Starting phenix.real_space_refine on Mon Mar 25 02:41:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj4_20087/03_2024/6oj4_20087.pdb" } resolution = 3.3 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= 0.028 sd= 0.730 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 74461 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 TYR 714": "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 PHE 219": "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 TYR 751": "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 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: 148556 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: {'CIS': 1, 'PTRANS': 30, 'TRANS': 784} Chain: "P" Number of atoms: 17650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 17650 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: 45.82, per 1000 atoms: 0.31 Number of scatterers: 148556 At special positions: 0 Unit cell: (288.486, 327.36, 194.37, 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 74461 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: 94.84 Conformation dependent library (CDL) restraints added in 10.4 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: 385 helices and 112 sheets defined 50.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.82 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.627A 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: 3.765A 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 280 removed outlier: 3.928A pdb=" N PHE A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.613A pdb=" N THR A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.867A pdb=" N ILE A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.190A 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: 3.660A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.745A pdb=" N LEU A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.532A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.790A pdb=" N GLY A 448 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.900A 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: 3.553A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 545 removed outlier: 3.782A pdb=" N LYS A 533 " --> pdb=" O PRO A 529 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.636A 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 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 677 removed outlier: 3.816A pdb=" N MET A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.634A pdb=" N ILE A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 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 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.837A pdb=" N VAL A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 810 through 814 removed outlier: 4.380A 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: 4.066A pdb=" N ASP A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.787A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.520A pdb=" N MET B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 225 through 235 removed outlier: 3.720A 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 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 321 through 338 removed outlier: 3.964A pdb=" N THR B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.619A 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: 3.715A pdb=" N LEU B 374 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.805A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.698A pdb=" N MET B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.502A 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: 3.627A pdb=" N ILE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.561A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 545 removed outlier: 3.728A pdb=" N LYS B 533 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.862A pdb=" N LEU B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 637 removed outlier: 3.664A 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: 3.912A pdb=" N MET B 669 " --> pdb=" O PRO B 665 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 4.897A pdb=" N GLU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.853A 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: 4.749A pdb=" N ILE B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 784 Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.878A 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: 4.401A 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: 3.890A 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: 3.616A pdb=" N ARG C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 348 through 361 removed outlier: 3.898A pdb=" N LYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.592A pdb=" N PHE C 373 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.903A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 421 removed outlier: 3.615A pdb=" N LEU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.548A 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: 3.631A pdb=" N ILE C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 3.618A 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 Processing helix chain 'C' and resid 529 through 545 removed outlier: 3.626A pdb=" N LYS C 533 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 3.986A 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: 3.696A pdb=" N ASN C 614 " --> pdb=" O TYR C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 655 removed outlier: 3.728A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 677 removed outlier: 4.017A pdb=" N TYR C 670 " --> pdb=" O ASP C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 694 Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.700A 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: 4.234A pdb=" N VAL C 794 " --> pdb=" O PHE C 790 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 795 " --> pdb=" O ALA C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.829A pdb=" N ALA C 820 " --> pdb=" O PHE C 816 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 823 " --> pdb=" O VAL C 819 " (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: 3.642A pdb=" N LYS D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 4.317A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (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 220 Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.840A 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: 3.808A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.505A pdb=" N ARG D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 removed outlier: 3.767A pdb=" N SER D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 360 removed outlier: 3.581A 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: 3.779A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.870A pdb=" N LEU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.608A pdb=" N LEU D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 3.553A 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 468 removed outlier: 3.508A pdb=" N ILE D 465 " --> pdb=" O THR D 461 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN D 468 " --> pdb=" O GLN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 508 through 523 removed outlier: 3.682A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 545 removed outlier: 3.642A 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: 3.719A 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: 3.821A pdb=" N ARG D 663 " --> pdb=" O ASP D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 678 removed outlier: 3.778A pdb=" N TYR D 670 " --> pdb=" O ASP D 666 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 678 " --> pdb=" O ASP D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.695A pdb=" N MET D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLU D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) removed outlier: 5.559A 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: 3.825A pdb=" N ALA D 787 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 3.733A 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 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: 4.273A 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: 3.788A 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 281 removed outlier: 3.676A pdb=" N ILE E 281 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 321 through 338 removed outlier: 3.846A pdb=" N LEU E 335 " --> pdb=" O SER E 331 " (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: 3.724A pdb=" N ILE E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 421 removed outlier: 4.141A pdb=" N LEU E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 443 Processing helix chain 'E' and resid 461 through 470 removed outlier: 4.141A pdb=" N GLN E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 469 " --> pdb=" O ILE E 465 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.554A pdb=" N GLN E 512 " --> pdb=" O HIS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 545 removed outlier: 3.546A 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 Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.542A pdb=" N VAL E 664 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 678 removed outlier: 3.742A pdb=" N MET E 669 " --> pdb=" O PRO E 665 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 678 " --> pdb=" O ASP E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 702 removed outlier: 4.749A pdb=" N GLU E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLN E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) removed outlier: 3.689A 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 Processing helix chain 'E' and resid 787 through 790 removed outlier: 3.754A 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: 4.088A 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 860 through 864 removed outlier: 3.877A pdb=" N PHE E 864 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 875 removed outlier: 3.520A pdb=" N ALA E 875 " --> pdb=" O PRO E 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.548A pdb=" N LYS F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 93 " --> pdb=" O HIS F 89 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 removed outlier: 3.974A pdb=" N LYS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 184 removed outlier: 3.869A pdb=" N GLN F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 removed outlier: 3.569A pdb=" N ALA F 212 " --> pdb=" O ASP F 208 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 4.145A 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: 3.590A pdb=" N ILE F 277 " --> pdb=" O ASN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.552A pdb=" N ARG F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 338 removed outlier: 3.614A pdb=" N SER F 338 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 361 removed outlier: 3.511A pdb=" N GLN F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 365 removed outlier: 3.816A 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: 3.697A pdb=" N ILE F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 removed outlier: 3.844A pdb=" N LEU F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 417 " --> pdb=" O SER F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 440 Processing helix chain 'F' and resid 442 through 448 removed outlier: 3.569A pdb=" N ALA F 446 " --> pdb=" O ILE F 442 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.788A pdb=" N GLN F 468 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 508 through 523 removed outlier: 3.910A pdb=" N GLN F 512 " --> pdb=" O HIS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 545 removed outlier: 3.790A pdb=" N SER F 535 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 536 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 543 " --> pdb=" O GLY F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 566 Processing helix chain 'F' and resid 585 through 592 removed outlier: 3.825A pdb=" N LEU F 591 " --> pdb=" O SER F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 638 removed outlier: 3.526A pdb=" N LEU F 607 " --> pdb=" O SER F 603 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 608 " --> pdb=" O PRO F 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 656 removed outlier: 3.657A pdb=" N ASP F 651 " --> pdb=" O SER F 647 " (cutoff:3.500A) removed outlier: 3.557A 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 700 removed outlier: 3.687A pdb=" N PHE F 689 " --> pdb=" O ARG F 685 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN F 695 " --> pdb=" O LEU F 691 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU F 697 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN F 698 " --> pdb=" O MET F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 748 removed outlier: 3.870A pdb=" N ARG F 747 " --> pdb=" O GLU F 743 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 748 " --> pdb=" O GLU F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 759 removed outlier: 4.781A pdb=" N MET F 757 " --> pdb=" O GLN F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 784 Processing helix chain 'F' and resid 785 through 789 removed outlier: 4.053A pdb=" N VAL F 789 " --> pdb=" O ASP F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 821 Processing helix chain 'G' and resid 87 through 100 removed outlier: 4.041A pdb=" N GLN G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 3.862A pdb=" N LEU G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 184 removed outlier: 3.875A pdb=" N GLN G 179 " --> pdb=" O ASN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 221 removed outlier: 3.544A pdb=" N ALA G 212 " --> pdb=" O ASP G 208 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.655A 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: 3.841A pdb=" N LEU G 264 " --> pdb=" O ASN G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 281 Processing helix chain 'G' and resid 321 through 340 removed outlier: 3.801A pdb=" N SER G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL G 339 " --> pdb=" O LEU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 361 removed outlier: 3.740A pdb=" N GLN G 352 " --> pdb=" O SER G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 365 removed outlier: 3.716A 