Starting phenix.real_space_refine on Sat Mar 23 17:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oik_3817/03_2024/5oik_3817.pdb" } resolution = 3.7 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= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 223 5.16 5 C 23677 2.51 5 N 6675 2.21 5 O 7300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B ARG 1131": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37988 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11261 Classifications: {'peptide': 1421} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9142 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 53, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2079 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1341 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 709 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Incomplete info: {'p_only': 9} Link IDs: {'rna3p': 42} Unresolved chain links: 9 Chain breaks: 1 Unresolved chain link angles: 39 Unresolved chain link dihedrals: 29 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan2': 1, ' DA:plan2': 2, ' DC:plan': 1, ' DT:plan': 5, ' DA:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "P" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "T" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 874 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3894 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 49.511 81.483 106.979 1.00174.43 S ATOM 486 SG CYS A 74 50.403 84.666 107.735 1.00166.79 S ATOM 533 SG CYS A 81 51.588 82.683 104.644 1.00162.13 S ATOM 768 SG CYS A 111 97.442 76.724 119.493 1.00183.09 S ATOM 796 SG CYS A 114 96.217 78.258 122.283 1.00182.27 S ATOM 1142 SG CYS A 184 98.201 74.807 122.510 1.00191.04 S ATOM 19973 SG CYS B1119 62.230 93.692 113.752 1.00148.10 S ATOM 19995 SG CYS B1122 64.520 91.088 113.113 1.00143.35 S ATOM 20110 SG CYS B1137 61.443 90.437 114.352 1.00165.79 S ATOM 20131 SG CYS B1140 64.951 91.110 116.464 1.00167.23 S ATOM 28452 SG CYS I 17 127.473 41.022 72.012 1.00155.52 S ATOM 28476 SG CYS I 20 124.329 40.644 74.643 1.00158.58 S ATOM 28637 SG CYS I 39 125.783 43.572 75.599 1.00159.23 S ATOM 28662 SG CYS I 42 128.090 40.618 75.763 1.00157.72 S ATOM 29014 SG CYS I 86 116.889 57.626 31.731 1.00154.36 S ATOM 29038 SG CYS I 89 116.360 54.569 29.565 1.00162.90 S ATOM 29242 SG CYS I 114 113.566 56.706 32.138 1.00146.80 S ATOM 29277 SG CYS I 119 116.034 54.241 33.009 1.00147.95 S ATOM 29387 SG CYS J 7 46.132 82.678 34.017 1.00 75.68 S ATOM 29411 SG CYS J 10 44.572 85.387 31.875 1.00 78.13 S ATOM 29675 SG CYS J 44 47.875 85.233 31.328 1.00 83.70 S ATOM 29681 SG CYS J 45 45.513 82.751 30.060 1.00 86.52 S ATOM 30834 SG CYS L 19 35.307 48.394 59.744 1.00138.04 S ATOM 30853 SG CYS L 22 33.360 46.285 57.805 1.00137.85 S ATOM 30970 SG CYS L 36 32.063 47.083 61.394 1.00146.22 S ATOM 30996 SG CYS L 39 35.347 45.135 60.694 1.00145.80 S ATOM 33293 SG CYS Y 16 75.126 24.130 126.306 1.00484.94 S ATOM 33315 SG CYS Y 19 78.449 24.783 124.495 1.00462.52 S ATOM 33427 SG CYS Y 33 76.998 21.604 123.861 1.00506.45 S ATOM 33449 SG CYS Y 36 78.411 22.354 127.424 1.00521.18 S Time building chain proxies: 18.42, per 1000 atoms: 0.48 Number of scatterers: 37988 At special positions: 0 Unit cell: (163.35, 167.4, 168.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 223 16.00 P 104 15.00 Mg 1 11.99 O 7300 8.00 N 6675 7.00 C 23677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.35 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 39 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8474 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 57 sheets defined 35.0% alpha, 19.9% beta 40 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 14.60 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.621A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.931A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 4.068A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.536A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.535A pdb=" N ILE A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.571A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.763A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.774A pdb=" N ASN A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.804A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.903A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.870A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 removed outlier: 3.556A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.113A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 665 through 678 removed outlier: 3.539A pdb=" N TYR A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.749A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 722 removed outlier: 3.530A pdb=" N THR A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 758 removed outlier: 3.649A pdb=" N ASN A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 747 " --> pdb=" O ARG A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.769A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.710A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.730A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 3.671A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.631A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.538A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.164A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 993 removed outlier: 3.682A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.735A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.566A pdb=" N ALA A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.737A pdb=" N LEU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1056 removed outlier: 3.530A pdb=" N ALA A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.545A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1071 " --> pdb=" O TRP A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.527A pdb=" N LEU A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1130 removed outlier: 3.855A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.063A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.361A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.507A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.829A pdb=" N GLU A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.175A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.674A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.588A pdb=" N VAL A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1387 removed outlier: 3.579A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.653A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.886A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.640A pdb=" N GLU A1441 " --> pdb=" O ASP A1437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1445 " --> pdb=" O GLU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.780A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.589A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.989A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.502A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.552A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.686A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.674A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 356 through 378 removed outlier: 4.191A pdb=" N LYS B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.307A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.551A pdb=" N GLY B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.985A pdb=" N SER B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.226A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.673A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.562A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.805A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.577A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 