: 0.8147 (t80) cc_final: 0.7834 (t80) REVERT: F 874 ASN cc_start: 0.9146 (m-40) cc_final: 0.8917 (t0) REVERT: G 142 ARG cc_start: 0.8707 (ptt180) cc_final: 0.8498 (ptp90) REVERT: G 201 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6950 (ptm160) REVERT: G 256 ASP cc_start: 0.8657 (m-30) cc_final: 0.8371 (m-30) REVERT: G 265 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8005 (tt0) REVERT: G 295 MET cc_start: 0.7298 (mmm) cc_final: 0.6081 (mmm) REVERT: G 318 HIS cc_start: 0.7921 (p-80) cc_final: 0.7695 (p-80) REVERT: G 394 LEU cc_start: 0.9287 (mt) cc_final: 0.8994 (tt) REVERT: G 396 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8574 (mm-40) REVERT: G 402 ASP cc_start: 0.8402 (m-30) cc_final: 0.8137 (m-30) REVERT: G 567 CYS cc_start: 0.9049 (m) cc_final: 0.8716 (m) REVERT: G 582 LYS cc_start: 0.8524 (mmtt) cc_final: 0.7907 (mmtm) REVERT: G 583 LEU cc_start: 0.9204 (tt) cc_final: 0.8763 (tt) REVERT: G 605 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 621 TYR cc_start: 0.8877 (t80) cc_final: 0.8619 (t80) REVERT: G 687 ASP cc_start: 0.9043 (m-30) cc_final: 0.8517 (m-30) REVERT: G 694 MET cc_start: 0.6964 (mtp) cc_final: 0.6535 (mtm) REVERT: G 746 MET cc_start: 0.8474 (tmm) cc_final: 0.8039 (tmm) REVERT: H 121 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7117 (mm-30) REVERT: H 140 VAL cc_start: 0.7772 (m) cc_final: 0.6126 (m) REVERT: H 221 ASP cc_start: 0.7853 (t0) cc_final: 0.7530 (t0) REVERT: H 224 THR cc_start: 0.8621 (m) cc_final: 0.7813 (p) REVERT: H 277 ILE cc_start: 0.9035 (mt) cc_final: 0.8685 (mm) REVERT: H 321 PHE cc_start: 0.8737 (m-10) cc_final: 0.8454 (m-80) REVERT: H 493 ASP cc_start: 0.7871 (t0) cc_final: 0.7446 (t0) REVERT: H 541 LEU cc_start: 0.8136 (mt) cc_final: 0.7887 (mt) REVERT: H 696 MET cc_start: 0.8723 (ptp) cc_final: 0.8511 (ptp) REVERT: H 723 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6065 (tm-30) REVERT: H 724 MET cc_start: 0.7791 (ttt) cc_final: 0.7057 (tpp) REVERT: H 759 LEU cc_start: 0.8522 (mt) cc_final: 0.8303 (tp) REVERT: H 807 TYR cc_start: 0.8352 (m-80) cc_final: 0.7683 (m-80) REVERT: H 868 ASP cc_start: 0.7538 (t70) cc_final: 0.7203 (t70) REVERT: I 220 GLN cc_start: 0.8349 (mt0) cc_final: 0.8041 (mp10) REVERT: I 234 GLU cc_start: 0.8280 (mp0) cc_final: 0.8049 (mp0) REVERT: I 294 ASN cc_start: 0.7638 (m-40) cc_final: 0.6810 (m-40) REVERT: I 295 MET cc_start: 0.8239 (mmt) cc_final: 0.6472 (tmm) REVERT: I 356 MET cc_start: 0.7727 (mmp) cc_final: 0.7389 (mmp) REVERT: I 394 LEU cc_start: 0.8650 (mt) cc_final: 0.8199 (mt) REVERT: I 407 ASN cc_start: 0.8166 (t0) cc_final: 0.7817 (t0) REVERT: I 423 ASN cc_start: 0.8920 (m110) cc_final: 0.8546 (t0) REVERT: I 440 ASN cc_start: 0.8922 (m-40) cc_final: 0.8306 (p0) REVERT: I 443 ILE cc_start: 0.9241 (mm) cc_final: 0.8982 (mp) REVERT: I 468 GLN cc_start: 0.9351 (tp40) cc_final: 0.8879 (tp-100) REVERT: I 518 MET cc_start: 0.8318 (mtm) cc_final: 0.8003 (ttm) REVERT: I 570 MET cc_start: 0.8035 (mpp) cc_final: 0.7734 (mpp) REVERT: I 608 PHE cc_start: 0.8400 (m-80) cc_final: 0.8188 (m-80) REVERT: I 637 ARG cc_start: 0.8786 (mtt180) cc_final: 0.6979 (tpt170) REVERT: I 655 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.7567 (mmp80) REVERT: I 830 THR cc_start: 0.8256 (m) cc_final: 0.7761 (m) REVERT: J 274 ASN cc_start: 0.8641 (m110) cc_final: 0.8413 (m110) REVERT: J 346 LEU cc_start: 0.7915 (mp) cc_final: 0.7709 (mp) REVERT: J 574 HIS cc_start: 0.6924 (m-70) cc_final: 0.6685 (m-70) REVERT: J 581 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7557 (mm-30) REVERT: J 658 ILE cc_start: 0.8822 (pt) cc_final: 0.8612 (mp) REVERT: J 