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: 3.794A pdb=" N ILE G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 421 removed outlier: 3.641A pdb=" N LEU G 411 " --> pdb=" O ASN G 407 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP G 416 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 426 Processing helix chain 'G' and resid 427 through 448 removed outlier: 6.087A pdb=" N TYR G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Proline residue: G 445 - end of helix Processing helix chain 'G' and resid 461 through 470 removed outlier: 4.141A pdb=" N GLN G 468 " --> pdb=" O GLN G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 484 removed outlier: 3.543A pdb=" N ASN G 477 " --> pdb=" O PHE G 473 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 522 removed outlier: 3.957A pdb=" N GLN G 512 " --> pdb=" O HIS G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.763A 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 removed outlier: 3.744A pdb=" N ALA G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 594 removed outlier: 3.671A 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 Processing helix chain 'G' and resid 665 through 677 removed outlier: 3.568A pdb=" N MET G 669 " --> pdb=" O PRO G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 694 removed outlier: 3.782A pdb=" N PHE G 689 " --> pdb=" O ARG G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 701 Processing helix chain 'G' and resid 751 through 761 removed outlier: 4.560A 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: 3.616A pdb=" N THR G 788 " --> pdb=" O LEU G 785 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL G 789 " --> pdb=" O ASP G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 790 through 796 removed outlier: 4.085A pdb=" N VAL G 794 " --> pdb=" O PHE G 790 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 795 " --> pdb=" O ALA G 791 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU G 796 " --> pdb=" O GLN G 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 790 through 796' Processing helix chain 'G' and resid 816 through 822 removed outlier: 3.835A pdb=" N TYR G 822 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 100 removed outlier: 3.869A pdb=" N GLU H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 94 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 118 removed outlier: 4.110A pdb=" N LEU H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 183 removed outlier: 3.696A pdb=" N GLN H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'H' and resid 208 through 219 removed outlier: 4.262A pdb=" N ILE H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.654A pdb=" N ILE H 277 " --> pdb=" O ASN H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.746A pdb=" N ARG H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 338 removed outlier: 3.971A pdb=" N SER H 338 " --> pdb=" O ILE H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 361 removed outlier: 3.606A pdb=" N LYS H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 396 removed outlier: 3.661A pdb=" N ILE H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 421 removed outlier: 3.588A pdb=" N LEU H 411 " --> pdb=" O ASN H 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 426 removed outlier: 3.565A 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: 3.753A pdb=" N GLN H 468 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 4.423A pdb=" N TRP H 478 " --> pdb=" O GLN H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 523 removed outlier: 3.864A pdb=" N GLN H 512 " --> pdb=" O HIS H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 546 removed outlier: 3.793A pdb=" N SER H 535 " --> pdb=" O ASP H 531 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.681A pdb=" N ASN H 614 " --> pdb=" O TYR H 610 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 656 removed outlier: 3.577A pdb=" N ASP H 651 " --> pdb=" O SER H 647 " (cutoff:3.500A) removed outlier: 3.692A 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 removed outlier: 3.678A pdb=" N PHE H 689 " --> pdb=" O ARG H 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 695 through 701 removed outlier: 3.605A pdb=" N ARG H 701 " --> pdb=" O GLU H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 742 through 748 removed outlier: 3.655A pdb=" N ARG H 747 " --> pdb=" O GLU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 759 removed outlier: 4.086A pdb=" N MET H 757 " --> pdb=" O GLN H 753 " (cutoff:3.500A) Processing helix chain 'H' and resid 778 through 783 Processing helix chain 'H' and resid 790 through 796 removed outlier: 3.949A pdb=" N VAL H 794 " --> pdb=" O PHE H 790 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 819 Processing helix chain 'H' and resid 861 through 865 Processing helix chain 'H' and resid 871 through 875 removed outlier: 3.700A pdb=" N ALA H 875 " --> pdb=" O PRO H 872 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.711A 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: 3.794A pdb=" N LYS I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 183 removed outlier: 3.666A 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: 3.610A pdb=" N ALA I 212 " --> pdb=" O ASP I 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.716A pdb=" N ARG I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.670A pdb=" N LEU I 264 " --> pdb=" O ASN I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 281 Processing helix chain 'I' and resid 282 through 287 removed outlier: 3.663A pdb=" N ARG I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 340 removed outlier: 3.832A pdb=" N SER I 338 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL I 339 " --> pdb=" O LEU I 335 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 361 removed outlier: 3.693A pdb=" N GLN I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 365 removed outlier: 3.543A 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: 3.611A pdb=" N ILE I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 421 removed outlier: 3.635A pdb=" N LEU I 411 " --> pdb=" O ASN I 407 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP I 416 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.600A 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: 4.294A pdb=" N GLN I 468 " --> pdb=" O GLN I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 484 removed outlier: 3.523A pdb=" N TRP I 478 " --> pdb=" O GLN I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 522 removed outlier: 4.151A pdb=" N GLN I 512 " --> pdb=" O HIS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 545 removed outlier: 3.682A pdb=" N SER I 535 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.828A 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 removed outlier: 3.512A pdb=" N VAL I 588 " --> pdb=" O GLN I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 603 through 637 Processing helix chain 'I' and resid 645 through 656 removed outlier: 3.537A pdb=" N ASP I 651 " --> pdb=" O SER I 647 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU I 656 " --> pdb=" O PHE I 652 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 664 removed outlier: 3.704A pdb=" N ARG I 663 " --> pdb=" O ASP I 660 " (cutoff:3.500A) removed outlier: 3.988A 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: 3.933A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 700 removed outlier: 3.693A pdb=" N PHE I 689 " --> pdb=" O ARG I 685 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU I 697 " --> pdb=" O LEU I 693 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN I 698 " --> pdb=" O MET I 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 742 through 748 removed outlier: 3.779A pdb=" N ARG I 747 " --> pdb=" O GLU I 743 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 760 removed outlier: 4.324A 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: 3.956A pdb=" N VAL I 789 " --> pdb=" O ASP I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 791 through 796 removed outlier: 3.774A 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 Processing helix chain 'J' and resid 73 through 86 removed outlier: 3.747A pdb=" N LEU J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 100 removed outlier: 3.847A pdb=" N VAL J 93 " --> pdb=" O HIS J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 removed outlier: 4.042A pdb=" N LEU J 112 " --> pdb=" O LYS J 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 183 removed outlier: 3.940A pdb=" N GLN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 3.503A pdb=" N ASP J 192 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 221 removed outlier: 3.643A pdb=" N ALA J 212 " --> pdb=" O ASP J 208 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 235 removed outlier: 3.598A 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: 3.522A pdb=" N ILE J 277 " --> pdb=" O ASN J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 340 removed outlier: 3.631A pdb=" N SER J 338 " --> pdb=" O ILE J 334 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 339 " --> pdb=" O LEU J 335 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 361 removed outlier: 3.847A pdb=" N GLN J 352 " --> pdb=" O SER J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 396 removed outlier: 3.711A pdb=" N ILE J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 421 removed outlier: 3.680A pdb=" N LEU J 411 " --> pdb=" O ASN J 407 " (cutoff:3.500A) removed outlier: 4.046A 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: 3.664A pdb=" N PHE J 447 " --> pdb=" O ILE J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 470 removed outlier: 4.287A 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: 3.920A pdb=" N GLN J 512 " --> pdb=" O HIS J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 545 removed outlier: 3.636A pdb=" N SER J 535 " --> pdb=" O ASP J 531 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J 536 " --> pdb=" O TYR J 532 " (cutoff:3.500A) removed outlier: 3.865A 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 removed outlier: 3.689A pdb=" N VAL J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 603 through 638 removed outlier: 3.583A pdb=" N ASN J 614 " --> pdb=" O TYR J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 645 through 653 removed outlier: 3.611A pdb=" N VAL J 649 " --> pdb=" O MET J 645 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 678 removed outlier: 3.513A pdb=" N LEU J 678 " --> pdb=" O ASP J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 702 removed outlier: 3.810A pdb=" N ASN J 695 " --> pdb=" O LEU J 691 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU J 697 " --> pdb=" O LEU J 693 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN J 698 " --> pdb=" O MET J 694 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 702 " --> pdb=" O GLN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 748 removed outlier: 3.710A pdb=" N ARG J 747 " --> pdb=" O GLU J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 760 removed outlier: 3.616A 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: 3.826A pdb=" N VAL J 789 " --> pdb=" O ASP J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 821 Processing helix chain 'J' and resid 871 through 875 Processing helix chain 'P' and resid 3 through 17 Processing helix chain 'P' and resid 31 through 50 Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.928A pdb=" N GLU P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 69 Processing helix chain 'P' and resid 83 through 90 removed outlier: 3.547A pdb=" N ARG P 87 " --> pdb=" O ASN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 94 removed outlier: 4.258A 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: 3.518A 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: 3.629A pdb=" N ARG P 165 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.663A pdb=" N MET P 196 " --> pdb=" O GLU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 215 removed outlier: 3.581A pdb=" N TRP P 206 " --> pdb=" O TYR P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 231 removed outlier: 3.633A 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: 3.574A pdb=" N GLY P 299 " --> pdb=" O MET P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 311 removed outlier: 3.658A pdb=" N TRP P 310 " --> pdb=" O MET P 306 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU P 311 " --> pdb=" O ILE P 307 " (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: 3.808A pdb=" N GLU P 362 " --> pdb=" O GLU P 358 " (cutoff:3.500A) removed outlier: 5.321A 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 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: 3.873A pdb=" N ALA P 429 " --> pdb=" O MET P 425 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN P 430 " --> pdb=" O ASP P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 467 through 487 removed outlier: 3.773A pdb=" N ILE P 471 " --> pdb=" O TYR P 467 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA P 475 " --> pdb=" O ILE P 471 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL P 476 " --> pdb=" O ALA P 472 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS P 486 " --> pdb=" O ILE P 482 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR P 487 " --> pdb=" O TYR P 483 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 547 removed outlier: 3.691A pdb=" N ARG P 535 " --> pdb=" O THR P 531 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE P 538 " --> pdb=" O PHE P 534 " (cutoff:3.500A) Processing helix chain 'P' and resid 551 through 569 removed outlier: 3.626A pdb=" N ILE P 555 " --> pdb=" O ASP P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 595 through 612 Processing helix chain 'P' and resid 613 through 618 removed outlier: 4.601A pdb=" N SER P 616 " --> pdb=" O SER P 613 " (cutoff:3.500A) Processing helix chain 'P' and resid 644 through 661 Processing helix chain 'P' and resid 705 through 724 removed outlier: 3.649A pdb=" N GLN P 709 " --> pdb=" O THR P 705 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA P 710 " --> pdb=" O GLN P 706 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA P 711 " --> pdb=" O TRP P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 741 removed outlier: 3.643A 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: 