3.613A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 718 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.662A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 725 " --> pdb=" O ARG B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 874 through 879 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.659A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.703A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 993 removed outlier: 3.540A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.727A pdb=" N LEU B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1097 removed outlier: 3.561A pdb=" N ALA B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.785A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.514A pdb=" N SER B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.566A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.575A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.565A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 241 through 271 removed outlier: 3.896A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.654A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.507A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.148A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.677A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.822A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 74 removed outlier: 3.581A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.545A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.539A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 removed outlier: 3.788A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.084A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.651A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.845A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.554A pdb=" N ILE K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.702A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 231 through 240 removed outlier: 3.561A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 5.202A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 Processing helix chain 'Z' and resid 261 through 265 Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 573 through 575 No H-bonds generated for 'chain 'Z' and resid 573 through 575' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.560A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.161A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.579A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.754A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.872A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.707A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.812A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.766A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.902A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.796A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.399A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB8, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.675A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.512A pdb=" N GLN B 468 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.832A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.565A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 572 through 577 removed outlier: 7.029A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.215A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.215A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.026A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.602A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.608A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.654A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.557A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.609A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.609A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.210A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.552A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.522A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.609A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.523A pdb=" N ASP G 120 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF1, first strand: chain 'I' and resid 94 through 97 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF4, first strand: chain 'Y' and resid 83 through 89 removed outlier: 7.072A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 115 through 116 removed outlier: 7.315A pdb=" N ILE Y 115 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Z' and resid 352 through 355 removed outlier: 4.704A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS Z 306 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL Z 293 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'Z' and resid 510 through 513 removed outlier: 3.548A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.065A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AG2, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.382A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.789A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) 1355 hydrogen bonds defined for protein. 3696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 23.99 Time building geometry restraints manager: 16.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9660 1.33 - 1.45: 8634 1.45 - 1.58: 20057 1.58 - 1.70: 187 1.70 - 1.83: 353 Bond restraints: 38891 Sorted by residual: bond pdb=" CA GLY Y 105 " pdb=" C GLY Y 105 " ideal model delta sigma weight residual 1.511 1.685 -0.174 1.40e-02 5.10e+03 1.54e+02 bond pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.16e-02 7.43e+03 4.09e+01 bond pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.17e-02 7.31e+03 3.71e+01 bond pdb=" O3' DA T 30 " pdb=" P DT T 31 " ideal model delta sigma weight residual 1.607 1.535 0.072 1.50e-02 4.44e+03 2.32e+01 bond pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " ideal model delta sigma weight residual 1.458 1.402 0.056 1.20e-02 6.94e+03 2.21e+01 ... (remaining 38886 not shown) Histogram of bond angle deviations from ideal: 94.18 - 102.51: 446 102.51 - 110.84: 14404 110.84 - 119.17: 18214 119.17 - 127.50: 19360 127.50 - 135.83: 520 Bond angle restraints: 52944 Sorted by residual: angle pdb=" N ARG Y 104 " pdb=" CA ARG Y 104 " pdb=" C ARG Y 104 " ideal model delta sigma weight residual 113.15 128.35 -15.20 1.19e+00 7.06e-01 1.63e+02 angle pdb=" N THR Z 449 " pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 111.28 94.49 16.79 1.35e+00 5.49e-01 1.55e+02 angle pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 109.21 94.18 15.03 1.36e+00 5.41e-01 1.22e+02 angle pdb=" N GLY Z 423 " pdb=" CA GLY Z 423 " pdb=" C GLY Z 423 " ideal model delta sigma weight residual 114.69 127.01 -12.32 1.19e+00 7.06e-01 1.07e+02 angle pdb=" N LYS Z 447 " pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 109.15 96.48 12.67 1.44e+00 4.82e-01 7.74e+01 ... (remaining 52939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 22639 23.28 - 46.57: 746 46.57 - 69.85: 204 69.85 - 93.14: 23 93.14 - 116.42: 1 Dihedral angle restraints: 23613 sinusoidal: 10503 harmonic: 13110 Sorted by residual: dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 136.96 43.04 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA VAL A1341 " pdb=" C VAL A1341 " pdb=" N SER A1342 " pdb=" CA SER A1342 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP C 189 " pdb=" C ASP C 189 " pdb=" N ASN C 190 " pdb=" CA ASN C 190 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 23610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5114 0.087 - 0.175: 767 0.175 - 0.262: 41 