659 PHE cc_start: 0.8824 (m-10) cc_final: 0.8428 (m-10) REVERT: J 742 LEU cc_start: 0.9226 (tt) cc_final: 0.9006 (tt) REVERT: J 827 THR cc_start: 0.8217 (p) cc_final: 0.7898 (t) REVERT: J 833 TYR cc_start: 0.7575 (t80) cc_final: 0.6028 (t80) REVERT: P 143 ASN cc_start: 0.7914 (t0) cc_final: 0.7512 (t0) REVERT: P 215 MET cc_start: 0.8574 (mmp) cc_final: 0.8369 (mmp) REVERT: P 257 ILE cc_start: 0.8743 (mt) cc_final: 0.8448 (mt) REVERT: P 258 ASN cc_start: 0.5714 (t0) cc_final: 0.5368 (p0) REVERT: P 283 GLN cc_start: 0.7887 (pp30) cc_final: 0.7624 (pp30) REVERT: P 293 ASP cc_start: 0.7366 (m-30) cc_final: 0.7135 (t0) REVERT: P 308 GLN cc_start: 0.8844 (tt0) cc_final: 0.8199 (tm-30) REVERT: P 359 MET cc_start: 0.7791 (mmt) cc_final: 0.7410 (mpp) REVERT: P 365 MET cc_start: 0.7362 (ttt) cc_final: 0.6656 (ttt) REVERT: P 374 MET cc_start: 0.8734 (mmt) cc_final: 0.8520 (mmt) REVERT: P 385 LEU cc_start: 0.8621 (mt) cc_final: 0.8407 (mt) REVERT: P 477 VAL cc_start: 0.8795 (t) cc_final: 0.8293 (p) REVERT: P 540 MET cc_start: 0.8213 (mtp) cc_final: 0.7884 (mtt) REVERT: P 548 MET cc_start: 0.7894 (ttp) cc_final: 0.7016 (tmm) REVERT: P 561 TYR cc_start: 0.7705 (t80) cc_final: 0.7387 (t80) REVERT: P 617 ASN cc_start: 0.8000 (m-40) cc_final: 0.6842 (t0) REVERT: P 646 GLN cc_start: 0.8874 (mt0) cc_final: 0.8236 (tp40) REVERT: P 763 PHE cc_start: 0.8596 (m-10) cc_final: 0.8096 (m-10) REVERT: P 818 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8623 (tm-30) REVERT: P 863 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7932 (mmmm) REVERT: P 1051 TRP cc_start: 0.8710 (m100) cc_final: 0.8052 (m100) outliers start: 2 outliers final: 0 residues processed: 2540 average time/residue: 1.7442 time to fit residues: 7334.4837 Evaluate side-chains 2265 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2264 time to evaluate : 8.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 0.0370 chunk 763 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 661 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 718 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 737 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 199 ASN A 267 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN B 695 ASN ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN D 614 ASN D 695 ASN ** D 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 GLN G 523 GLN H 151 ASN ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN I 396 GLN I 480 HIS I 486 GLN I 576 GLN I 739 GLN ** I 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134656 restraints weight = 558697.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138840 restraints weight = 251421.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141242 restraints weight = 128873.068| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 75455 Z= 0.193 Angle : 0.575 10.006 102320 Z= 0.310 Chirality : 0.040 0.165 11722 Planarity : 0.005 0.110 13254 Dihedral : 5.371 60.328 9999 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.56 % Favored : 92.43 % Rotamer: Outliers : 0.04 % Allowed : 0.30 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % 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: -1.24 (0.09), residues: 9050 helix: 0.36 (0.08), residues: 4287 sheet: -1.37 (0.18), residues: 755 loop : -2.05 (0.10), residues: 4008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 416 HIS 0.012 0.001 HIS J 257 PHE 0.033 0.001 PHE A 263 TYR 0.043 0.002 TYR I 610 ARG 0.012 0.001 ARG B 522 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 93855.70 seconds wall clock time: 1595 minutes 18.54 seconds (95718.54 seconds total)