3.889A pdb=" N VAL P 782 " --> pdb=" O THR P 778 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER P 790 " --> pdb=" O ARG P 786 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU P 791 " --> pdb=" O ALA P 787 " (cutoff:3.500A) removed outlier: 4.272A 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 805 through 820 removed outlier: 3.930A pdb=" N LYS P 809 " --> pdb=" O SER P 805 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 840 removed outlier: 3.677A pdb=" N ALA P 837 " --> pdb=" O LEU P 833 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS P 838 " --> pdb=" O THR P 834 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN P 840 " --> pdb=" O LYS P 836 " (cutoff:3.500A) Processing helix chain 'P' and resid 842 through 862 removed outlier: 3.560A pdb=" N MET P 860 " --> pdb=" O ALA P 856 " (cutoff:3.500A) Processing helix chain 'P' and resid 873 through 882 removed outlier: 3.722A pdb=" N ILE P 877 " --> pdb=" O THR P 873 " (cutoff:3.500A) removed outlier: 3.600A 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: 4.034A pdb=" N ILE P 934 " --> pdb=" O ILE P 930 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS P 936 " --> pdb=" O ARG P 932 " (cutoff:3.500A) Processing helix chain 'P' and resid 943 through 951 Processing helix chain 'P' and resid 956 through 964 removed outlier: 3.680A pdb=" N LEU P 960 " --> pdb=" O ASN P 956 " (cutoff:3.500A) Processing helix chain 'P' and resid 968 through 979 removed outlier: 3.904A pdb=" N ALA P 972 " --> pdb=" O PRO P 968 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS P 979 " --> pdb=" O TYR P 975 " (cutoff:3.500A) Processing helix chain 'P' and resid 984 through 997 removed outlier: 3.502A pdb=" N LEU P 997 " --> pdb=" O VAL P 993 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1007 removed outlier: 3.683A pdb=" N PHE P1007 " --> pdb=" O TYR P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1011 through 1017 removed outlier: 3.656A pdb=" N GLU P1015 " --> pdb=" O SER P1011 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU P1017 " --> pdb=" O ASP P1013 " (cutoff:3.500A) Processing helix chain 'P' and resid 1026 through 1049 removed outlier: 3.697A pdb=" N THR P1030 " --> pdb=" O ILE P1026 " (cutoff:3.500A) Processing helix chain 'P' and resid 1059 through 1071 removed outlier: 3.674A pdb=" N LYS P1068 " --> pdb=" O ILE P1064 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS P1069 " --> pdb=" O LYS P1065 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP P1071 " --> pdb=" O TRP P1067 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1082 removed outlier: 3.630A 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: 4.091A pdb=" N VAL A 140 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.153A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 402 removed outlier: 6.493A 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: 3.564A pdb=" N GLY A 709 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 768 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 711 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 766 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 740 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 8.739A 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 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 774 removed outlier: 6.525A pdb=" N ILE A 773 " --> pdb=" O LEU A 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 141 removed outlier: 4.038A pdb=" N VAL B 140 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 5.871A 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: 7.014A 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: 3.542A pdb=" N GLY B 709 " --> pdb=" O TYR B 833 " (cutoff:3.500A) removed outlier: 6.074A 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 Processing sheet with id=AC4, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.601A 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: 4.046A pdb=" N VAL C 140 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.082A 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 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: 6.319A 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: 6.768A 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: 4.123A pdb=" N VAL D 140 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 6.058A 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: 6.916A 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 removed outlier: 6.634A pdb=" N SER D 400 " --> pdb=" O LEU D 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 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 706 through 707 Processing sheet with id=AE8, first strand: chain 'D' and resid 710 through 712 removed outlier: 6.633A pdb=" N ILE D 740 " --> pdb=" O VAL D 767 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 717 through 718 Processing sheet with id=AF1, first strand: chain 'D' and resid 727 through 728 Processing sheet with id=AF2, first strand: chain 'D' and resid 730 through 731 Processing sheet with id=AF3, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.876A pdb=" N VAL P 580 " --> pdb=" O ASP P 577 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE P 584 " --> pdb=" O VAL P 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL P 573 " --> pdb=" O ILE P 584 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 133 through 141 removed outlier: 4.165A pdb=" N VAL E 140 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG E 150 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AF6, first strand: chain 'E' and resid 238 through 240 Processing sheet with id=AF7, first strand: chain 'E' and resid 270 through 271 removed outlier: 6.796A pdb=" N ARG E 304 " --> pdb=" O TYR E 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 291 through 294 Processing sheet with id=AF9, first strand: chain 'E' and resid 399 through 402 removed outlier: 6.126A pdb=" N SER E 400 " --> pdb=" O LEU E 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 488 through 492 Processing sheet with id=AG2, first strand: chain 'E' and resid 706 through 712 removed outlier: 6.525A pdb=" N GLY E 768 " --> pdb=" O GLY E 709 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE E 711 " --> pdb=" O LEU E 766 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 766 " --> pdb=" O ILE E 711 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE E 740 " --> pdb=" O VAL E 767 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ALA E 769 " --> pdb=" O ILE E 740 " (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: 6.641A 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 removed outlier: 4.533A pdb=" N GLN F 838 " --> pdb=" O TRP F 155 " (cutoff:3.500A) 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 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 399 through 402 Processing sheet with id=AH3, first strand: chain 'F' and resid 488 through 492 Processing sheet with id=AH4, first strand: chain 'F' and resid 706 through 712 removed outlier: 3.635A pdb=" N GLY F 709 " --> pdb=" O GLY F 768 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY F 768 " --> pdb=" O GLY F 709 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE F 711 " --> pdb=" O LEU F 766 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU F 766 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE F 740 " --> pdb=" O VAL F 767 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ALA F 769 " --> pdb=" O ILE F 740 " (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 727 through 728 removed outlier: 3.576A pdb=" N ILE F 809 " --> pdb=" O TYR F 727 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 773 " --> pdb=" O LEU F 806 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 808 " --> pdb=" O ILE F 773 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP F 775 " --> pdb=" O LYS F 808 " (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 'G' and resid 133 through 138 Processing sheet with id=AH9, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AI1, first strand: chain 'G' and resid 238 through 240 Processing sheet with id=AI2, first strand: chain 'G' and resid 270 through 271 Processing sheet with id=AI3, first strand: chain 'G' and resid 291 through 294 Processing sheet with id=AI4, first strand: chain 'G' and resid 488 through 492 Processing sheet with id=AI5, first strand: chain 'G' and resid 730 through 731 removed outlier: 3.612A pdb=" N LEU G 770 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY G 709 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY G 768 " --> pdb=" O GLY G 709 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE G 711 " --> pdb=" O LEU G 766 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU G 766 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE G 740 " --> pdb=" O VAL G 767 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ALA G 769 " --> pdb=" O ILE G 740 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 717 through 718 Processing sheet with id=AI7, first strand: chain 'G' and resid 720 through 721 removed outlier: 3.539A pdb=" N VAL G 728 " --> pdb=" O GLU G 720 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 133 through 138 removed outlier: 4.563A pdb=" N GLN H 838 " --> pdb=" O TRP H 155 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 195 through 196 Processing sheet with id=AJ1, first strand: chain 'H' and resid 238 through 240 Processing sheet with id=AJ2, first strand: chain 'H' and resid 270 through 271 Processing sheet with id=AJ3, first strand: chain 'H' and resid 291 through 294 Processing sheet with id=AJ4, first strand: chain 'H' and resid 488 through 492 Processing sheet with id=AJ5, first strand: chain 'H' and resid 710 through 712 Processing sheet with id=AJ6, first strand: chain 'H' and resid 720 through 721 Processing sheet with id=AJ7, first strand: chain 'H' and resid 730 through 731 Processing sheet with id=AJ8, first strand: chain 'I' and resid 133 through 142 removed outlier: 4.409A pdb=" N VAL I 140 " --> pdb=" O ARG I 150 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG I 150 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ARG I 142 " --> pdb=" O GLU I 148 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU I 148 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AK1, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AK2, first strand: chain 'I' and resid 270 through 271 Processing sheet with id=AK3, first strand: chain 'I' and resid 291 through 295 Processing sheet with id=AK4, first strand: chain 'I' and resid 488 through 492 Processing sheet with id=AK5, first strand: chain 'I' and resid 706 through 712 removed outlier: 4.718A pdb=" N ILE I 706 " --> pdb=" O LEU I 770 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU I 770 " --> pdb=" O ILE I 706 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN I 708 " --> pdb=" O GLY I 768 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY I 768 " --> pdb=" O GLN I 708 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE I 740 " --> pdb=" O VAL I 767 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ALA I 769 " --> pdb=" O ILE I 740 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'I' and resid 720 through 721 Processing sheet with id=AK7, first strand: chain 'I' and resid 730 through 731 Processing sheet with id=AK8, first strand: chain 'J' and resid 133 through 138 removed outlier: 4.402A pdb=" N GLN J 838 " --> pdb=" O TRP J 155 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 195 through 196 Processing sheet with id=AL1, first strand: chain 'J' and resid 238 through 240 Processing sheet with id=AL2, first strand: chain 'J' and resid 270 through 271 Processing sheet with id=AL3, first strand: chain 'J' and resid 291 through 295 Processing sheet with id=AL4, first strand: chain 'J' and resid 488 through 492 Processing sheet with id=AL5, first strand: chain 'J' and resid 730 through 731 removed outlier: 3.527A pdb=" N GLY J 709 " --> pdb=" O TYR J 833 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 709 " --> pdb=" O GLY J 768 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY J 768 " --> pdb=" O GLY J 709 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE J 711 " --> pdb=" O LEU J 766 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU J 766 " --> pdb=" O ILE J 711 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 720 through 721 removed outlier: 3.580A pdb=" N GLU J 720 " --> pdb=" O VAL J 728 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 773 through 774 removed outlier: 6.413A pdb=" N ILE J 773 " --> pdb=" O LEU J 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'P' and resid 22 through 28 removed outlier: 6.826A pdb=" N VAL P 22 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER P 76 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE P 24 " --> pdb=" O ILE P 74 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE P 74 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE P 26 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'P' and resid 257 through 260 removed outlier: 4.528A pdb=" N ASN P 258 " --> pdb=" O LYS P 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS P 274 " --> pdb=" O ASN P 258 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'P' and resid 449 through 452 Processing sheet with id=AM2, first strand: chain 'P' and resid 621 through 628 removed outlier: 6.800A pdb=" N VAL P 636 " --> pdb=" O LYS P 624 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE P 626 " --> pdb=" O TYR P 634 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR P 634 " --> pdb=" O ILE P 626 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU P 669 " --> pdb=" O TYR P 518 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 675 through 676 removed outlier: 3.706A pdb=" N ILE P 675 " --> pdb=" O ILE P 682 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR P 681 " --> pdb=" O PHE P 688 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'P' and resid 888 through 890 removed outlier: 3.598A pdb=" N ASN P 888 " --> pdb=" O SER P1053 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP P1051 " --> pdb=" O ALA P 890 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ARG P1019 " --> pdb=" O ILE P1052 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU P1054 " --> pdb=" O ARG P1019 " (cutoff:3.500A) 3196 hydrogen bonds defined for protein. 