0.262 - 0.350: 6 0.350 - 0.437: 3 Chirality restraints: 5931 Sorted by residual: chirality pdb=" CA ARG Y 104 " pdb=" N ARG Y 104 " pdb=" C ARG Y 104 " pdb=" CB ARG Y 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS Z 268 " pdb=" N LYS Z 268 " pdb=" C LYS Z 268 " pdb=" CB LYS Z 268 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA SER Y 20 " pdb=" N SER Y 20 " pdb=" C SER Y 20 " pdb=" CB SER Y 20 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5928 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 105 " 0.031 2.00e-02 2.50e+03 7.03e-02 4.95e+01 pdb=" C GLY Y 105 " -0.121 2.00e-02 2.50e+03 pdb=" O GLY Y 105 " 0.047 2.00e-02 2.50e+03 pdb=" N VAL Y 106 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 30 " 0.053 2.00e-02 2.50e+03 2.69e-02 1.98e+01 pdb=" N9 DA T 30 " -0.056 2.00e-02 2.50e+03 pdb=" C8 DA T 30 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 30 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 30 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DA T 30 " 0.036 2.00e-02 2.50e+03 pdb=" N6 DA T 30 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA T 30 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 30 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 30 " -0.020 2.00e-02 2.50e+03 pdb=" C4 DA T 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 872 " 0.019 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C THR B 872 " -0.063 2.00e-02 2.50e+03 pdb=" O THR B 872 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 873 " 0.021 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 162 2.45 - 3.06: 25349 3.06 - 3.68: 53589 3.68 - 4.29: 85449 4.29 - 4.90: 141160 Nonbonded interactions: 305709 Sorted by model distance: nonbonded pdb=" OE2 GLU Z 417 " pdb=" NH1 ARG Z 516 " model vdw 1.841 2.520 nonbonded pdb=" OH TYR B 367 " pdb=" OE2 GLU B 611 " model vdw 2.038 2.440 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.059 2.440 nonbonded pdb=" NZ LYS B 327 " pdb=" CE3 TRP Z 250 " model vdw 2.090 3.420 nonbonded pdb=" OE1 GLN G 60 " pdb=" NH2 ARG G 63 " model vdw 2.094 2.520 ... (remaining 305704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 5.810 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 121.270 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 0.174 38891 Z= 0.739 Angle : 1.066 17.703 52944 Z= 0.622 Chirality : 0.061 0.437 5931 Planarity : 0.006 0.086 6516 Dihedral : 12.584 116.421 15139 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.28 % Favored : 95.48 % Rotamer: Outliers : 0.33 % Allowed : 0.88 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -3.26 (0.10), residues: 4467 helix: -3.80 (0.09), residues: 1332 sheet: -1.58 (0.16), residues: 706 loop : -1.26 (0.11), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 570 HIS 0.021 0.003 HIS G 9 PHE 0.044 0.004 PHE B 805 TYR 0.045 0.004 TYR B 752 ARG 0.027 0.001 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 803 time to evaluate : 4.533 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: A 58 MET cc_start: 0.8974 (ttp) cc_final: 0.8692 (ttp) REVERT: A 321 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8366 (tm-30) REVERT: A 341 GLN cc_start: 0.8974 (mt0) cc_final: 0.8569 (mp10) REVERT: A 393 ILE cc_start: 0.9561 (mt) cc_final: 0.8953 (tp) REVERT: A 514 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7297 (mt-10) REVERT: A 637 MET cc_start: 0.8612 (ptm) cc_final: 0.8352 (ptp) REVERT: A 796 LYS cc_start: 0.9315 (mttt) cc_final: 0.8899 (mtpp) REVERT: A 845 GLU cc_start: 0.8588 (tt0) cc_final: 0.8204 (tt0) REVERT: A 959 MET cc_start: 0.8712 (mtp) cc_final: 0.7799 (mtp) REVERT: A 1095 LEU cc_start: 0.9355 (mt) cc_final: 0.9095 (mt) REVERT: A 1161 LEU cc_start: 0.9740 (mt) cc_final: 0.9463 (mt) REVERT: A 1243 LEU cc_start: 0.9510 (tp) cc_final: 0.9078 (mt) REVERT: A 1292 MET cc_start: 0.9089 (mtm) cc_final: 0.8763 (mtp) REVERT: A 1296 MET cc_start: 0.8755 (mmm) cc_final: 0.8375 (mmm) REVERT: A 1361 ASP cc_start: 0.8311 (t0) cc_final: 0.7443 (t0) REVERT: A 1422 GLN cc_start: 0.8807 (mt0) cc_final: 0.8522 (mt0) REVERT: A 1437 ASP cc_start: 0.9279 (m-30) cc_final: 0.8381 (m-30) REVERT: A 1447 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8290 (mp0) REVERT: A 1451 MET cc_start: 0.8980 (mmm) cc_final: 0.8385 (mmm) REVERT: B 54 SER cc_start: 0.9180 (m) cc_final: 0.8951 (p) REVERT: B 200 MET cc_start: 0.8541 (ttm) cc_final: 0.8273 (ttm) REVERT: B 674 MET cc_start: 0.8136 (mmm) cc_final: 0.7845 (tpt) REVERT: B 796 MET cc_start: 0.8142 (mtm) cc_final: 0.7655 (mtp) REVERT: B 802 ASP cc_start: 0.8518 (m-30) cc_final: 0.8200 (m-30) REVERT: B 1092 ASP cc_start: 0.8791 (m-30) cc_final: 0.8236 (m-30) REVERT: B 1101 GLN cc_start: 0.8389 (mt0) cc_final: 0.7697 (mt0) REVERT: B 1118 VAL cc_start: 0.9651 (t) cc_final: 0.9308 (p) REVERT: B 1130 THR cc_start: 0.9181 (m) cc_final: 0.8706 (t) REVERT: B 1151 MET cc_start: 0.9107 (ptm) cc_final: 0.8527 (ptm) REVERT: B 1165 MET cc_start: 0.9313 (mtm) cc_final: 0.9039 (mtt) REVERT: D 64 THR cc_start: 0.8893 (m) cc_final: 0.8606 (p) REVERT: G 7 LEU cc_start: 0.9288 (mt) cc_final: 0.8685 (tp) REVERT: G 8 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7892 (mm-30) REVERT: G 21 ASN cc_start: 0.9074 (m-40) cc_final: 0.8499 (t0) REVERT: G 28 GLN cc_start: 0.9153 (mt0) cc_final: 0.8753 (mt0) REVERT: G 34 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7543 (p) REVERT: G 52 ASP cc_start: 0.6871 (m-30) cc_final: 0.6387 (m-30) REVERT: G 72 TYR cc_start: 0.8304 (p90) cc_final: 0.7085 (p90) REVERT: G 81 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8338 (tptp) REVERT: G 86 ASP cc_start: 0.6925 (m-30) cc_final: 0.6044 (p0) REVERT: G 116 GLU cc_start: 0.9183 (mp0) cc_final: 0.8878 (pm20) REVERT: G 166 ASP cc_start: 0.9440 (m-30) cc_final: 0.9064 (p0) REVERT: H 43 VAL cc_start: 0.9353 (t) cc_final: 0.9128 (p) REVERT: H 60 ILE cc_start: 0.9603 (mt) cc_final: 0.9383 (tp) REVERT: H 98 ARG cc_start: 0.8509 (ttt90) cc_final: 0.8294 (ttt180) REVERT: I 25 TYR cc_start: 0.8297 (m-80) cc_final: 0.5348 (m-80) REVERT: I 57 LYS cc_start: 0.9386 (mttt) cc_final: 0.9029 (mtmm) REVERT: I 78 LEU cc_start: 0.9425 (mt) cc_final: 0.8679 (mt) REVERT: K 24 ASP cc_start: 0.8317 (t0) cc_final: 0.8023 (t0) REVERT: L 16 ILE cc_start: 0.9222 (mt) cc_final: 0.9001 (tp) REVERT: L 21 GLU cc_start: 0.9116 (tp30) cc_final: 0.8856 (tm-30) REVERT: Z 627 LYS cc_start: 0.8947 (pttt) cc_final: 0.8177 (tmtt) REVERT: Z 705 LEU cc_start: 0.9267 (tp) cc_final: 0.9040 (tp) REVERT: Z 738 SER cc_start: 0.8910 (m) cc_final: 0.8387 (p) outliers start: 13 outliers final: 5 residues processed: 815 average time/residue: 0.5705 time to fit residues: 721.6914 Evaluate side-chains 434 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 428 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain Y residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1163 HIS A1230 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 111 ASN B 265 GLN B 312 GLN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS B1094 GLN B1097 HIS B1142 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 34 ASN D 38 HIS F 72 GLN G 4 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS K 69 HIS Y 12 HIS Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38891 Z= 0.232 Angle : 0.727 13.216 52944 Z= 0.378 Chirality : 0.046 0.281 5931 Planarity : 0.005 0.074 6516 Dihedral : 14.520 113.559 6071 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 1.66 % Allowed : 7.92 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.73 (0.11), residues: 4467 helix: -1.62 (0.12), residues: 1386 sheet: -1.03 (0.16), residues: 715 loop : -0.75 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 49 HIS 0.013 0.002 HIS B 370 PHE 0.027 0.002 PHE Z 583 TYR 0.026 0.002 TYR A 669 ARG 0.011 0.001 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 