9024 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: 68.35 Time building geometry restraints manager: 100.48 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: 74405 1.02 - 1.22: 95 1.22 - 1.42: 31210 1.42 - 1.62: 43464 1.62 - 1.81: 742 Bond restraints: 149916 Sorted by residual: bond pdb=" C ARG I 882 " pdb=" N ILE I 883 " ideal model delta sigma weight residual 1.329 1.269 0.060 2.19e-02 2.09e+03 7.55e+00 bond pdb=" CA LEU C 806 " pdb=" CB LEU C 806 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.46e+00 bond pdb=" C SER H 662 " pdb=" N ARG H 663 " ideal model delta sigma weight residual 1.332 1.298 0.035 1.40e-02 5.10e+03 6.13e+00 bond pdb=" CB THR G 329 " pdb=" CG2 THR G 329 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 bond pdb=" CG1 ILE E 442 " pdb=" CD1 ILE E 442 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 ... (remaining 149911 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.62: 996 103.62 - 111.26: 162383 111.26 - 118.89: 42895 118.89 - 126.53: 63841 126.53 - 134.16: 845 Bond angle restraints: 270960 Sorted by residual: angle pdb=" C ILE J 367 " pdb=" N GLN J 368 " pdb=" CA GLN J 368 " ideal model delta sigma weight residual 121.70 130.85 -9.15 1.80e+00 3.09e-01 2.58e+01 angle pdb=" C ALA G 143 " pdb=" N ASN G 144 " pdb=" CA ASN G 144 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ALA H 143 " pdb=" N ASN H 144 " pdb=" CA ASN H 144 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C GLU P 265 " pdb=" N GLU P 266 " pdb=" CA GLU P 266 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" N ASN B 378 " pdb=" CA ASN B 378 " pdb=" C ASN B 378 " ideal model delta sigma weight residual 110.24 115.55 -5.31 1.30e+00 5.92e-01 1.67e+01 ... (remaining 270955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 65001 17.19 - 34.38: 4300 34.38 - 51.56: 826 51.56 - 68.75: 142 68.75 - 85.94: 30 Dihedral angle restraints: 70299 sinusoidal: 38863 harmonic: 31436 Sorted by residual: 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 -121.24 -58.76 0 5.00e+00 4.00e-02 1.38e+02 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 -121.75 -58.25 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA GLU G 106 " pdb=" C GLU G 106 " pdb=" N PRO G 107 " pdb=" CA PRO G 107 " ideal model delta harmonic sigma weight residual -180.00 -128.76 -51.24 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 70296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 6717 0.044 - 0.088: 3754 0.088 - 0.132: 1070 0.132 - 0.176: 174 0.176 - 0.220: 7 Chirality restraints: 11722 Sorted by residual: chirality pdb=" CB ILE P 303 " pdb=" CA ILE P 303 " pdb=" CG1 ILE P 303 " pdb=" CG2 ILE P 303 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO F 526 " pdb=" N PRO F 526 " pdb=" C PRO F 526 " pdb=" CB PRO F 526 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL H 764 " pdb=" CA VAL H 764 " pdb=" CG1 VAL H 764 " pdb=" CG2 VAL H 764 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 11719 not shown) Planarity restraints: 21987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 106 " -0.072 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO G 107 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO G 107 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO G 107 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 106 " 0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO F 107 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO F 107 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO F 107 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 102 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO D 103 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.055 5.00e-02 4.00e+02 ... (remaining 21984 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 12001 2.22 - 2.81: 333777 2.81 - 3.41: 384824 3.41 - 4.00: 537349 4.00 - 4.60: 846184 Nonbonded interactions: 2114135 Sorted by model distance: nonbonded pdb=" O ASN J 810 " pdb=" HG SER J 813 " model vdw 1.624 1.850 nonbonded pdb=" H LEU I 496 " pdb=" OD1 ASN I 571 " model vdw 1.643 1.850 nonbonded pdb=" O LEU J 818 " pdb=" HE1 TRP J 824 " model vdw 1.656 1.850 nonbonded pdb=" OE2 GLU C 682 " pdb=" HE ARG C 685 " model vdw 1.660 1.850 nonbonded pdb=" O ARG C 201 " pdb="HE21 GLN G 642 " model vdw 1.667 1.850 ... (remaining 2114130 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 individual isotropic 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.550 Extract box with map and model: 14.570 Check model and map are aligned: 1.580 Set scattering table: 0.990 Process input model: 369.530 Find NCS groups from input model: 6.280 Set up NCS constraints: 0.390 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 400.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.011 0.112 75455 Z= 0.739 Angle : 0.901 9.629 102320 Z= 0.483 Chirality : 0.055 0.220 11722 Planarity : 0.006 0.111 13254 Dihedral : 10.204 78.080 28629 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.29 % Favored : 90.66 % Rotamer: Outliers : 0.01 % Allowed : 1.36 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.08 % 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: -3.56 (0.08), residues: 9050 helix: -1.85 (0.07), residues: 4293 sheet: -2.84 (0.14), residues: 839 loop : -2.75 (0.09), residues: 3918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 148 HIS 0.015 0.002 HIS H 266 PHE 0.049 0.003 PHE B 373 TYR 0.035 0.004 TYR A 444 ARG 0.016 0.002 ARG C 675 *********************** 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 2640 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2639 time to evaluate : 8.721 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: A 349 THR cc_start: 0.8648 (p) cc_final: 0.8378 (t) REVERT: A 355 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7563 (tttp) REVERT: A 795 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7844 (mttt) REVERT: A 868 ASP cc_start: 0.7773 (t70) cc_final: 0.7517 (t0) REVERT: A 884 MET cc_start: 0.7017 (mmt) cc_final: 0.6760 (mmt) REVERT: B 270 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 320 ASN cc_start: 0.7811 (t160) cc_final: 0.7393 (t0) REVERT: B 375 THR cc_start: 0.8939 (m) cc_final: 0.8705 (p) REVERT: B 470 ILE cc_start: 0.8018 (pt) cc_final: 0.7764 (pt) REVERT: B 639 ASN cc_start: 0.8054 (t0) cc_final: 0.7853 (t0) REVERT: B 723 GLU cc_start: 0.7301 (pp20) cc_final: 0.6057 (pp20) REVERT: C 402 ASP cc_start: 0.7375 (p0) cc_final: 0.7002 (p0) REVERT: C 706 ILE cc_start: 0.9140 (pp) cc_final: 0.8869 (pt) REVERT: C 817 TYR cc_start: 0.8071 (p90) cc_final: 0.7854 (p90) REVERT: D 280 TYR cc_start: 0.8557 (t80) cc_final: 0.8275 (t80) REVERT: D 334 ILE cc_start: 0.9194 (tt) cc_final: 0.8975 (mm) REVERT: D 393 MET cc_start: 0.8276 (mtm) cc_final: 0.8012 (mtm) REVERT: D 420 VAL cc_start: 0.9177 (m) cc_final: 0.8835 (t) REVERT: D 581 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 661 ILE cc_start: 0.8624 (mp) cc_final: 0.8417 (mt) REVERT: D 741 ASN cc_start: 0.8164 (t0) cc_final: 0.7903 (t0) REVERT: D 815 ASP cc_start: 0.7165 (m-30) cc_final: 0.6921 (m-30) REVERT: E 248 TYR cc_start: 0.8942 (m-80) cc_final: 0.8458 (m-80) REVERT: E 320 ASN cc_start: 0.8182 (t0) cc_final: 0.7864 (t0) REVERT: E 326 ASP cc_start: 0.7910 (t70) cc_final: 0.7536 (t0) REVERT: E 344 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7550 (mmtp) REVERT: E 490 VAL cc_start: 0.8997 (p) cc_final: 0.8698 (m) REVERT: E 542 LEU cc_start: 0.8938 (mt) cc_final: 0.8603 (mt) REVERT: E 574 HIS cc_start: 0.8037 (t70) cc_final: 0.7685 (t70) REVERT: E 696 MET cc_start: 0.8491 (ptm) cc_final: 0.8286 (ptm) REVERT: F 100 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8301 (mmtm) REVERT: F 222 GLU cc_start: 0.5477 (tm-30) cc_final: 0.5132 (tm-30) REVERT: F 319 ASP cc_start: 0.7935 (p0) cc_final: 0.7707 (p0) REVERT: F 593 MET cc_start: 0.8146 (mmm) cc_final: 0.7859 (mmt) REVERT: F 703 SER cc_start: 0.8265 (t) cc_final: 0.8025 (p) REVERT: F 756 ASN cc_start: 0.8221 (t0) cc_final: 0.7839 (t0) REVERT: F 879 ASP cc_start: 0.7697 (p0) cc_final: 0.7381 (p0) REVERT: G 184 MET cc_start: 0.7609 (ttm) cc_final: 0.7402 (ttt) REVERT: G 637 ARG cc_start: 0.8425 (mtt180) cc_final: 0.7518 (mmp-170) REVERT: G 741 ASN cc_start: 0.7501 (t0) cc_final: 0.7147 (t0) REVERT: H 442 ILE cc_start: 0.9001 (mm) cc_final: 0.8712 (mt) REVERT: H 486 GLN cc_start: 0.8430 (mp10) cc_final: 0.8173 (mp10) REVERT: I 429 GLU cc_start: 0.8323 (mp0) cc_final: 0.7923 (mp0) REVERT: I 621 TYR cc_start: 0.8753 (t80) cc_final: 0.8368 (t80) REVERT: I 833 TYR cc_start: 0.8632 (t80) cc_final: 0.8402 (t80) REVERT: J 178 ASP cc_start: 0.7572 (p0) cc_final: 0.7195 (p0) REVERT: J 326 ASP cc_start: 0.7811 (t0) cc_final: 0.7600 (t0) REVERT: J 580 THR cc_start: 0.8321 (m) cc_final: 0.7805 (p) REVERT: J 621 TYR cc_start: 0.8294 (t80) cc_final: 0.7739 (t80) REVERT: J 651 ASP cc_start: 0.7575 (t70) cc_final: 0.7329 (t0) REVERT: J 669 MET cc_start: 0.7914 (mmm) cc_final: 0.7558 (mmt) REVERT: J 778 VAL cc_start: 0.9050 (t) cc_final: 0.8829 (t) REVERT: J 815 ASP cc_start: 0.8012 (p0) cc_final: 0.7788 (p0) REVERT: P 6 LEU cc_start: 0.7621 (mp) cc_final: 0.7368 (mt) REVERT: P 365 MET cc_start: 0.7385 (ttt) cc_final: 0.6813 (ttp) REVERT: P 383 ASP cc_start: 0.7543 (t70) cc_final: 0.7162 (t0) REVERT: P 384 HIS cc_start: 0.6939 (p-80) cc_final: 0.6721 (p-80) REVERT: P 937 TYR cc_start: 0.7524 (m-80) cc_final: 0.7321 (m-80) REVERT: P 1010 ASN cc_start: 0.7962 (m110) cc_final: 0.7747 (m-40) outliers start: 1 outliers final: 0 residues processed: 2640 average time/residue: 1.9897 time to fit residues: 8529.2937 Evaluate side-chains 1686 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1686 time to evaluate : 8.499 ------------------------------------------------------------------------------- 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: 0.7980 chunk 685 optimal weight: 0.8980 chunk 380 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 462 optimal weight: 0.7980 chunk 366 optimal weight: 0.7980 chunk 708 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 430 optimal weight: 0.8980 chunk 527 optimal weight: 0.7980 chunk 820 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 484 ASN A 584 GLN A 609 HIS ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN B 361 GLN B 469 GLN B 484 ASN B 880 ASN C 287 ASN C 290 ASN C 423 ASN C 484 ASN ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN C 574 HIS C 874 ASN C 880 ASN D 179 GLN D 244 ASN D 352 GLN D 484 ASN D 756 ASN D 792 GLN E 179 GLN E 287 ASN E 484 ASN E 519 GLN E 636 ASN E 821 ASN F 266 HIS F 290 ASN F 294 ASN F 440 ASN F 486 GLN F 545 ASN F 605 GLN F 733 ASN F 761 ASN F 838 GLN F 874 ASN G 354 GLN G 423 ASN G 549 GLN G 733 ASN G 739 GLN G 814 ASN G 852 ASN H 257 HIS H 318 HIS H 361 GLN H 423 ASN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 739 GLN H 838 GLN I 266 HIS I 620 ASN I 636 ASN J 266 HIS J 287 ASN J 523 GLN J 537 GLN P 17 ASN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 430 ASN P 532 GLN P 703 GLN P 862 GLN P 920 GLN P1044 HIS ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 75455 Z= 0.182 Angle : 0.579 7.966 102320 Z= 0.313 Chirality : 0.040 0.189 11722 Planarity : 0.005 0.093 13254 Dihedral : 5.952 77.715 9999 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.98 % Rotamer: Outliers : 0.85 % Allowed : 7.43 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.02 % 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: -2.22 (0.08), residues: 9050 helix: -0.53 (0.08), residues: 4309 sheet: -2.38 (0.15), residues: 838 loop : -2.30 (0.09), residues: 3903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 478 HIS 0.005 0.001 HIS J 453 PHE 0.016 0.001 PHE B 373 TYR 0.019 0.001 TYR A 714 ARG 0.014 0.001 ARG B 637 *********************** 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 1922 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1851 time to evaluate : 8.744 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: A 349 THR cc_start: 0.8532 (p) cc_final: 0.8264 (t) REVERT: A 795 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8045 (mptt) REVERT: A 884 MET cc_start: 0.7155 (mmt) cc_final: 0.6915 (mmt) REVERT: B 234 GLU cc_start: 0.6721 (tt0) cc_final: 0.6381 (tt0) REVERT: B 375 THR cc_start: 0.8985 (m) cc_final: 0.8619 (p) REVERT: B 431 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7767 (pt) REVERT: B 627 ASP cc_start: 0.8139 (m-30) cc_final: 0.7817 (m-30) REVERT: B 757 MET cc_start: 0.7884 (mtm) cc_final: 0.7609 (mtm) REVERT: B 796 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 268 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 326 ASP cc_start: 0.8207 (t70) cc_final: 0.7637 (t70) REVERT: C 452 MET cc_start: 0.6153 (ttt) cc_final: 0.5547 (ttt) REVERT: C 579 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 706 ILE cc_start: 0.9221 (pp) cc_final: 0.8982 (pt) REVERT: C 854 THR cc_start: 0.7742 (m) cc_final: 0.7381 (p) REVERT: D 252 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8426 (pp) REVERT: D 268 LEU cc_start: 0.8859 (pp) cc_final: 0.8510 (mt) REVERT: D 280 TYR cc_start: 0.8661 (t80) cc_final: 0.8134 (t80) REVERT: D 645 MET cc_start: 0.8259 (mtt) cc_final: 0.7819 (mmt) REVERT: E 101 THR cc_start: 0.8308 (m) cc_final: 0.7980 (t) REVERT: E 248 TYR cc_start: 0.8931 (m-80) cc_final: 0.8605 (m-80) REVERT: E 320 ASN cc_start: 0.8323 (t0) cc_final: 0.7823 (t0) REVERT: E 344 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7778 (mmtp) REVERT: E 490 VAL cc_start: 0.9004 (p) cc_final: 0.8733 (m) REVERT: E 716 ASP cc_start: 0.7965 (t0) cc_final: 0.7752 (t0) REVERT: F 100 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8313 (mmtm) REVERT: F 220 GLN cc_start: 0.8105 (mm110) cc_final: 0.7825 (mp10) REVERT: F 354 GLN cc_start: 0.7330 (mp10) cc_final: 0.7100 (mp10) REVERT: F 450 GLN cc_start: 0.8131 (pt0) cc_final: 0.7802 (pt0) REVERT: F 593 MET cc_start: 0.8199 (mmm) cc_final: 0.7828 (mmt) REVERT: F 756 ASN cc_start: 0.8071 (t0) cc_final: 0.7817 (t0) REVERT: F 812 ASP cc_start: 0.7351 (p0) cc_final: 0.7050 (p0) REVERT: G 171 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6904 (tt0) REVERT: G 218 ILE cc_start: 0.9206 (mt) cc_final: 0.8989 (mt) REVERT: G 464 GLN cc_start: 0.8343 (mt0) cc_final: 0.7851 (mt0) REVERT: G 637 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7554 (mmp-170) REVERT: G 744 GLU cc_start: 0.7456 (mp0) cc_final: 0.7128 (mp0) REVERT: G 807 TYR cc_start: 0.8453 (m-80) cc_final: 0.8250 (m-80) REVERT: H 150 ARG cc_start: 0.5967 (ptp-170) cc_final: 0.5626 (ptp-170) REVERT: H 774 THR cc_start: 0.8712 (p) cc_final: 0.8383 (p) REVERT: I 833 TYR cc_start: 0.8683 (t80) cc_final: 0.8331 (t80) REVERT: J 178 ASP cc_start: 0.7589 (p0) cc_final: 0.7263 (p0) REVERT: J 193 MET cc_start: 0.7603 (ptp) cc_final: 0.6864 (ptp) REVERT: J 425 MET cc_start: 0.8516 (tpt) cc_final: 0.8281 (tpt) REVERT: J 580 THR cc_start: 0.8040 (m) cc_final: 0.7701 (p) REVERT: J 621 TYR cc_start: 0.8342 (t80) cc_final: 0.7886 (t80) REVERT: J 651 ASP cc_start: 0.7658 (t70) cc_final: 0.7303 (t0) REVERT: P 365 MET cc_start: 0.7410 (ttt) cc_final: 0.6917 (ttp) REVERT: P 500 LEU cc_start: 0.7898 (mt) cc_final: 0.7521 (mt) REVERT: P 1010 ASN cc_start: 0.8080 (m110) cc_final: 0.7609 (m-40) outliers start: 71 outliers final: 46 residues processed: 1883 average time/residue: 1.9335 time to fit residues: 5993.3202 Evaluate side-chains 1654 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1603 time to evaluate : 8.