503 time to evaluate : 4.010 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: A 34 MET cc_start: 0.8999 (tmm) cc_final: 0.8567 (tmm) REVERT: A 48 GLU cc_start: 0.8917 (tt0) cc_final: 0.8501 (pt0) REVERT: A 58 MET cc_start: 0.9053 (ttp) cc_final: 0.8148 (tmm) REVERT: A 238 MET cc_start: 0.7924 (mpp) cc_final: 0.7708 (mpp) REVERT: A 493 ASN cc_start: 0.9021 (t0) cc_final: 0.8796 (t0) REVERT: A 514 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 565 MET cc_start: 0.8635 (tpp) cc_final: 0.8237 (tpp) REVERT: A 849 ASP cc_start: 0.9010 (m-30) cc_final: 0.8578 (m-30) REVERT: A 1199 MET cc_start: 0.8980 (ppp) cc_final: 0.8727 (tmm) REVERT: A 1292 MET cc_start: 0.9059 (mtm) cc_final: 0.8732 (ptp) REVERT: A 1437 ASP cc_start: 0.8917 (m-30) cc_final: 0.8709 (m-30) REVERT: A 1441 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 1451 MET cc_start: 0.8887 (mmm) cc_final: 0.8569 (tpp) REVERT: A 1472 ASP cc_start: 0.8352 (p0) cc_final: 0.7891 (p0) REVERT: B 54 SER cc_start: 0.9332 (m) cc_final: 0.8779 (p) REVERT: B 297 MET cc_start: 0.8704 (mtp) cc_final: 0.8115 (mmt) REVERT: B 300 MET cc_start: 0.9258 (mmp) cc_final: 0.9040 (mmm) REVERT: B 508 MET cc_start: 0.8466 (mtp) cc_final: 0.8129 (mtp) REVERT: B 796 MET cc_start: 0.8101 (mtm) cc_final: 0.7814 (mtp) REVERT: B 1092 ASP cc_start: 0.8494 (m-30) cc_final: 0.8136 (m-30) REVERT: B 1101 GLN cc_start: 0.8152 (mt0) cc_final: 0.7793 (mt0) REVERT: B 1109 GLU cc_start: 0.7994 (mp0) cc_final: 0.7772 (mp0) REVERT: B 1118 VAL cc_start: 0.9718 (t) cc_final: 0.9463 (p) REVERT: B 1138 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8899 (mmm-85) REVERT: B 1171 MET cc_start: 0.9191 (mtm) cc_final: 0.8904 (mtm) REVERT: D 34 ASN cc_start: 0.5102 (OUTLIER) cc_final: 0.4849 (t0) REVERT: D 64 THR cc_start: 0.8888 (m) cc_final: 0.8587 (p) REVERT: D 128 GLN cc_start: 0.9788 (tp-100) cc_final: 0.9471 (mm110) REVERT: F 95 LYS cc_start: 0.9363 (ttmm) cc_final: 0.9076 (ttpt) REVERT: G 21 ASN cc_start: 0.9066 (m-40) cc_final: 0.8434 (t0) REVERT: G 28 GLN cc_start: 0.9080 (mt0) cc_final: 0.8716 (mt0) REVERT: G 29 LYS cc_start: 0.8640 (tppt) cc_final: 0.8405 (mmtm) REVERT: G 81 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8333 (tptp) REVERT: G 85 VAL cc_start: 0.9572 (OUTLIER) cc_final: 0.9355 (t) REVERT: G 86 ASP cc_start: 0.7504 (m-30) cc_final: 0.6568 (p0) REVERT: H 145 MET cc_start: 0.7317 (mtp) cc_final: 0.7105 (ttt) REVERT: I 23 MET cc_start: 0.7335 (pmm) cc_final: 0.7123 (pmm) REVERT: I 25 TYR cc_start: 0.7645 (m-80) cc_final: 0.7259 (m-80) REVERT: I 46 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8209 (tm-30) REVERT: I 74 GLN cc_start: 0.8605 (mp10) cc_final: 0.8398 (mp10) REVERT: I 75 ASP cc_start: 0.7777 (t0) cc_final: 0.7232 (t0) REVERT: K 24 ASP cc_start: 0.8243 (t0) cc_final: 0.7957 (t0) REVERT: K 103 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8139 (mm-30) REVERT: L 16 ILE cc_start: 0.9281 (mt) cc_final: 0.8838 (tt) REVERT: L 21 GLU cc_start: 0.9079 (tp30) cc_final: 0.8819 (tm-30) REVERT: L 44 MET cc_start: 0.8767 (mmm) cc_final: 0.7652 (mmm) REVERT: Z 288 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.8821 (t70) REVERT: Z 508 MET cc_start: 0.9174 (pmm) cc_final: 0.8947 (pmm) REVERT: Z 627 LYS cc_start: 0.8737 (pttt) cc_final: 0.8201 (tmtt) REVERT: Z 738 SER cc_start: 0.8832 (m) cc_final: 0.8494 (p) outliers start: 66 outliers final: 32 residues processed: 547 average time/residue: 0.5031 time to fit residues: 447.6814 Evaluate side-chains 428 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 393 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 37 ASP Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 342 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 445 optimal weight: 20.0000 chunk 367 optimal weight: 6.9990 chunk 408 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 353 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 945 ASN A1034 GLN A1077 ASN A1093 GLN A1230 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 350 HIS B 471 ASN B 948 GLN B1120 ASN C 265 HIS D 34 ASN F 72 GLN ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 45 GLN I 60 HIS J 52 HIS ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 38891 Z= 0.469 Angle : 0.753 13.328 52944 Z= 0.388 Chirality : 0.047 0.239 5931 Planarity : 0.005 0.060 6516 Dihedral : 14.475 112.696 6069 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 2.72 % Allowed : 8.87 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.89 (0.12), residues: 4467 helix: -0.33 (0.13), residues: 1396 sheet: -0.75 (0.17), residues: 729 loop : -0.58 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 27 HIS 0.010 0.002 HIS A 84 PHE 0.021 0.002 PHE G 119 TYR 0.028 0.002 TYR B 160 ARG 0.010 0.001 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 388 time to evaluate : 4.397 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: A 48 GLU cc_start: 0.8799 (tt0) cc_final: 0.8318 (pt0) REVERT: A 58 MET cc_start: 0.9063 (ttp) cc_final: 0.8028 (tmm) REVERT: A 216 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9221 (mm) REVERT: A 238 MET cc_start: 0.7825 (mpp) cc_final: 0.7456 (mpp) REVERT: A 266 MET cc_start: 0.5891 (mmm) cc_final: 0.5662 (mmt) REVERT: A 514 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 845 GLU cc_start: 0.8474 (pp20) cc_final: 0.8178 (pp20) REVERT: A 849 ASP cc_start: 0.9008 (m-30) cc_final: 0.8629 (m-30) REVERT: A 1038 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 1292 MET cc_start: 0.9162 (mtm) cc_final: 0.8838 (mtp) REVERT: A 1296 MET cc_start: 0.8562 (mmm) cc_final: 0.8078 (mmm) REVERT: A 1441 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 1451 MET cc_start: 0.8944 (mmm) cc_final: 0.8744 (tpp) REVERT: B 365 LEU cc_start: 0.9816 (OUTLIER) cc_final: 0.9514 (tt) REVERT: B 410 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.8841 (t0) REVERT: B 471 ASN cc_start: 0.8855 (t0) cc_final: 0.8243 (t0) REVERT: B 508 MET cc_start: 0.8741 (mtp) cc_final: 0.8284 (mtp) REVERT: B 767 LEU cc_start: 0.9509 (mt) cc_final: 0.8752 (tt) REVERT: B 840 MET cc_start: 0.8197 (mtp) cc_final: 0.7900 (mtt) REVERT: B 1089 MET cc_start: 0.8953 (mmm) cc_final: 0.8751 (mmm) REVERT: B 1092 ASP cc_start: 0.8469 (m-30) cc_final: 0.8182 (m-30) REVERT: B 1101 GLN cc_start: 0.8470 (mt0) cc_final: 0.7603 (mt0) REVERT: B 1109 GLU cc_start: 0.8172 (mp0) cc_final: 0.7840 (mp0) REVERT: D 64 THR cc_start: 0.8847 (m) cc_final: 0.8627 (p) REVERT: D 128 GLN cc_start: 0.9809 (tp-100) cc_final: 0.9443 (mm110) REVERT: E 18 MET cc_start: 0.8904 (mtm) cc_final: 0.8685 (ttm) REVERT: F 52 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9101 (tp) REVERT: F 84 GLU cc_start: 0.8623 (pm20) cc_final: 0.8390 (pm20) REVERT: F 95 LYS cc_start: 0.9384 (ttmm) cc_final: 0.8931 (ttpt) REVERT: F 98 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8096 (mtmm) REVERT: G 21 ASN cc_start: 0.9170 (m-40) cc_final: 0.8174 (p0) REVERT: G 24 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8798 (p0) REVERT: G 28 GLN cc_start: 0.9070 (mt0) cc_final: 0.8803 (mt0) REVERT: G 81 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8412 (ttmt) REVERT: G 85 VAL cc_start: 0.9590 (OUTLIER) cc_final: 0.9359 (t) REVERT: G 86 ASP cc_start: 0.7543 (m-30) cc_final: 0.6543 (p0) REVERT: G 139 GLN cc_start: 0.7832 (tp40) cc_final: 0.7393 (tp40) REVERT: I 23 MET cc_start: 0.7626 (pmm) cc_final: 0.7260 (pmm) REVERT: I 25 TYR cc_start: 0.8136 (m-80) cc_final: 0.7691 (m-80) REVERT: K 24 ASP cc_start: 0.8394 (t0) cc_final: 0.8105 (t0) REVERT: L 21 GLU cc_start: 0.9264 (tp30) cc_final: 0.9017 (tm-30) REVERT: L 44 MET cc_start: 0.8998 (mmm) cc_final: 0.8062 (mmm) REVERT: Z 197 MET cc_start: 0.8116 (tpp) cc_final: 0.7814 (tpt) REVERT: Z 288 ASP cc_start: 0.9424 (OUTLIER) cc_final: 0.8743 (t0) REVERT: Z 451 MET cc_start: 0.9243 (mmm) cc_final: 0.8769 (mmm) REVERT: Z 460 MET cc_start: 0.8846 (mmp) cc_final: 0.7670 (tpp) REVERT: Z 508 MET cc_start: 0.9235 (pmm) cc_final: 0.8941 (pmm) REVERT: Z 726 ASP cc_start: 0.8478 (p0) cc_final: 0.8118 (p0) outliers start: 108 outliers final: 63 residues processed: 465 average time/residue: 0.5209 time to fit residues: 400.9470 Evaluate side-chains 416 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 344 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 20.0000 chunk 309 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 413 optimal weight: 0.0970 chunk 437 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 391 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 273 GLN A 472 HIS A 757 GLN A 804 HIS A 945 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 22 ASN I 50 ASN Y 41 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38891 Z= 0.206 Angle : 0.616 10.870 52944 Z= 0.317 Chirality : 0.043 0.208 5931 Planarity : 0.004 0.067 6516 Dihedral : 14.330 110.074 6067 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.92 % Allowed : 11.09 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.37 (0.12), residues: 4467 helix: 0.34 (0.14), residues: 1402 sheet: -0.44 (0.18), residues: 722 loop : -0.45 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.015 0.001 HIS Y 12 PHE 0.025 0.001 PHE A 458 TYR 0.019 0.001 TYR A 413 ARG 0.007 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 398 time to evaluate : 4.538 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: A 48 GLU cc_start: 0.8762 (tt0) cc_final: 0.8299 (pt0) REVERT: A 58 MET cc_start: 0.8973 (ttp) cc_final: 0.8253 (tmm) REVERT: A 148 CYS cc_start: 0.8779 (m) cc_final: 0.8197 (p) REVERT: A 216 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9221 (mm) REVERT: A 238 MET cc_start: 0.8274 (mpp) cc_final: 0.7848 (mpp) REVERT: A 514 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 845 GLU cc_start: 0.8426 (pp20) cc_final: 0.8025 (pp20) REVERT: A 849 ASP cc_start: 0.9104 (m-30) cc_final: 0.8757 (m-30) REVERT: A 1038 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 1071 GLU cc_start: 0.8053 (tp30) cc_final: 0.7643 (tp30) REVERT: A 1292 MET cc_start: 0.9042 (mtm) cc_final: 0.8821 (ptp) REVERT: A 1364 GLU cc_start: 0.8617 (mp0) cc_final: 0.8367 (mp0) REVERT: A 1451 MET cc_start: 0.8832 (mmm) cc_final: 0.8541 (tpp) REVERT: B 410 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.8863 (t0) REVERT: B 471 ASN cc_start: 0.8783 (t0) cc_final: 0.8221 (t0) REVERT: B 508 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8276 (mtp) REVERT: B 767 LEU cc_start: 0.9458 (mt) cc_final: 0.8737 (tt) REVERT: B 840 MET cc_start: 0.8155 (mtp) cc_final: 0.7941 (mtt) REVERT: B 1092 ASP cc_start: 0.8437 (m-30) cc_final: 0.8157 (m-30) REVERT: B 1101 GLN cc_start: 0.8353 (mt0) cc_final: 0.7899 (mt0) REVERT: B 1109 GLU cc_start: 0.8101 (mp0) cc_final: 0.7722 (mp0) REVERT: F 68 THR cc_start: 0.9636 (m) cc_final: 0.9349 (t) REVERT: F 95 LYS cc_start: 0.9383 (ttmm) cc_final: 0.8936 (ttpt) REVERT: G 21 ASN cc_start: 0.9101 (m-40) cc_final: 0.8131 (p0) REVERT: G 24 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8752 (p0) REVERT: G 28 GLN cc_start: 0.9108 (mt0) cc_final: 0.8796 (mt0) REVERT: G 81 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8433 (ttmt) REVERT: G 104 MET cc_start: 0.8050 (tmm) cc_final: 0.7742 (tmm) REVERT: H 90 TYR cc_start: 0.8835 (t80) cc_final: 0.8345 (t80) REVERT: H 95 LYS cc_start: 0.9411 (ttmt) cc_final: 0.9175 (ttmm) REVERT: I 25 TYR cc_start: 0.7955 (m-80) cc_final: 0.7659 (m-80) REVERT: J 28 GLU cc_start: 0.8328 (mp0) cc_final: 0.8121 (mp0) REVERT: K 24 ASP cc_start: 0.8241 (t0) cc_final: 0.7986 (t0) REVERT: K 102 GLU cc_start: 0.8082 (pp20) cc_final: 0.7876 (pp20) REVERT: L 21 GLU cc_start: 0.9197 (tp30) cc_final: 0.8810 (tm-30) REVERT: L 44 MET cc_start: 0.9033 (mmm) cc_final: 0.8048 (mmm) REVERT: Z 288 ASP cc_start: 0.9410 (OUTLIER) cc_final: 0.8745 (t0) REVERT: Z 460 MET cc_start: 0.8953 (mmp) cc_final: 0.8630 (mmp) REVERT: Z 481 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9185 (mp) REVERT: Z 508 MET cc_start: 0.9238 (pmm) cc_final: 0.8946 (pmm) REVERT: Z 726 ASP cc_start: 0.8562 (p0) cc_final: 0.8273 (p0) outliers start: 76 outliers final: 41 residues processed: 451 average time/residue: 0.4879 time to fit residues: 363.4016 Evaluate side-chains 411 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 302 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 110 optimal weight: 0.0870 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 945 ASN A1034 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN B 731 GLN D 128 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 60 HIS ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38891 Z= 0.181 Angle : 0.592 10.774 52944 Z= 0.303 Chirality : 0.043 0.175 5931 Planarity : 0.004 0.065 6516 Dihedral : 14.130 108.478 6066 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.27 % Allowed : 11.34 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 4467 helix: 0.69 (0.14), residues: 1418 sheet: -0.26 (0.18), residues: 728 loop : -0.38 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.010 0.001 HIS I 60 PHE 0.023 0.001 PHE A 458 TYR 0.018 0.001 TYR F 115 ARG 0.013 0.000 ARG E 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 389 time to evaluate : 4.695 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: A 48 GLU cc_start: 0.8806 (tt0) cc_final: 0.8421 (pt0) REVERT: A 58 MET cc_start: 0.8866 (ttp) cc_final: 0.8263 (tmm) REVERT: A 148 CYS cc_start: 0.8853 (m) cc_final: 0.8256 (p) REVERT: A 238 MET cc_start: 0.8167 (mpp) cc_final: 0.7850 (mpp) REVERT: A 329 MET cc_start: 0.8424 (ptt) cc_final: 0.7951 (ptt) REVERT: A 467 MET cc_start: 0.8588 (mmt) cc_final: 0.8241 (mmt) REVERT: A 514 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 559 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7573 (mp0) REVERT: A 845 GLU cc_start: 0.8444 (pp20) cc_final: 0.8012 (pp20) REVERT: A 849 ASP cc_start: 0.9051 (m-30) cc_final: 0.8699 (m-30) REVERT: A 986 MET cc_start: 0.8536 (mtm) cc_final: 0.7277 (mtm) REVERT: A 1038 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (p) REVERT: A 1085 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 1451 MET cc_start: 0.8707 (mmm) cc_final: 0.8064 (mmm) REVERT: B 410 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.9023 (t0) REVERT: B 471 ASN cc_start: 0.8775 (t0) cc_final: 0.8159 (t0) REVERT: B 508 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: B 767 LEU cc_start: 0.9382 (mt) cc_final: 0.8715 (tt) REVERT: B 844 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9315 (tp) REVERT: B 1092 ASP cc_start: 0.8410 (m-30) cc_final: 0.8190 (m-30) REVERT: B 1101 GLN cc_start: 0.8250 (mt0) cc_final: 0.7842 (mt0) REVERT: D 128 GLN cc_start: 0.9854 (tp40) cc_final: 0.9544 (mm-40) REVERT: E 94 MET cc_start: 0.8327 (ppp) cc_final: 0.8080 (ppp) REVERT: F 52 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9145 (tp) REVERT: F 56 TYR cc_start: 0.8653 (m-80) cc_final: 0.8293 (m-80) REVERT: F 68 THR cc_start: 0.9620 (m) cc_final: 0.9342 (t) REVERT: F 95 LYS cc_start: 0.9356 (ttmm) cc_final: 0.8945 (ttpt) REVERT: F 98 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8065 (mtmm) REVERT: G 9 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7478 (m-70) REVERT: G 21 ASN cc_start: 0.9097 (m-40) cc_final: 0.8131 (p0) REVERT: G 24 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8689 (p0) REVERT: G 28 GLN cc_start: 0.9060 (mt0) cc_final: 0.8748 (mt0) REVERT: G 90 THR cc_start: 0.8566 (p) cc_final: 0.7873 (p) REVERT: G 139 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7531 (tp40) REVERT: H 90 TYR cc_start: 0.8825 (t80) cc_final: 0.8440 (t80) REVERT: H 95 LYS cc_start: 