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 774 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain F residue 89 HIS Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain F residue 874 ASN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 836 ILE Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 785 LEU Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 757 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 780 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 862 GLN Chi-restraints excluded: chain P residue 973 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 683 optimal weight: 5.9990 chunk 559 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 822 optimal weight: 6.9990 chunk 888 optimal weight: 10.0000 chunk 732 optimal weight: 3.9990 chunk 815 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 659 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 352 GLN A 560 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN A 880 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 358 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 760 ASN C 260 ASN C 477 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN D 94 GLN D 244 ASN D 290 ASN D 497 ASN ** D 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D 609 HIS D 762 GLN E 179 GLN E 316 ASN E 358 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 GLN E 821 ASN F 484 ASN F 501 ASN F 549 GLN F 584 GLN ** F 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 ASN F 838 GLN ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN G 485 ASN G 537 GLN G 761 ASN G 814 ASN ** H 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 838 GLN I 423 ASN I 440 ASN I 484 ASN I 549 GLN I 636 ASN J 137 GLN J 380 GLN J 440 ASN P 17 ASN P 51 ASN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 703 GLN ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 75455 Z= 0.435 Angle : 0.649 9.399 102320 Z= 0.354 Chirality : 0.044 0.184 11722 Planarity : 0.006 0.098 13254 Dihedral : 5.803 88.762 9999 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 1.85 % Allowed : 9.17 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.08), residues: 9050 helix: -0.20 (0.08), residues: 4376 sheet: -2.07 (0.16), residues: 751 loop : -2.21 (0.09), residues: 3923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 707 HIS 0.007 0.001 HIS G 508 PHE 0.020 0.002 PHE G 173 TYR 0.029 0.002 TYR I 621 ARG 0.009 0.001 ARG E 238 *********************** 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 1841 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1687 time to evaluate : 10.258 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: A 349 THR cc_start: 0.8567 (p) cc_final: 0.8277 (t) REVERT: A 795 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8034 (mmtp) REVERT: A 868 ASP cc_start: 0.7945 (t70) cc_final: 0.7719 (t0) REVERT: A 884 MET cc_start: 0.7523 (mmt) cc_final: 0.7156 (mmt) REVERT: B 234 GLU cc_start: 0.6833 (tt0) cc_final: 0.6517 (tt0) REVERT: B 278 PHE cc_start: 0.7823 (m-10) cc_final: 0.7211 (m-80) REVERT: B 375 THR cc_start: 0.9043 (m) cc_final: 0.8655 (p) REVERT: B 431 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8285 (pt) REVERT: B 627 ASP cc_start: 0.8245 (m-30) cc_final: 0.7947 (m-30) REVERT: B 747 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8216 (ttm110) REVERT: B 795 LYS cc_start: 0.6815 (mmtt) cc_final: 0.6483 (mmtt) REVERT: B 796 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 268 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8719 (pp) REVERT: C 334 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9244 (mm) REVERT: C 706 ILE cc_start: 0.9411 (pp) cc_final: 0.9208 (pt) REVERT: C 854 THR cc_start: 0.8120 (m) cc_final: 0.7740 (p) REVERT: D 216 ASP cc_start: 0.7207 (m-30) cc_final: 0.6803 (m-30) REVERT: D 252 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8441 (pp) REVERT: D 255 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 540 ILE cc_start: 0.9012 (pt) cc_final: 0.8692 (mt) REVERT: D 854 THR cc_start: 0.8741 (p) cc_final: 0.8539 (t) REVERT: E 248 TYR cc_start: 0.9024 (m-80) cc_final: 0.8694 (m-80) REVERT: E 268 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8965 (pp) REVERT: E 320 ASN cc_start: 0.8691 (t0) cc_final: 0.8385 (t0) REVERT: E 384 ASP cc_start: 0.8421 (t70) cc_final: 0.7999 (t0) REVERT: E 687 ASP cc_start: 0.7395 (m-30) cc_final: 0.7177 (m-30) REVERT: E 796 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7344 (pp) REVERT: F 100 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8432 (mmtm) REVERT: F 486 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7954 (mp-120) REVERT: F 593 MET cc_start: 0.8859 (mmm) cc_final: 0.8368 (mmt) REVERT: F 756 ASN cc_start: 0.8380 (t0) cc_final: 0.7921 (t0) REVERT: F 812 ASP cc_start: 0.7865 (p0) cc_final: 0.7510 (p0) REVERT: G 268 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8745 (pp) REVERT: G 464 GLN cc_start: 0.8586 (mt0) cc_final: 0.8249 (mt0) REVERT: G 627 ASP cc_start: 0.8407 (m-30) cc_final: 0.7862 (m-30) REVERT: G 637 ARG cc_start: 0.8606 (mtt180) cc_final: 0.7726 (mmp-170) REVERT: G 739 GLN cc_start: 0.8451 (mp-120) cc_final: 0.8235 (mp-120) REVERT: G 744 GLU cc_start: 0.7504 (mp0) cc_final: 0.7258 (mp0) REVERT: H 216 ASP cc_start: 0.8050 (p0) cc_final: 0.7820 (p0) REVERT: H 493 ASP cc_start: 0.7403 (t0) cc_final: 0.7159 (t0) REVERT: H 663 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8045 (ttt90) REVERT: H 774 THR cc_start: 0.8846 (p) cc_final: 0.8589 (p) REVERT: I 261 GLU cc_start: 0.7121 (pp20) cc_final: 0.6690 (pt0) REVERT: I 344 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8476 (ptpp) REVERT: I 637 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8344 (mtm-85) REVERT: I 795 LYS cc_start: 0.8378 (tttt) cc_final: 0.7973 (mmtp) REVERT: I 833 TYR cc_start: 0.8873 (t80) cc_final: 0.8569 (t80) REVERT: J 178 ASP cc_start: 0.7788 (p0) cc_final: 0.7575 (p0) REVERT: J 425 MET cc_start: 0.8767 (tpt) cc_final: 0.8418 (tpt) REVERT: J 580 THR cc_start: 0.8237 (m) cc_final: 0.7965 (p) REVERT: J 639 ASN cc_start: 0.8208 (t0) cc_final: 0.7998 (t0) REVERT: J 651 ASP cc_start: 0.8142 (t70) cc_final: 0.7742 (t0) REVERT: P 365 MET cc_start: 0.7545 (ttt) cc_final: 0.7298 (ttp) REVERT: P 500 LEU cc_start: 0.7780 (mt) cc_final: 0.7306 (mt) REVERT: P 664 THR cc_start: 0.8949 (m) cc_final: 0.8742 (p) REVERT: P 1010 ASN cc_start: 0.8270 (m110) cc_final: 0.7818 (m-40) outliers start: 154 outliers final: 101 residues processed: 1763 average time/residue: 1.9116 time to fit residues: 5580.0729 Evaluate side-chains 1654 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1542 time to evaluate : 8.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 754 ILE Chi-restraints excluded: chain C residue 774 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 824 TRP Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 572 MET Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 869 THR Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 275 ASP Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 704 ASP Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 827 THR Chi-restraints excluded: chain H residue 836 ILE Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 535 SER Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 785 LEU Chi-restraints excluded: chain I residue 809 ILE Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain J residue 137 GLN Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 740 ILE Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 757 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 780 SER Chi-restraints excluded: chain P residue 17 ASN Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 736 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 3.9990 chunk 618 optimal weight: 4.9990 chunk 426 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 392 optimal weight: 2.9990 chunk 552 optimal weight: 3.9990 chunk 825 optimal weight: 4.9990 chunk 873 optimal weight: 7.9990 chunk 431 optimal weight: 4.9990 chunk 782 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 260 ASN B 380 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 497 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 ASN C 756 ASN D 368 GLN D 423 ASN D 571 ASN E 179 GLN E 584 GLN E 636 ASN E 874 ASN F 523 GLN F 838 GLN G 318 HIS ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 ASN H 90 GLN H 657 GLN H 739 GLN I 423 ASN I 477 ASN I 636 ASN J 137 GLN J 760 ASN P 273 ASN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 794 GLN ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 75455 Z= 0.375 Angle : 0.600 9.538 102320 Z= 0.326 Chirality : 0.042 0.160 11722 Planarity : 0.005 0.096 13254 Dihedral : 5.597 85.327 9999 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 2.21 % Allowed : 10.41 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.09), residues: 9050 helix: 0.10 (0.08), residues: 4403 sheet: -1.77 (0.17), residues: 716 loop : -2.10 (0.09), residues: 3931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 478 HIS 0.008 0.001 HIS J 453 PHE 0.018 0.002 PHE G 173 TYR 0.019 0.002 TYR P 363 ARG 0.008 0.001 ARG H 721 *********************** 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 1823 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1639 time to evaluate : 8.771 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: A 240 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: A 349 THR cc_start: 0.8559 (p) cc_final: 0.8305 (t) REVERT: A 450 GLN cc_start: 0.7327 (mt0) cc_final: 0.7053 (tt0) REVERT: A 723 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: A 795 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8074 (mmtp) REVERT: A 884 MET cc_start: 0.7605 (mmt) cc_final: 0.7165 (mmt) REVERT: B 234 GLU cc_start: 0.6825 (tt0) cc_final: 0.6563 (tt0) REVERT: B 278 PHE cc_start: 0.7973 (m-10) cc_final: 0.7426 (m-80) REVERT: B 627 ASP cc_start: 0.8298 (m-30) cc_final: 0.8017 (m-30) REVERT: B 795 LYS cc_start: 0.6867 (mmtt) cc_final: 0.6621 (mmtt) REVERT: B 796 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8506 (pp) REVERT: B 881 MET cc_start: 0.7565 (tpt) cc_final: 0.7353 (tpt) REVERT: C 268 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8767 (pp) REVERT: C 817 TYR cc_start: 0.7919 (p90) cc_final: 0.7718 (p90) REVERT: C 854 THR cc_start: 0.8033 (m) cc_final: 0.7652 (p) REVERT: D 252 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8429 (pp) REVERT: D 431 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8629 (pt) REVERT: D 540 ILE cc_start: 0.9064 (pt) cc_final: 0.8739 (mt) REVERT: D 796 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7004 (pp) REVERT: D 854 THR cc_start: 0.8644 (p) cc_final: 0.8366 (t) REVERT: E 248 TYR cc_start: 0.9030 (m-80) cc_final: 0.8658 (m-80) REVERT: E 320 ASN cc_start: 0.8753 (t0) cc_final: 0.8451 (t0) REVERT: E 384 ASP cc_start: 0.8340 (t70) cc_final: 0.8087 (t0) REVERT: E 796 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7389 (pp) REVERT: F 425 MET cc_start: 0.8669 (tpt) cc_final: 0.8406 (tpt) REVERT: F 486 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7919 (mp-120) REVERT: F 593 MET cc_start: 0.8959 (mmm) cc_final: 0.8432 (mmt) REVERT: F 756 ASN cc_start: 0.8493 (t0) cc_final: 0.7986 (t0) REVERT: F 812 ASP cc_start: 0.7954 (p0) cc_final: 0.7533 (p0) REVERT: G 268 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8795 (pp) REVERT: G 493 ASP cc_start: 0.7005 (t0) cc_final: 0.6706 (t0) REVERT: G 627 ASP cc_start: 0.8375 (m-30) cc_final: 0.7793 (m-30) REVERT: G 637 ARG cc_start: 0.8607 (mtt180) cc_final: 0.7798 (mmp-170) REVERT: G 661 ILE cc_start: 0.8716 (mm) cc_final: 0.8262 (pt) REVERT: G 739 GLN cc_start: 0.8539 (mp-120) cc_final: 0.8303 (mp-120) REVERT: G 760 ASN cc_start: 0.8564 (m-40) cc_final: 0.8214 (m110) REVERT: G 777 SER cc_start: 0.8670 (t) cc_final: 0.8343 (p) REVERT: H 216 ASP cc_start: 0.8037 (p0) cc_final: 0.7821 (p0) REVERT: H 222 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6194 (tt0) REVERT: H 355 LYS cc_start: 0.8396 (tttm) cc_final: 0.7895 (tttp) REVERT: H 359 ASP cc_start: 0.7511 (m-30) cc_final: 0.7093 (m-30) REVERT: H 493 ASP cc_start: 0.7422 (t0) cc_final: 0.7153 (t0) REVERT: H 663 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8218 (ttt90) REVERT: H 722 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7539 (t0) REVERT: H 774 THR cc_start: 0.8971 (p) cc_final: 0.8722 (p) REVERT: I 344 LYS cc_start: 0.8722 (ptpp) cc_final: 0.8517 (ptpp) REVERT: I 580 THR cc_start: 0.8359 (m) cc_final: 0.8045 (p) REVERT: I 795 LYS cc_start: 0.8413 (tttt) cc_final: 0.7990 (mmtp) REVERT: I 833 TYR cc_start: 0.8900 (t80) cc_final: 0.8603 (t80) REVERT: J 425 MET cc_start: 0.8819 (tpt) cc_final: 0.8458 (tpt) REVERT: J 580 THR cc_start: 0.8250 (m) cc_final: 0.7969 (p) REVERT: J 639 ASN cc_start: 0.8307 (t0) cc_final: 0.8056 (t0) REVERT: J 651 ASP cc_start: 0.8164 (t70) cc_final: 0.7757 (t0) REVERT: P 365 MET cc_start: 0.7667 (ttt) cc_final: 0.7389 (ttp) REVERT: P 500 LEU cc_start: 0.7725 (mt) cc_final: 0.7322 (mt) REVERT: P 664 THR cc_start: 0.9062 (m) cc_final: 0.8817 (p) REVERT: P 1010 ASN cc_start: 0.8307 (m110) cc_final: 0.7737 (m-40) outliers start: 184 outliers final: 121 residues processed: 1740 average time/residue: 1.8458 time to fit residues: 5281.5510 Evaluate side-chains 1674 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1541 time to evaluate : 8.