0.9378 (ttmt) cc_final: 0.9169 (ttmm) REVERT: I 25 TYR cc_start: 0.8130 (m-80) cc_final: 0.7829 (m-80) REVERT: I 81 THR cc_start: 0.9518 (p) cc_final: 0.9306 (t) REVERT: K 21 ILE cc_start: 0.9439 (mt) cc_final: 0.8929 (mt) REVERT: K 24 ASP cc_start: 0.8222 (t0) cc_final: 0.7968 (t0) REVERT: K 103 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7904 (mm-30) REVERT: Z 288 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.8742 (t0) REVERT: Z 460 MET cc_start: 0.8985 (mmp) cc_final: 0.8660 (mmp) REVERT: Z 481 ILE cc_start: 0.9695 (OUTLIER) cc_final: 0.9230 (mp) REVERT: Z 508 MET cc_start: 0.9252 (pmm) cc_final: 0.8945 (pmm) outliers start: 90 outliers final: 54 residues processed: 451 average time/residue: 0.4851 time to fit residues: 364.1752 Evaluate side-chains 429 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 365 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 538 GLU Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 3.9990 chunk 394 optimal weight: 50.0000 chunk 86 optimal weight: 7.9990 chunk 257 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 438 optimal weight: 0.0020 chunk 363 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A1093 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.003 0.039 38891 Z= 0.179 Angle : 0.579 10.731 52944 Z= 0.297 Chirality : 0.042 0.157 5931 Planarity : 0.004 0.042 6516 Dihedral : 13.985 106.419 6066 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 2.24 % Allowed : 11.82 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 4467 helix: 1.03 (0.14), residues: 1417 sheet: -0.13 (0.18), residues: 727 loop : -0.31 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 278 HIS 0.005 0.001 HIS A 84 PHE 0.020 0.001 PHE A 458 TYR 0.018 0.001 TYR F 115 ARG 0.009 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 384 time to evaluate : 4.429 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: A 148 CYS cc_start: 0.8911 (m) cc_final: 0.8323 (p) REVERT: A 216 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9226 (mm) REVERT: A 238 MET cc_start: 0.8304 (mpp) cc_final: 0.7679 (mmp) REVERT: A 329 MET cc_start: 0.8450 (ptt) cc_final: 0.7975 (ptt) REVERT: A 467 MET cc_start: 0.8577 (mmt) cc_final: 0.8312 (mmt) REVERT: A 565 MET cc_start: 0.8584 (tpp) cc_final: 0.8226 (tpp) REVERT: A 845 GLU cc_start: 0.8445 (pp20) cc_final: 0.8021 (pp20) REVERT: A 849 ASP cc_start: 0.9085 (m-30) cc_final: 0.8822 (m-30) REVERT: A 988 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.8945 (t60) REVERT: A 1038 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 1364 GLU cc_start: 0.8640 (mp0) cc_final: 0.8329 (mp0) REVERT: A 1398 LEU cc_start: 0.9355 (mt) cc_final: 0.9014 (mm) REVERT: A 1451 MET cc_start: 0.8616 (mmm) cc_final: 0.8009 (mmm) REVERT: B 410 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9117 (t0) REVERT: B 471 ASN cc_start: 0.8708 (t0) cc_final: 0.8098 (t0) REVERT: B 508 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: B 529 MET cc_start: 0.8592 (mmm) cc_final: 0.8378 (mmm) REVERT: B 616 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9058 (p) REVERT: B 767 LEU cc_start: 0.9441 (mt) cc_final: 0.8849 (tt) REVERT: B 844 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9330 (tp) REVERT: B 1092 ASP cc_start: 0.8407 (m-30) cc_final: 0.8156 (m-30) REVERT: B 1138 ARG cc_start: 0.9488 (mmt90) cc_final: 0.9280 (mmt90) REVERT: F 52 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9134 (tp) REVERT: F 56 TYR cc_start: 0.8624 (m-80) cc_final: 0.8288 (m-80) REVERT: F 68 THR cc_start: 0.9639 (m) cc_final: 0.9422 (p) REVERT: F 95 LYS cc_start: 0.9386 (ttmm) cc_final: 0.8955 (ttpt) REVERT: G 9 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7593 (m-70) REVERT: G 21 ASN cc_start: 0.9100 (m-40) cc_final: 0.8163 (p0) REVERT: G 24 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8679 (p0) REVERT: G 28 GLN cc_start: 0.9055 (mt0) cc_final: 0.8722 (mt0) REVERT: G 90 THR cc_start: 0.8632 (p) cc_final: 0.8252 (p) REVERT: G 139 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7724 (tp40) REVERT: H 95 LYS cc_start: 0.9391 (ttmt) cc_final: 0.9146 (ttmm) REVERT: I 31 GLU cc_start: 0.9518 (mp0) cc_final: 0.9291 (mp0) REVERT: I 60 HIS cc_start: 0.8145 (t70) cc_final: 0.7935 (t70) REVERT: K 24 ASP cc_start: 0.8163 (t0) cc_final: 0.7916 (t0) REVERT: K 102 GLU cc_start: 0.8051 (pp20) cc_final: 0.7795 (pp20) REVERT: Z 260 MET cc_start: 0.8804 (mmm) cc_final: 0.8604 (mmm) REVERT: Z 288 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.8744 (t0) REVERT: Z 451 MET cc_start: 0.9296 (mmm) cc_final: 0.8698 (mmm) REVERT: Z 460 MET cc_start: 0.8783 (mmp) cc_final: 0.8429 (mmp) REVERT: Z 481 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9246 (mp) REVERT: Z 508 MET cc_start: 0.9269 (pmm) cc_final: 0.8963 (pmm) REVERT: Z 726 ASP cc_start: 0.8377 (t0) cc_final: 0.8148 (p0) outliers start: 89 outliers final: 61 residues processed: 444 average time/residue: 0.4867 time to fit residues: 359.0535 Evaluate side-chains 435 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 362 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 988 TRP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 729 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 368 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 436 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 780 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 631 GLN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 38891 Z= 0.402 Angle : 0.686 14.759 52944 Z= 0.345 Chirality : 0.044 0.162 5931 Planarity : 0.004 0.047 6516 Dihedral : 14.049 105.542 6066 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.72 % Allowed : 12.02 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4467 helix: 1.13 (0.14), residues: 1419 sheet: -0.32 (0.18), residues: 743 loop : -0.34 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Z 278 HIS 0.005 0.001 HIS A 84 PHE 0.019 0.002 PHE A 458 TYR 0.023 0.002 TYR H 90 ARG 0.011 0.001 ARG B1141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 355 time to evaluate : 4.166 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: A 148 CYS cc_start: 0.9003 (m) cc_final: 0.8477 (p) REVERT: A 216 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9231 (mm) REVERT: A 238 MET cc_start: 0.8381 (mpp) cc_final: 0.7662 (mmp) REVERT: A 329 MET cc_start: 0.8462 (ptt) cc_final: 0.7979 (ptt) REVERT: A 360 ASP cc_start: 0.8446 (t0) cc_final: 0.8189 (t70) REVERT: A 467 MET cc_start: 0.8600 (mmt) cc_final: 0.8350 (mmt) REVERT: A 514 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 845 GLU cc_start: 0.8513 (pp20) cc_final: 0.7684 (pp20) REVERT: A 849 ASP cc_start: 0.9123 (m-30) cc_final: 0.8446 (m-30) REVERT: A 1038 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8866 (p) REVERT: A 1085 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 1364 GLU cc_start: 0.8662 (mp0) cc_final: 0.8351 (mp0) REVERT: A 1451 MET cc_start: 0.8664 (mmm) cc_final: 0.8422 (tpp) REVERT: B 239 MET cc_start: 0.9075 (ttm) cc_final: 0.8867 (ttt) REVERT: B 297 MET cc_start: 0.8882 (mmm) cc_final: 0.8572 (mmm) REVERT: B 410 ASN cc_start: 0.9410 (OUTLIER) cc_final: 0.9186 (t0) REVERT: B 508 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: B 844 ILE cc_start: 0.9560 (OUTLIER) cc_final: 0.9358 (tp) REVERT: B 1092 ASP cc_start: 0.8352 (m-30) cc_final: 0.8145 (m-30) REVERT: B 1131 ARG cc_start: 0.8884 (mmm160) cc_final: 0.8613 (mmm160) REVERT: E 94 MET cc_start: 0.8432 (ppp) cc_final: 0.8107 (ppp) REVERT: F 95 LYS cc_start: 0.9376 (ttmm) cc_final: 0.8910 (ttpt) REVERT: G 9 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7672 (m-70) REVERT: G 21 ASN cc_start: 0.9132 (m-40) cc_final: 0.8100 (p0) REVERT: G 24 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8694 (p0) REVERT: G 28 GLN cc_start: 