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 380 GLN Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 824 TRP Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 523 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 809 ILE Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 722 ASP Chi-restraints excluded: chain H residue 827 THR Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 535 SER Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain I residue 785 LEU Chi-restraints excluded: chain I residue 809 ILE Chi-restraints excluded: chain I residue 811 SER Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 757 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 827 THR Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 17 ASN Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 356 ASP Chi-restraints excluded: chain P residue 442 ASN Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 676 GLU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 840 ASN Chi-restraints excluded: chain P residue 1074 THR 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: 2.9990 chunk 650 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 745 optimal weight: 5.9990 chunk 604 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 446 optimal weight: 0.9980 chunk 784 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 753 GLN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 639 ASN C 477 ASN C 571 ASN D 372 GLN D 571 ASN E 179 GLN F 838 GLN G 545 ASN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 423 ASN H 484 ASN H 739 GLN I 423 ASN I 636 ASN J 519 GLN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 640 ASN ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 75455 Z= 0.309 Angle : 0.566 9.146 102320 Z= 0.306 Chirality : 0.041 0.160 11722 Planarity : 0.005 0.097 13254 Dihedral : 5.410 83.666 9999 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.48 % Favored : 92.50 % Rotamer: Outliers : 2.18 % Allowed : 11.57 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 9050 helix: 0.36 (0.08), residues: 4431 sheet: -1.62 (0.17), residues: 711 loop : -1.95 (0.09), residues: 3908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 478 HIS 0.004 0.001 HIS J 453 PHE 0.016 0.001 PHE F 447 TYR 0.018 0.002 TYR G 95 ARG 0.008 0.000 ARG A 637 *********************** 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 1779 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1597 time to evaluate : 8.738 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: A 409 MET cc_start: 0.8697 (tpt) cc_final: 0.8354 (tpt) REVERT: A 450 GLN cc_start: 0.7483 (mt0) cc_final: 0.7259 (tt0) REVERT: A 780 SER cc_start: 0.8904 (m) cc_final: 0.8356 (t) REVERT: A 795 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8097 (mmtp) REVERT: A 884 MET cc_start: 0.7581 (mmt) cc_final: 0.7187 (mmt) REVERT: B 278 PHE cc_start: 0.8070 (m-10) cc_final: 0.7643 (m-80) REVERT: B 627 ASP cc_start: 0.8284 (m-30) cc_final: 0.7957 (m-30) REVERT: B 795 LYS cc_start: 0.6897 (mmtt) cc_final: 0.6697 (mmtt) REVERT: B 796 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 268 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8767 (pp) REVERT: C 547 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8056 (tp) REVERT: C 854 THR cc_start: 0.7956 (m) cc_final: 0.7592 (p) REVERT: D 252 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8407 (pp) REVERT: D 255 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8745 (mp) REVERT: D 431 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8590 (pt) REVERT: D 540 ILE cc_start: 0.9012 (pt) cc_final: 0.8720 (mt) REVERT: D 663 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7566 (mmt-90) REVERT: D 796 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6972 (pp) REVERT: E 248 TYR cc_start: 0.9019 (m-80) cc_final: 0.8627 (m-80) REVERT: E 268 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8936 (pp) REVERT: E 320 ASN cc_start: 0.8759 (t0) cc_final: 0.8490 (t0) REVERT: E 345 GLU cc_start: 0.8054 (pm20) cc_final: 0.7813 (pm20) REVERT: E 384 ASP cc_start: 0.8370 (t70) cc_final: 0.8124 (t0) REVERT: E 458 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: E 490 VAL cc_start: 0.9025 (p) cc_final: 0.8748 (m) REVERT: E 796 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (pp) REVERT: F 150 ARG cc_start: 0.7687 (ptt180) cc_final: 0.7426 (ptp-170) REVERT: F 216 ASP cc_start: 0.7833 (p0) cc_final: 0.7483 (p0) REVERT: F 486 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7894 (mp-120) REVERT: F 593 MET cc_start: 0.9000 (mmm) cc_final: 0.8482 (mmt) REVERT: F 756 ASN cc_start: 0.8560 (t0) cc_final: 0.8000 (t0) REVERT: G 202 ASP cc_start: 0.7254 (t0) cc_final: 0.7004 (t0) REVERT: G 268 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8797 (pp) REVERT: G 493 ASP cc_start: 0.6976 (t0) cc_final: 0.6668 (t0) REVERT: G 532 TYR cc_start: 0.8340 (t80) cc_final: 0.8109 (t80) REVERT: G 637 ARG cc_start: 0.8595 (mtt180) cc_final: 0.7817 (mmp-170) REVERT: G 661 ILE cc_start: 0.8697 (mm) cc_final: 0.8257 (pt) REVERT: G 739 GLN cc_start: 0.8579 (mp-120) cc_final: 0.8351 (mp-120) REVERT: G 760 ASN cc_start: 0.8569 (m-40) cc_final: 0.8126 (m110) REVERT: G 777 SER cc_start: 0.8662 (t) cc_final: 0.8366 (p) REVERT: H 222 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6114 (tt0) REVERT: H 355 LYS cc_start: 0.8375 (tttm) cc_final: 0.7904 (tttp) REVERT: H 359 ASP cc_start: 0.7573 (m-30) cc_final: 0.7150 (m-30) REVERT: H 493 ASP cc_start: 0.7445 (t0) cc_final: 0.7183 (t0) REVERT: H 627 ASP cc_start: 0.7111 (m-30) cc_final: 0.6850 (m-30) REVERT: H 663 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8033 (mtt180) REVERT: H 774 THR cc_start: 0.9005 (p) cc_final: 0.8765 (p) REVERT: H 830 THR cc_start: 0.8824 (m) cc_final: 0.8447 (p) REVERT: I 344 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8513 (ptpp) REVERT: I 477 ASN cc_start: 0.7800 (m-40) cc_final: 0.7541 (m110) REVERT: I 580 THR cc_start: 0.8361 (m) cc_final: 0.8040 (p) REVERT: I 795 LYS cc_start: 0.8445 (tttt) cc_final: 0.8007 (mmtp) REVERT: I 833 TYR cc_start: 0.8883 (t80) cc_final: 0.8604 (t80) REVERT: J 580 THR cc_start: 0.8302 (m) cc_final: 0.7948 (p) REVERT: J 639 ASN cc_start: 0.8310 (t0) cc_final: 0.8054 (t0) REVERT: J 651 ASP cc_start: 0.8202 (t70) cc_final: 0.7790 (t0) REVERT: J 822 TYR cc_start: 0.7757 (m-80) cc_final: 0.7511 (m-80) REVERT: P 365 MET cc_start: 0.7727 (ttt) cc_final: 0.7474 (ttp) REVERT: P 394 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8387 (tt) REVERT: P 500 LEU cc_start: 0.7625 (mt) cc_final: 0.7263 (mt) REVERT: P 664 THR cc_start: 0.9059 (m) cc_final: 0.8755 (p) REVERT: P 1001 TYR cc_start: 0.7796 (m-80) cc_final: 0.7515 (m-80) REVERT: P 1010 ASN cc_start: 0.8275 (m110) cc_final: 0.7738 (m-40) outliers start: 182 outliers final: 126 residues processed: 1698 average time/residue: 1.8224 time to fit residues: 5093.4213 Evaluate side-chains 1693 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1553 time to evaluate : 8.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 824 TRP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 824 TRP Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 572 MET Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 693 LEU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 809 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 704 ASP Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 827 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain I residue 785 LEU Chi-restraints excluded: chain I residue 811 SER Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 692 ILE Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 356 ASP Chi-restraints excluded: chain P residue 383 ASP Chi-restraints excluded: chain P residue 394 LEU Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 640 ASN Chi-restraints excluded: chain P residue 1074 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 2.9990 chunk 786 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 513 optimal weight: 0.0570 chunk 215 optimal weight: 5.9990 chunk 874 optimal weight: 4.9990 chunk 726 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 459 optimal weight: 3.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 639 ASN C 378 ASN C 477 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN D 571 ASN E 423 ASN F 512 GLN F 523 GLN F 695 ASN F 838 GLN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 90 GLN H 423 ASN I 636 ASN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN J 760 ASN P 17 ASN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 75455 Z= 0.215 Angle : 0.526 8.803 102320 Z= 0.283 Chirality : 0.040 0.157 11722 Planarity : 0.005 0.095 13254 Dihedral : 5.202 80.813 9999 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.05 % Favored : 92.94 % Rotamer: Outliers : 2.04 % Allowed : 12.30 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 9050 helix: 0.65 (0.08), residues: 4424 sheet: -1.41 (0.18), residues: 707 loop : -1.85 (0.10), residues: 3919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 478 HIS 0.004 0.001 HIS J 453 PHE 0.014 0.001 PHE D 855 TYR 0.019 0.001 TYR G 95 ARG 0.009 0.000 ARG H 721 *********************** 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 1771 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1601 time to evaluate : 8.864 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: A 359 ASP cc_start: 0.7656 (m-30) cc_final: 0.7294 (m-30) REVERT: A 409 MET cc_start: 0.8717 (tpt) cc_final: 0.8371 (tpt) REVERT: A 780 SER cc_start: 0.8896 (m) cc_final: 0.8382 (t) REVERT: A 795 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8055 (mmtt) REVERT: A 884 MET cc_start: 0.7564 (mmt) cc_final: 0.7161 (mmt) REVERT: B 278 PHE cc_start: 0.8040 (m-10) cc_final: 0.7581 (m-80) REVERT: B 627 ASP cc_start: 0.8274 (m-30) cc_final: 0.7946 (m-30) REVERT: B 795 LYS cc_start: 0.6856 (mmtt) cc_final: 0.6540 (mmtt) REVERT: B 796 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8531 (pp) REVERT: C 268 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8756 (pp) REVERT: C 547 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 854 THR cc_start: 0.7870 (m) cc_final: 0.7538 (p) REVERT: D 252 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8376 (pp) REVERT: D 255 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 431 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8596 (pt) REVERT: D 540 ILE cc_start: 0.8969 (pt) cc_final: 0.8713 (mt) REVERT: D 663 ARG cc_start: 0.7795 (mmt180) cc_final: 0.7586 (mmt-90) REVERT: D 796 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6957 (pp) REVERT: E 216 ASP cc_start: 0.7997 (m-30) cc_final: 0.7786 (m-30) REVERT: E 248 TYR cc_start: 0.9009 (m-80) cc_final: 0.8681 (m-80) REVERT: E 268 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8978 (pp) REVERT: E 320 ASN cc_start: 0.8734 (t0) cc_final: 0.8450 (t0) REVERT: E 367 ILE cc_start: 0.7781 (mm) cc_final: 0.7569 (mm) REVERT: E 384 ASP cc_start: 0.8370 (t70) cc_final: 0.8126 (t0) REVERT: E 490 VAL cc_start: 0.9029 (p) cc_final: 0.8757 (m) REVERT: E 796 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7301 (pp) REVERT: F 150 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7446 (ptp-170) REVERT: F 216 ASP cc_start: 0.7799 (p0) cc_final: 0.7421 (p0) REVERT: F 486 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7866 (mp-120) REVERT: F 593 MET cc_start: 0.8995 (mmm) cc_final: 0.8477 (mmt) REVERT: F 756 ASN cc_start: 0.8558 (t0) cc_final: 0.7947 (t0) REVERT: G 268 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8805 (pp) REVERT: G 637 ARG cc_start: 0.8554 (mtt180) cc_final: 0.7912 (mmp-170) REVERT: G 661 ILE cc_start: 0.8566 (mm) cc_final: 0.8185 (pt) REVERT: G 739 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8337 (mp-120) REVERT: G 760 ASN cc_start: 0.8572 (m-40) cc_final: 0.8116 (m110) REVERT: G 777 SER cc_start: 0.8600 (t) cc_final: 0.8336 (p) REVERT: H 176 LEU cc_start: 0.9245 (tp) cc_final: 0.9030 (tp) REVERT: H 355 LYS cc_start: 0.8365 (tttm) cc_final: 0.7823 (tttp) REVERT: H 359 ASP cc_start: 0.7578 (m-30) cc_final: 0.7135 (m-30) REVERT: H 493 ASP cc_start: 0.7451 (t0) cc_final: 0.7193 (t0) REVERT: H 627 ASP cc_start: 0.7078 (m-30) cc_final: 0.6815 (m-30) REVERT: H 722 ASP cc_start: 0.7865 (t0) cc_final: 0.7567 (t0) REVERT: H 774 THR cc_start: 0.9010 (p) cc_final: 0.8781 (p) REVERT: H 830 THR cc_start: 0.8773 (m) cc_final: 0.8419 (p) REVERT: I 216 ASP cc_start: 0.8156 (p0) cc_final: 0.7900 (p0) REVERT: I 580 THR cc_start: 0.8327 (m) cc_final: 0.8002 (p) REVERT: I 695 ASN cc_start: 0.8873 (m-40) cc_final: 0.8341 (m110) REVERT: I 795 LYS cc_start: 0.8442 (tttt) cc_final: 0.8002 (mmtp) REVERT: I 833 TYR cc_start: 0.8895 (t80) cc_final: 0.8614 (t80) REVERT: J 580 THR cc_start: 0.8254 (m) cc_final: 0.7901 (p) REVERT: J 639 ASN cc_start: 0.8307 (t0) cc_final: 0.8045 (t0) REVERT: J 651 ASP cc_start: 0.8169 (t70) cc_final: 0.7773 (t0) REVERT: P 365 MET cc_start: 0.7665 (ttt) cc_final: 0.7439 (ttp) REVERT: P 500 LEU cc_start: 0.7536 (mt) cc_final: 0.7170 (mt) REVERT: P 647 MET cc_start: 0.8165 (mtp) cc_final: 0.7962 (mtp) REVERT: P 664 THR cc_start: 0.9045 (m) cc_final: 0.8746 (p) REVERT: P 1001 TYR cc_start: 0.7823 (m-80) cc_final: 0.7577 (m-80) REVERT: P 1010 ASN cc_start: 0.8271 (m110) cc_final: 0.7743 (m-40) outliers start: 170 outliers final: 125 residues processed: 1697 average time/residue: 1.8432 time to fit residues: 5137.0019 Evaluate side-chains 1690 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1553 time to evaluate : 8.