0.9051 (mt0) cc_final: 0.8728 (mt0) REVERT: G 90 THR cc_start: 0.8589 (p) cc_final: 0.8178 (p) REVERT: G 105 SER cc_start: 0.8428 (m) cc_final: 0.8133 (p) REVERT: G 139 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7788 (tp40) REVERT: I 60 HIS cc_start: 0.8321 (t70) cc_final: 0.8118 (t70) REVERT: K 24 ASP cc_start: 0.8220 (t0) cc_final: 0.7971 (t0) REVERT: Y 63 MET cc_start: 0.8925 (tpp) cc_final: 0.8616 (tpp) REVERT: Z 197 MET cc_start: 0.8410 (tpp) cc_final: 0.7717 (tpt) REVERT: Z 278 TRP cc_start: 0.8771 (m-90) cc_final: 0.8075 (m-90) REVERT: Z 288 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.8694 (t0) REVERT: Z 460 MET cc_start: 0.8996 (mmp) cc_final: 0.8741 (mmp) REVERT: Z 481 ILE cc_start: 0.9710 (OUTLIER) cc_final: 0.9255 (mp) REVERT: Z 508 MET cc_start: 0.9211 (pmm) cc_final: 0.8896 (pmm) REVERT: Z 726 ASP cc_start: 0.8580 (t0) cc_final: 0.8347 (p0) outliers start: 108 outliers final: 71 residues processed: 429 average time/residue: 0.4782 time to fit residues: 342.2587 Evaluate side-chains 418 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 338 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain Z residue 729 GLU Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 277 optimal weight: 0.0270 chunk 297 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 330 GLN A 472 HIS ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38891 Z= 0.204 Angle : 0.602 11.504 52944 Z= 0.305 Chirality : 0.043 0.161 5931 Planarity : 0.004 0.042 6516 Dihedral : 13.969 103.878 6066 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.14 % Allowed : 12.83 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4467 helix: 1.32 (0.14), residues: 1422 sheet: -0.09 (0.18), residues: 723 loop : -0.27 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 988 HIS 0.005 0.001 HIS A 84 PHE 0.013 0.001 PHE A 668 TYR 0.017 0.001 TYR F 115 ARG 0.007 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 366 time to evaluate : 4.424 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: A 148 CYS cc_start: 0.8946 (m) cc_final: 0.8426 (p) REVERT: A 216 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9239 (mm) REVERT: A 238 MET cc_start: 0.8412 (mpp) cc_final: 0.7770 (mmp) REVERT: A 329 MET cc_start: 0.8507 (ptt) cc_final: 0.8074 (ptt) REVERT: A 484 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9170 (pp) REVERT: A 514 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 565 MET cc_start: 0.8472 (tpp) cc_final: 0.8087 (tpp) REVERT: A 845 GLU cc_start: 0.8481 (pp20) cc_final: 0.8154 (pp20) REVERT: A 849 ASP cc_start: 0.9150 (m-30) cc_final: 0.8921 (m-30) REVERT: A 1038 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 1085 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 1364 GLU cc_start: 0.8637 (mp0) cc_final: 0.8293 (mp0) REVERT: A 1451 MET cc_start: 0.8580 (mmm) cc_final: 0.8078 (mmm) REVERT: B 297 MET cc_start: 0.8833 (mmm) cc_final: 0.8556 (mmm) REVERT: B 410 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9160 (t0) REVERT: B 508 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: B 616 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9220 (p) REVERT: B 844 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9337 (tp) REVERT: B 908 MET cc_start: 0.8766 (ppp) cc_final: 0.8491 (ppp) REVERT: B 1058 LYS cc_start: 0.9115 (mttm) cc_final: 0.8891 (mtmt) REVERT: B 1131 ARG cc_start: 0.8867 (mmm160) cc_final: 0.8632 (mmm160) REVERT: D 128 GLN cc_start: 0.9883 (tp-100) cc_final: 0.9379 (mm110) REVERT: E 94 MET cc_start: 0.8308 (ppp) cc_final: 0.8055 (ppp) REVERT: F 95 LYS cc_start: 0.9288 (ttmm) cc_final: 0.8871 (ttpt) REVERT: G 21 ASN cc_start: 0.9086 (m-40) cc_final: 0.8113 (p0) REVERT: G 24 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8647 (p0) REVERT: G 28 GLN cc_start: 0.9045 (mt0) cc_final: 0.8704 (mt0) REVERT: G 90 THR cc_start: 0.8569 (p) cc_final: 0.8158 (p) REVERT: G 104 MET cc_start: 0.7232 (tpt) cc_final: 0.7009 (tpt) REVERT: G 105 SER cc_start: 0.8569 (m) cc_final: 0.8292 (p) REVERT: G 139 GLN cc_start: 0.8524 (mm-40) cc_final: 0.7982 (tp40) REVERT: I 35 LEU cc_start: 0.9248 (tp) cc_final: 0.9029 (mt) REVERT: I 60 HIS cc_start: 0.8285 (t70) cc_final: 0.7993 (t-170) REVERT: K 24 ASP cc_start: 0.8146 (t0) cc_final: 0.7900 (t0) REVERT: K 102 GLU cc_start: 0.8077 (pp20) cc_final: 0.7818 (pp20) REVERT: Y 50 TYR cc_start: 0.7238 (m-80) cc_final: 0.6991 (m-80) REVERT: Z 197 MET cc_start: 0.8403 (tpp) cc_final: 0.7781 (tpt) REVERT: Z 288 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.8626 (t0) REVERT: Z 451 MET cc_start: 0.9295 (mmm) cc_final: 0.8649 (mmm) REVERT: Z 460 MET cc_start: 0.8847 (mmp) cc_final: 0.8568 (mmp) REVERT: Z 481 ILE cc_start: 0.9715 (OUTLIER) cc_final: 0.9248 (mp) REVERT: Z 508 MET cc_start: 0.9189 (pmm) cc_final: 0.8851 (pmm) REVERT: Z 726 ASP cc_start: 0.8418 (t0) cc_final: 0.8214 (p0) outliers start: 85 outliers final: 58 residues processed: 424 average time/residue: 0.4755 time to fit residues: 334.4760 Evaluate side-chains 418 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 350 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 603 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 2.9990 chunk 418 optimal weight: 7.9990 chunk 381 optimal weight: 4.9990 chunk 406 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 0.0470 chunk 319 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 367 optimal weight: 3.9990 chunk 384 optimal weight: 20.0000 chunk 405 optimal weight: 30.0000 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 41 ASN Z 337 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 38891 Z= 0.272 Angle : 0.630 11.987 52944 Z= 0.318 Chirality : 0.043 0.211 5931 Planarity : 0.004 0.039 6516 Dihedral : 13.890 103.193 6066 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 2.09 % Allowed : 13.08 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4467 helix: 1.30 (0.14), residues: 1437 sheet: -0.04 (0.19), residues: 718 loop : -0.29 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 278 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE B 805 TYR 0.019 0.001 TYR G 17 ARG 0.007 0.000 ARG E 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 353 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9628 (t0) cc_final: 0.9406 (t0) REVERT: A 78 MET cc_start: 0.9009 (tpp) cc_final: 0.8770 (tpp) REVERT: A 132 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8305 (ptmm) REVERT: A 148 CYS cc_start: 0.8959 (m) cc_final: 0.8464 (p) REVERT: A 216 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9242 (mm) REVERT: A 238 MET cc_start: 0.8316 (mpp) cc_final: 0.7634 (mmp) REVERT: A 329 MET cc_start: 0.8510 (ptt) cc_final: 0.8065 (ptt) REVERT: A 484 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9155 (pp) REVERT: A 514 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7524 (mt-10) REVERT: A 565 MET cc_start: 0.8575 (tpp) cc_final: 0.8210 (tpp) REVERT: A 845 GLU cc_start: 0.8452 (pp20) cc_final: 0.8190 (pp20) REVERT: A 849 ASP cc_start: 0.9154 (m-30) cc_final: 0.8927 (m-30) REVERT: A 1038 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 1085 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 1279 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: A 1292 MET cc_start: 0.9057 (mtp) cc_final: 0.8853 (ptp) REVERT: A 1364 GLU cc_start: 0.8659 (mp0) cc_final: 0.8312 (mp0) REVERT: A 1451 MET cc_start: 0.8723 (mmm) cc_final: 0.8267 (mmm) REVERT: B 297 MET cc_start: 0.8846 (mmm) cc_final: 0.8571 (mmm) REVERT: B 508 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: B 616 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9233 (p) REVERT: B 844 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9364 (tp) REVERT: B 908 MET cc_start: 0.8729 (ppp) cc_final: 0.8388 (ppp) REVERT: B 1058 LYS cc_start: 0.9194 (mttm) cc_final: 0.8971 (mtmt) REVERT: B 1131 ARG cc_start: 0.8902 (mmm160) cc_final: 0.8645 (mmm160) REVERT: D 128 GLN cc_start: 0.9886 (tp-100) cc_final: 0.9444 (mm-40) REVERT: F 95 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8928 (ttpt) REVERT: G 21 ASN cc_start: 0.9062 (m-40) cc_final: 0.8040 (p0) REVERT: G 24 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8659 (p0) REVERT: G 28 GLN cc_start: 0.9041 (mt0) cc_final: 0.8702 (mt0) REVERT: G 29 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8375 (mttt) REVERT: G 86 ASP cc_start: 0.8193 (m-30) cc_final: 0.7237 (p0) REVERT: G 90 THR cc_start: 0.8577 (p) cc_final: 0.7963 (p) REVERT: G 100 GLU cc_start: 0.7399 (mp0) cc_final: 0.7047 (mp0) REVERT: G 104 MET cc_start: 0.7334 (tpt) cc_final: 0.7023 (tpt) REVERT: G 105 SER cc_start: 0.8607 (m) cc_final: 0.8192 (p) REVERT: G 139 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8015 (tp40) REVERT: I 35 LEU cc_start: 0.9248 (tp) cc_final: 0.9037 (mt) REVERT: I 60 HIS cc_start: 0.8270 (t70) cc_final: 0.7993 (t-170) REVERT: K 24 ASP cc_start: 0.8149 (t0) cc_final: 0.7894 (t0) REVERT: Y 50 TYR cc_start: 0.7155 (m-80) cc_final: 0.6906 (m-80) REVERT: Z 197 MET cc_start: 0.8448 (tpp) cc_final: 0.8008 (tpp) REVERT: Z 278 TRP cc_start: 0.8709 (m-90) cc_final: 0.7945 (m-90) REVERT: Z 288 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.8713 (t0) REVERT: Z 451 MET cc_start: 0.9280 (mmm) cc_final: 0.8682 (mmm) REVERT: Z 460 MET cc_start: 0.8881 (mmp) cc_final: 0.8610 (mmp) REVERT: Z 481 ILE cc_start: 0.9718 (OUTLIER) cc_final: 0.9249 (mp) REVERT: Z 508 MET cc_start: 0.9197 (pmm) cc_final: 0.8864 (pmm) REVERT: Z 726 ASP cc_start: 0.8339 (t0) cc_final: 0.8073 (p0) outliers start: 83 outliers final: 56 residues processed: 410 average time/residue: 0.4880 time to fit residues: 332.5596 Evaluate side-chains 405 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 338 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain Z residue 739 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 3.9990 chunk 430 optimal weight: 20.0000 chunk 262 optimal weight: 0.7980 chunk 204 optimal weight: 0.3980 chunk 299 optimal weight: 8.9990 chunk 451 optimal weight: 10.0000 chunk 415 optimal weight: 20.0000 chunk 359 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38891 Z= 0.169 Angle : 0.614 12.176 52944 Z= 0.309 Chirality : 0.043 0.211 5931 Planarity : 0.004 0.043 6516 Dihedral : 13.778 101.635 6066 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 1.61 % Allowed : 13.74 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 4467 helix: 1.33 (0.14), residues: 1436 sheet: 0.02 (0.18), residues: 741 loop : -0.19 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Z 278 HIS 0.004 0.001 HIS A 84 PHE 0.014 0.001 PHE A 668 TYR 0.025 0.001 TYR G 17 ARG 0.012 0.000 ARG I 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8934 Ramachandran restraints generated. 4467 Oldfield, 0 Emsley, 4467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 370 time to evaluate : 6.626 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: A 77 ASN cc_start: 0.9620 (t0) cc_final: 0.9385 (t0) REVERT: A 132 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8277 (ptmm) REVERT: A 148 CYS cc_start: 0.8926 (m) cc_final: 0.8401 (p) REVERT: A 238 MET cc_start: 0.8337 (mpp) cc_final: 0.7806 (mmp) REVERT: A 355 MET cc_start: 0.8995 (mmm) cc_final: 0.8344 (mmm) REVERT: A 484 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8826 (pp) REVERT: A 514 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 565 MET cc_start: 0.8312 (tpp) cc_final: 0.7976 (tpp) REVERT: A 845 GLU cc_start: 0.8441 (pp20) cc_final: 0.8169 (pp20) REVERT: A 849 ASP cc_start: 0.9151 (m-30) cc_final: 0.8909 (m-30) REVERT: A 1038 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 1279 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6891 (tpp) REVERT: A 1364 GLU cc_start: 0.8630 (mp0) cc_final: 0.8291 (mp0) REVERT: A 1451 MET cc_start: 0.8653 (mmm) cc_final: 0.8210 (mmm) REVERT: B 297 MET cc_start: 0.8814 (mmm) cc_final: 0.8544 (mmm) REVERT: B 508 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: B 616 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9266 (p) REVERT: B 1058 LYS cc_start: 0.8993 (mttm) cc_final: 0.8777 (mtmt) REVERT: B 1131 ARG cc_start: 0.8893 (mmm160) cc_final: 0.8634 (mmm160) REVERT: F 95 LYS cc_start: 0.9285 (ttmm) cc_final: 0.9080 (ttpt) REVERT: G 9 HIS cc_start: 0.8885 (t-170) cc_final: 0.8501 (t-170) REVERT: G 21 ASN cc_start: 0.9071 (m-40) cc_final: 0.8109 (p0) REVERT: G 24 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8650 (p0) REVERT: G 28 GLN cc_start: 0.9040 (mt0) cc_final: 0.8710 (mt0) REVERT: G 29 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8381 (mttt) REVERT: G 86 ASP cc_start: 0.8174 (m-30) cc_final: 0.7208 (p0) REVERT: G 90 THR cc_start: 0.8570 (p) cc_final: 0.7979 (p) REVERT: G 94 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9224 (mmmt) REVERT: G 100 GLU cc_start: 0.7378 (mp0) cc_final: 0.7010 (mp0) REVERT: G 105 SER cc_start: 0.8480 (m) cc_final: 0.8186 (p) REVERT: G 120 ASP cc_start: 0.9381 (p0) cc_final: 0.9005 (p0) REVERT: G 139 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7636 (tp40) REVERT: I 35 LEU cc_start: 0.9184 (tp) cc_final: 0.8821 (mt) REVERT: I 47 GLU cc_start: 0.8783 (tp30) cc_final: 0.8469 (tm-30) REVERT: I 60 HIS cc_start: 0.8242 (t70) cc_final: 0.7980 (t-170) REVERT: K 24 ASP cc_start: 0.8116 (t0) cc_final: 0.7855 (t0) REVERT: K 102 GLU cc_start: 0.8255 (pp20) cc_final: 0.7961 (pp20) REVERT: L 44 MET cc_start: 0.9234 (mmm) cc_final: 0.8856 (mmm) REVERT: Y 50 TYR cc_start: 0.7249 (m-80) cc_final: 0.7006 (m-80) REVERT: Z 197 MET cc_start: 0.8429 (tpp) cc_final: 0.7996 (tpp) REVERT: Z 278 TRP cc_start: 0.8691 (m-90) cc_final: 0.7921 (m-90) REVERT: Z 451 MET cc_start: 0.9292 (mmm) cc_final: 0.8681 (mmm) REVERT: Z 460 MET cc_start: 0.8840 (mmp) cc_final: 0.8582 (mmp) REVERT: Z 481 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9251 (mp) REVERT: Z 508 MET cc_start: 0.9178 (pmm) cc_final: 0.8839 (pmm) REVERT: Z 726 ASP cc_start: 0.8359 (t0) cc_final: 0.8095 (p0) outliers start: 64 outliers final: 51 residues processed: 414 average time/residue: 0.4853 time to fit residues: 334.7256 Evaluate side-chains 409 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 350 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1084 LEU Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain Z residue 288 ASP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 580 ASP Chi-restraints excluded: chain Z residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 10.0000 chunk 382 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 331 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 359 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 HIS ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052957 restraints weight = 133954.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054859 restraints weight = 63250.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056076 restraints weight = 39992.067| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 38891 Z= 0.276 Angle : 0.645 12.335 52944 Z= 0.324 Chirality : 0.043 0.187 5931 Planarity : 0.004 0.054 6516 Dihedral : 13.735 101.077 6066 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 1.66 % Allowed : 13.91 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 4467 helix: 1.40 (0.14), residues: 1430 sheet: 0.01 (0.18), residues: 754 loop : -0.24 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Z 278 HIS 0.007 0.001 HIS B 939 PHE 0.020 0.001 PHE A1284 TYR 0.022 0.001 TYR G 17 ARG 0.006 0.000 ARG E 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7994.59 seconds wall clock time: 145 minutes 28.25 seconds (8728.25 seconds total)