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 737 PHE Chi-restraints excluded: chain C residue 824 TRP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 808 LYS Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 739 GLN Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 373 PHE Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain H residue 452 MET Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 803 LYS Chi-restraints excluded: chain H residue 827 THR Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 663 ARG Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain I residue 785 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 345 GLU Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 356 ASP Chi-restraints excluded: chain P residue 399 SER Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 874 ILE Chi-restraints excluded: chain P residue 1048 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 498 optimal weight: 3.9990 chunk 638 optimal weight: 6.9990 chunk 494 optimal weight: 0.3980 chunk 736 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 871 optimal weight: 5.9990 chunk 545 optimal weight: 5.9990 chunk 531 optimal weight: 1.9990 chunk 402 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 320 ASN B 380 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 477 ASN D 501 ASN D 571 ASN D 792 GLN E 179 GLN E 453 HIS F 396 GLN F 838 GLN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 396 GLN H 423 ASN H 814 ASN I 642 GLN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 959 GLN ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 75455 Z= 0.291 Angle : 0.547 8.490 102320 Z= 0.295 Chirality : 0.041 0.158 11722 Planarity : 0.005 0.096 13254 Dihedral : 5.176 82.624 9999 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.35 % Favored : 92.64 % Rotamer: Outliers : 2.21 % Allowed : 12.42 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.09), residues: 9050 helix: 0.72 (0.08), residues: 4427 sheet: -1.46 (0.18), residues: 710 loop : -1.77 (0.10), residues: 3913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 478 HIS 0.005 0.001 HIS P 384 PHE 0.015 0.001 PHE G 173 TYR 0.017 0.002 TYR G 95 ARG 0.010 0.000 ARG H 721 *********************** 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 1757 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1573 time to evaluate : 8.502 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: A 283 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7385 (tp30) REVERT: A 359 ASP cc_start: 0.7608 (m-30) cc_final: 0.7279 (m-30) REVERT: A 409 MET cc_start: 0.8729 (tpt) cc_final: 0.8397 (tpt) REVERT: A 780 SER cc_start: 0.8913 (m) cc_final: 0.8439 (t) REVERT: A 795 LYS cc_start: 0.8463 (ttmm) cc_final: 0.7994 (mmtt) REVERT: A 817 TYR cc_start: 0.8060 (p90) cc_final: 0.7777 (p90) REVERT: A 884 MET cc_start: 0.7588 (mmt) cc_final: 0.7132 (mmt) REVERT: B 278 PHE cc_start: 0.8096 (m-10) cc_final: 0.7743 (m-80) REVERT: B 320 ASN cc_start: 0.8446 (t0) cc_final: 0.7981 (t0) REVERT: B 627 ASP cc_start: 0.8272 (m-30) cc_final: 0.7961 (m-30) REVERT: B 795 LYS cc_start: 0.6872 (mmtt) cc_final: 0.6659 (mmtt) REVERT: B 796 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8531 (pp) REVERT: C 268 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8746 (pp) REVERT: C 278 PHE cc_start: 0.8962 (m-80) cc_final: 0.8759 (m-80) REVERT: C 547 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8107 (tp) REVERT: C 854 THR cc_start: 0.8003 (m) cc_final: 0.7692 (p) REVERT: D 252 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8423 (pp) REVERT: D 255 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8742 (mp) REVERT: D 431 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8610 (pt) REVERT: D 540 ILE cc_start: 0.8975 (pt) cc_final: 0.8733 (mt) REVERT: E 268 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (pp) REVERT: E 320 ASN cc_start: 0.8793 (t0) cc_final: 0.8508 (t0) REVERT: E 367 ILE cc_start: 0.7811 (mm) cc_final: 0.7602 (mm) REVERT: E 384 ASP cc_start: 0.8390 (t70) cc_final: 0.8132 (t0) REVERT: E 458 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: E 490 VAL cc_start: 0.9019 (p) cc_final: 0.8758 (m) REVERT: E 796 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7370 (pp) REVERT: F 150 ARG cc_start: 0.7747 (ptt180) cc_final: 0.7469 (ptp-170) REVERT: F 216 ASP cc_start: 0.7824 (p0) cc_final: 0.7440 (p0) REVERT: F 486 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7884 (mp-120) REVERT: F 593 MET cc_start: 0.9036 (mmm) cc_final: 0.8494 (mmt) REVERT: F 756 ASN cc_start: 0.8653 (t0) cc_final: 0.8011 (t0) REVERT: G 268 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8805 (pp) REVERT: G 532 TYR cc_start: 0.8285 (t80) cc_final: 0.8046 (t80) REVERT: G 637 ARG cc_start: 0.8572 (mtt180) cc_final: 0.7925 (mmp-170) REVERT: G 661 ILE cc_start: 0.8558 (mm) cc_final: 0.8214 (pt) REVERT: G 739 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8324 (mp-120) REVERT: G 760 ASN cc_start: 0.8607 (m-40) cc_final: 0.8199 (m110) REVERT: G 777 SER cc_start: 0.8708 (t) cc_final: 0.8461 (p) REVERT: H 355 LYS cc_start: 0.8476 (tttm) cc_final: 0.7930 (tttp) REVERT: H 359 ASP cc_start: 0.7603 (m-30) cc_final: 0.7182 (m-30) REVERT: H 493 ASP cc_start: 0.7471 (t0) cc_final: 0.7200 (t0) REVERT: H 627 ASP cc_start: 0.7017 (m-30) cc_final: 0.6772 (m-30) REVERT: H 774 THR cc_start: 0.9013 (p) cc_final: 0.8790 (p) REVERT: H 830 THR cc_start: 0.8806 (m) cc_final: 0.8411 (p) REVERT: I 216 ASP cc_start: 0.8169 (p0) cc_final: 0.7932 (p0) REVERT: I 477 ASN cc_start: 0.7828 (m-40) cc_final: 0.7577 (m110) REVERT: I 580 THR cc_start: 0.8454 (m) cc_final: 0.8120 (p) REVERT: I 695 ASN cc_start: 0.8913 (m-40) cc_final: 0.8413 (m110) REVERT: I 795 LYS cc_start: 0.8494 (tttt) cc_final: 0.8010 (mmtp) REVERT: I 833 TYR cc_start: 0.8914 (t80) cc_final: 0.8666 (t80) REVERT: J 580 THR cc_start: 0.8303 (m) cc_final: 0.7941 (p) REVERT: J 639 ASN cc_start: 0.8347 (t0) cc_final: 0.8109 (t0) REVERT: J 651 ASP cc_start: 0.8201 (t70) cc_final: 0.7800 (t0) REVERT: P 500 LEU cc_start: 0.7578 (mt) cc_final: 0.7241 (mt) REVERT: P 632 ASP cc_start: 0.7819 (p0) cc_final: 0.7595 (p0) REVERT: P 664 THR cc_start: 0.9116 (m) cc_final: 0.8793 (p) REVERT: P 739 MET cc_start: 0.8412 (mtp) cc_final: 0.8197 (mtm) REVERT: P 1001 TYR cc_start: 0.7834 (m-80) cc_final: 0.7599 (m-80) REVERT: P 1010 ASN cc_start: 0.8303 (m110) cc_final: 0.7823 (m-40) outliers start: 184 outliers final: 146 residues processed: 1679 average time/residue: 1.7966 time to fit residues: 4968.8503 Evaluate side-chains 1702 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1544 time to evaluate : 8.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 824 TRP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 450 GLN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 792 GLN Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 866 SER Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 519 GLN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 808 LYS Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 824 TRP Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 485 ASN Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 739 GLN Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 452 MET Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 704 ASP Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 803 LYS Chi-restraints excluded: chain H residue 827 THR Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 663 ARG Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 345 GLU Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 356 ASP Chi-restraints excluded: chain P residue 383 ASP Chi-restraints excluded: chain P residue 399 SER Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 874 ILE Chi-restraints excluded: chain P residue 1074 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 520 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 553 optimal weight: 0.9980 chunk 593 optimal weight: 4.9990 chunk 430 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 684 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 ASN D 501 ASN D 571 ASN D 792 GLN ** E 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 423 ASN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 959 GLN ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 75455 Z= 0.188 Angle : 0.511 8.446 102320 Z= 0.274 Chirality : 0.039 0.165 11722 Planarity : 0.005 0.099 13254 Dihedral : 5.005 78.898 9999 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.70 % Favored : 93.29 % Rotamer: Outliers : 1.91 % Allowed : 13.16 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.09), residues: 9050 helix: 0.93 (0.08), residues: 4431 sheet: -1.24 (0.18), residues: 715 loop : -1.67 (0.10), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 478 HIS 0.004 0.001 HIS J 453 PHE 0.012 0.001 PHE D 790 TYR 0.025 0.001 TYR D 725 ARG 0.012 0.000 ARG P 508 *********************** 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 1755 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1596 time to evaluate : 8.746 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: A 359 ASP cc_start: 0.7579 (m-30) cc_final: 0.7266 (m-30) REVERT: A 409 MET cc_start: 0.8729 (tpt) cc_final: 0.8439 (tpt) REVERT: A 723 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: A 795 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7956 (mmtt) REVERT: A 817 TYR cc_start: 0.8009 (p90) cc_final: 0.7730 (p90) REVERT: A 884 MET cc_start: 0.7530 (mmt) cc_final: 0.7092 (mmt) REVERT: B 278 PHE cc_start: 0.8048 (m-10) cc_final: 0.7687 (m-80) REVERT: B 320 ASN cc_start: 0.8468 (t0) cc_final: 0.8013 (t0) REVERT: B 627 ASP cc_start: 0.8236 (m-30) cc_final: 0.7923 (m-30) REVERT: B 795 LYS cc_start: 0.6875 (mmtt) cc_final: 0.6584 (mmtt) REVERT: B 796 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8537 (pp) REVERT: B 807 TYR cc_start: 0.8225 (m-80) cc_final: 0.7721 (m-80) REVERT: C 268 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8807 (pp) REVERT: C 547 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8065 (tp) REVERT: D 252 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8412 (pp) REVERT: D 255 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8701 (mp) REVERT: D 431 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8605 (pt) REVERT: D 579 THR cc_start: 0.8807 (m) cc_final: 0.8580 (p) REVERT: E 268 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8957 (pp) REVERT: E 320 ASN cc_start: 0.8761 (t0) cc_final: 0.8477 (t0) REVERT: E 384 ASP cc_start: 0.8363 (t70) cc_final: 0.8109 (t0) REVERT: E 490 VAL cc_start: 0.9002 (p) cc_final: 0.8720 (m) REVERT: E 693 LEU cc_start: 0.8855 (mt) cc_final: 0.8595 (mt) REVERT: E 796 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7307 (pp) REVERT: F 150 ARG cc_start: 0.7738 (ptt180) cc_final: 0.7468 (ptp-170) REVERT: F 593 MET cc_start: 0.9021 (mmm) cc_final: 0.8506 (mmt) REVERT: F 756 ASN cc_start: 0.8562 (t0) cc_final: 0.7915 (t0) REVERT: G 268 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8800 (pp) REVERT: G 637 ARG cc_start: 0.8543 (mtt180) cc_final: 0.7930 (mmp-170) REVERT: G 661 ILE cc_start: 0.8532 (mm) cc_final: 0.8236 (pt) REVERT: G 739 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8320 (mp-120) REVERT: G 760 ASN cc_start: 0.8580 (m-40) cc_final: 0.8184 (m110) REVERT: G 777 SER cc_start: 0.8658 (t) cc_final: 0.8412 (p) REVERT: H 176 LEU cc_start: 0.9250 (tp) cc_final: 0.9031 (tp) REVERT: H 355 LYS cc_start: 0.8392 (tttm) cc_final: 0.7843 (tttp) REVERT: H 359 ASP cc_start: 0.7575 (m-30) cc_final: 0.7150 (m-30) REVERT: H 493 ASP cc_start: 0.7448 (t0) cc_final: 0.7179 (t0) REVERT: H 627 ASP cc_start: 0.6998 (m-30) cc_final: 0.6767 (m-30) REVERT: I 216 ASP cc_start: 0.8123 (p0) cc_final: 0.7903 (p0) REVERT: I 580 THR cc_start: 0.8410 (m) cc_final: 0.8099 (p) REVERT: I 695 ASN cc_start: 0.8851 (m-40) cc_final: 0.8316 (m110) REVERT: I 774 THR cc_start: 0.9184 (p) cc_final: 0.8959 (p) REVERT: I 795 LYS cc_start: 0.8475 (tttt) cc_final: 0.7975 (mmtp) REVERT: I 833 TYR cc_start: 0.8882 (t80) cc_final: 0.8665 (t80) REVERT: J 230 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7396 (ttp80) REVERT: J 580 THR cc_start: 0.8239 (m) cc_final: 0.7874 (p) REVERT: J 639 ASN cc_start: 0.8323 (t0) cc_final: 0.8082 (t0) REVERT: J 651 ASP cc_start: 0.8136 (t70) cc_final: 0.7736 (t0) REVERT: P 425 MET cc_start: 0.8139 (mtt) cc_final: 0.7811 (mtt) REVERT: P 500 LEU cc_start: 0.7466 (mt) cc_final: 0.7163 (mt) REVERT: P 632 ASP cc_start: 0.7782 (p0) cc_final: 0.7569 (p0) REVERT: P 664 THR cc_start: 0.9108 (m) cc_final: 0.8807 (p) REVERT: P 1010 ASN cc_start: 0.8192 (m110) cc_final: 0.7766 (m-40) outliers start: 159 outliers final: 126 residues processed: 1686 average time/residue: 1.7885 time to fit residues: 4959.2525 Evaluate side-chains 1675 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1538 time to evaluate : 8.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 737 PHE Chi-restraints excluded: chain C residue 824 TRP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 533 LYS Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 808 LYS Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 824 TRP Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 485 ASN Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 739 GLN Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 373 PHE Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain H residue 452 MET Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain H residue 803 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 663 ARG Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 732 ARG Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 356 ASP Chi-restraints excluded: chain P residue 383 ASP Chi-restraints excluded: chain P residue 399 SER Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 801 GLU Chi-restraints excluded: chain P residue 874 ILE Chi-restraints excluded: chain P residue 888 ASN Chi-restraints excluded: chain P residue 1074 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 0.9980 chunk 834 optimal weight: 5.9990 chunk 761 optimal weight: 2.9990 chunk 811 optimal weight: 6.9990 chunk 488 optimal weight: 3.9990 chunk 353 optimal weight: 3.9990 chunk 637 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 733 optimal weight: 0.7980 chunk 767 optimal weight: 0.7980 chunk 809 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 639 ASN D 501 ASN D 571 ASN E 179 GLN ** E 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 838 GLN ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 423 ASN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 703 GLN ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5184 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= 0.187 Angle : 0.504 8.378 102320 Z= 0.270 Chirality : 0.039 0.156 11722 Planarity : 0.005 0.097 13254 Dihedral : 4.862 77.793 9999 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.76 % Favored : 93.23 % Rotamer: Outliers : 1.66 % Allowed : 13.62 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.09), residues: 9050 helix: 1.08 (0.08), residues: 4433 sheet: -1.06 (0.18), residues: 665 loop : -1.59 (0.10), residues: 3952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 478 HIS 0.004 0.001 HIS H 257 PHE 0.016 0.001 PHE C 278 TYR 0.035 0.001 TYR A 621 ARG 0.014 0.000 ARG P 508 *********************** 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 1710 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1572 time to evaluate : 8.482 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: A 359 ASP cc_start: 0.7617 (m-30) cc_final: 0.7157 (m-30) REVERT: A 409 MET cc_start: 0.8724 (tpt) cc_final: 0.8450 (tpt) REVERT: A 723 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7358 (pp20) REVERT: A 795 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7953 (mmtt) REVERT: A 884 MET cc_start: 0.7585 (mmt) cc_final: 0.7163 (mmt) REVERT: B 278 PHE cc_start: 0.8041 (m-10) cc_final: 0.7633 (m-80) REVERT: B 320 ASN cc_start: 0.8475 (t0) cc_final: 0.8110 (t0) REVERT: B 627 ASP cc_start: 0.8217 (m-30) cc_final: 0.7834 (m-30) REVERT: B 795 LYS cc_start: 0.6895 (mmtt) cc_final: 0.6096 (mmtp) REVERT: B 796 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8509 (pp) REVERT: B 807 TYR cc_start: 0.8236 (m-80) cc_final: 0.7738 (m-80) REVERT: C 268 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8734 (pp) REVERT: C 452 MET cc_start: 0.6313 (ttt) cc_final: 0.5689 (ttt) REVERT: C 547 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8101 (tp) REVERT: D 252 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8439 (pp) REVERT: D 255 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 431 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8665 (pt) REVERT: E 268 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8952 (pp) REVERT: E 320 ASN cc_start: 0.8728 (t0) cc_final: 0.8426 (t0) REVERT: E 384 ASP cc_start: 0.8374 (t70) cc_final: 0.8126 (t0) REVERT: E 490 VAL cc_start: 0.9006 (p) cc_final: 0.8707 (m) REVERT: E 796 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7321 (pp) REVERT: F 150 ARG cc_start: 0.7747 (ptt180) cc_final: 0.7473 (ptp-170) REVERT: F 216 ASP cc_start: 0.7838 (p0) cc_final: 0.7568 (p0) REVERT: F 486 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7868 (mp-120) REVERT: F 593 MET cc_start: 0.9028 (mmm) cc_final: 0.8451 (mmt) REVERT: F 756 ASN cc_start: 0.8501 (t0) cc_final: 0.7888 (t0) REVERT: G 268 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8788 (pp) REVERT: G 637 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7942 (mmp-170) REVERT: G 739 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8329 (mp-120) REVERT: G 760 ASN cc_start: 0.8579 (m-40) cc_final: 0.8194 (m110) REVERT: G 777 SER cc_start: 0.8662 (t) cc_final: 0.8424 (p) REVERT: H 355 LYS cc_start: 0.8498 (tttm) cc_final: 0.7966 (tttp) REVERT: H 359 ASP cc_start: 0.7565 (m-30) cc_final: 0.7224 (m-30) REVERT: H 493 ASP cc_start: 0.7448 (t0) cc_final: 0.7184 (t0) REVERT: H 627 ASP cc_start: 0.6999 (m-30) cc_final: 0.6765 (m-30) REVERT: I 216 ASP cc_start: 0.8134 (p0) cc_final: 0.7906 (p0) REVERT: I 580 THR cc_start: 0.8424 (m) cc_final: 0.8108 (p) REVERT: I 691 LEU cc_start: 0.8889 (mt) cc_final: 0.8671 (mt) REVERT: I 695 ASN cc_start: 0.8821 (m-40) cc_final: 0.8292 (m110) REVERT: I 774 THR cc_start: 0.9189 (p) cc_final: 0.8967 (p) REVERT: I 795 LYS cc_start: 0.8440 (tttt) cc_final: 0.7967 (mmtp) REVERT: I 833 TYR cc_start: 0.8910 (t80) cc_final: 0.8657 (t80) REVERT: J 230 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7390 (ttp80) REVERT: J 580 THR cc_start: 0.8243 (m) cc_final: 0.7876 (p) REVERT: J 639 ASN cc_start: 0.8328 (t0) cc_final: 0.8091 (t0) REVERT: J 651 ASP cc_start: 0.8060 (t70) cc_final: 0.7670 (t0) REVERT: P 425 MET cc_start: 0.8156 (mtt) cc_final: 0.7803 (mtt) REVERT: P 488 ARG cc_start: 0.7466 (mmt90) cc_final: 0.7221 (mtt180) REVERT: P 500 LEU cc_start: 0.7361 (mt) cc_final: 0.7007 (mt) REVERT: P 664 THR cc_start: 0.9108 (m) cc_final: 0.8812 (p) REVERT: P 730 GLU cc_start: 0.7669 (mp0) cc_final: 0.7463 (mp0) REVERT: P 1010 ASN cc_start: 0.8204 (m110) cc_final: 0.7782 (m-40) outliers start: 138 outliers final: 110 residues processed: 1651 average time/residue: 1.8490 time to fit residues: 5027.8817 Evaluate side-chains 1655 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1533 time to evaluate : 7.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 533 LYS Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 808 LYS Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 485 ASN Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 739 GLN Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain H residue 452 MET Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 732 ARG Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 746 MET Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 383 ASP Chi-restraints excluded: chain P residue 399 SER Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 801 GLU Chi-restraints excluded: chain P residue 874 ILE Chi-restraints excluded: chain P residue 888 ASN Chi-restraints excluded: chain P residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 0.9980 chunk 858 optimal weight: 4.9990 chunk 524 optimal weight: 2.9990 chunk 407 optimal weight: 1.9990 chunk 596 optimal weight: 2.9990 chunk 900 optimal weight: 5.9990 chunk 828 optimal weight: 4.9990 chunk 717 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 553 optimal weight: 1.9990 chunk 439 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 469 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 ASN ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 ASN D 792 GLN ** E 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 ASN ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 473 GLN P 703 GLN ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5260 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= 0.187 Angle : 0.501 8.451 102320 Z= 0.268 Chirality : 0.039 0.159 11722 Planarity : 0.005 0.098 13254 Dihedral : 4.794 77.745 9999 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.59 % Favored : 93.40 % Rotamer: Outliers : 1.55 % Allowed : 13.91 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 9050 helix: 1.18 (0.08), residues: 4433 sheet: -1.06 (0.18), residues: 692 loop : -1.55 (0.10), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 478 HIS 0.004 0.001 HIS H 257 PHE 0.011 0.001 PHE D 481 TYR 0.023 0.001 TYR A 621 ARG 0.012 0.000 ARG P 508 ********************** 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 1697 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1568 time to evaluate : 8.737 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: A 359 ASP cc_start: 0.7560 (m-30) cc_final: 0.7175 (m-30) REVERT: A 409 MET cc_start: 0.8733 (tpt) cc_final: 0.8451 (tpt) REVERT: A 723 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: A 780 SER cc_start: 0.8859 (m) cc_final: 0.8481 (t) REVERT: A 795 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7946 (mmtt) REVERT: A 884 MET cc_start: 0.7568 (mmt) cc_final: 0.7151 (mmt) REVERT: B 278 PHE cc_start: 0.8033 (m-10) cc_final: 0.7605 (m-80) REVERT: B 627 ASP cc_start: 0.8197 (m-30) cc_final: 0.7865 (m-30) REVERT: B 795 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6106 (mmtp) REVERT: B 796 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 807 TYR cc_start: 0.8222 (m-80) cc_final: 0.7783 (m-80) REVERT: C 268 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8742 (pp) REVERT: C 547 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8065 (tp) REVERT: D 252 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8417 (pp) REVERT: D 255 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (mp) REVERT: D 431 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8682 (pt) REVERT: E 268 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8928 (pp) REVERT: E 320 ASN cc_start: 0.8754 (t0) cc_final: 0.8444 (t0) REVERT: E 384 ASP cc_start: 0.8377 (t70) cc_final: 0.8124 (t0) REVERT: E 490 VAL cc_start: 0.9023 (p) cc_final: 0.8718 (m) REVERT: E 796 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7318 (pp) REVERT: F 216 ASP cc_start: 0.7816 (p0) cc_final: 0.7536 (p0) REVERT: F 486 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7882 (mp-120) REVERT: F 593 MET cc_start: 0.9026 (mmm) cc_final: 0.8455 (mmt) REVERT: F 756 ASN cc_start: 0.8490 (t0) cc_final: 0.7874 (t0) REVERT: G 268 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9003 (pp) REVERT: G 637 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7938 (mmp-170) REVERT: G 721 ARG cc_start: 0.8332 (mpt-90) cc_final: 0.7459 (mpt-90) REVERT: G 739 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (mp-120) REVERT: G 760 ASN cc_start: 0.8573 (m-40) cc_final: 0.8188 (m110) REVERT: G 777 SER cc_start: 0.8673 (t) cc_final: 0.8425 (p) REVERT: H 355 LYS cc_start: 0.8496 (tttm) cc_final: 0.7948 (tttp) REVERT: H 359 ASP cc_start: 0.7566 (m-30) cc_final: 0.7248 (m-30) REVERT: H 423 ASN cc_start: 0.8166 (m110) cc_final: 0.7931 (m110) REVERT: H 493 ASP cc_start: 0.7443 (t0) cc_final: 0.7185 (t0) REVERT: H 627 ASP cc_start: 0.6988 (m-30) cc_final: 0.6760 (m-30) REVERT: H 756 ASN cc_start: 0.8275 (t0) cc_final: 0.7998 (t0) REVERT: I 216 ASP cc_start: 0.8161 (p0) cc_final: 0.7932 (p0) REVERT: I 580 THR cc_start: 0.8448 (m) cc_final: 0.8143 (p) REVERT: I 691 LEU cc_start: 0.8861 (mt) cc_final: 0.8640 (mt) REVERT: I 695 ASN cc_start: 0.8792 (m-40) cc_final: 0.8267 (m110) REVERT: I 774 THR cc_start: 0.9187 (p) cc_final: 0.8973 (p) REVERT: I 795 LYS cc_start: 0.8453 (tttt) cc_final: 0.7969 (mmtp) REVERT: I 833 TYR cc_start: 0.8904 (t80) cc_final: 0.8658 (t80) REVERT: J 230 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7394 (ttp80) REVERT: J 425 MET cc_start: 0.8867 (tpt) cc_final: 0.8564 (tpt) REVERT: J 580 THR cc_start: 0.8248 (m) cc_final: 0.7887 (p) REVERT: J 639 ASN cc_start: 0.8347 (t0) cc_final: 0.8135 (t0) REVERT: J 651 ASP cc_start: 0.8062 (t70) cc_final: 0.7758 (t0) REVERT: P 425 MET cc_start: 0.8165 (mtt) cc_final: 0.7817 (mtt) REVERT: P 488 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7190 (mtt180) REVERT: P 500 LEU cc_start: 0.7319 (mt) cc_final: 0.6997 (mt) REVERT: P 571 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (p) REVERT: P 664 THR cc_start: 0.9115 (m) cc_final: 0.8829 (p) REVERT: P 730 GLU cc_start: 0.7614 (mp0) cc_final: 0.7392 (mp0) REVERT: P 1010 ASN cc_start: 0.8193 (m110) cc_final: 0.7776 (m-40) outliers start: 129 outliers final: 107 residues processed: 1641 average time/residue: 1.8692 time to fit residues: 5065.6525 Evaluate side-chains 1642 residues out of total 8332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1522 time to evaluate : 8.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 737 PHE Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 533 LYS Chi-restraints excluded: chain E residue 647 SER Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 450 GLN Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 722 ASP Chi-restraints excluded: chain F residue 774 THR Chi-restraints excluded: chain F residue 815 ASP Chi-restraints excluded: chain F residue 859 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 485 ASN Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 694 MET Chi-restraints excluded: chain G residue 716 ASP Chi-restraints excluded: chain G residue 739 GLN Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain H residue 452 MET Chi-restraints excluded: chain H residue 527 THR Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 692 ILE Chi-restraints excluded: chain H residue 716 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain I residue 502 ASP Chi-restraints excluded: chain I residue 527 THR Chi-restraints excluded: chain I residue 720 GLU Chi-restraints excluded: chain I residue 722 ASP Chi-restraints excluded: chain I residue 725 TYR Chi-restraints excluded: chain I residue 732 ARG Chi-restraints excluded: chain I residue 764 VAL Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain J residue 662 SER Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 868 ASP Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 383 ASP Chi-restraints excluded: chain P residue 399 SER Chi-restraints excluded: chain P residue 506 VAL Chi-restraints excluded: chain P residue 517 LEU Chi-restraints excluded: chain P residue 571 SER Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 775 TYR Chi-restraints excluded: chain P residue 801 GLU Chi-restraints excluded: chain P residue 874 ILE Chi-restraints excluded: chain P residue 888 ASN Chi-restraints excluded: chain P residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 0.8980 chunk 763 optimal weight: 3.9990 chunk 219 optimal weight: 0.1980 chunk 661 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 718 optimal weight: 3.9990 chunk 300 optimal weight: 0.1980 chunk 737 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 469 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 ASN D 792 GLN E 179 GLN ** E 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN H 474 GLN I 240 GLN I 358 GLN I 636 ASN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 703 GLN ** P 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096969 restraints weight = 398524.029| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.02 r_work: 0.2956 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 75455 Z= 0.155 Angle : 0.491 8.303 102320 Z= 0.261 Chirality : 0.039 0.164 11722 Planarity : 0.005 0.097 13254 Dihedral : 4.666 75.720 9999 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.49 % Favored : 93.50 % Rotamer: Outliers : 1.54 % Allowed : 14.09 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 9050 helix: 1.31 (0.08), residues: 4435 sheet: -0.97 (0.18), residues: 686 loop : -1.47 (0.10), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 478 HIS 0.006 0.001 HIS J 453 PHE 0.013 0.001 PHE C 278 TYR 0.022 0.001 TYR A 621 ARG 0.013 0.000 ARG P 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 67807.11 seconds wall clock time: 1156 minutes 0.95 seconds (69360.95 seconds total)