Starting phenix.real_space_refine on Thu Jun 19 07:38:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwo_34318/06_2025/8gwo_34318.cif" } resolution = 3.8 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= 0.038 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 56 5.49 5 S 157 5.16 5 C 13689 2.51 5 N 3682 2.21 5 O 4288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'RNA': 1, 'peptide': 113} Modifications used: {'rna2p_pyr': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106, None: 1} Not linked: pdbres=" U G 0 " pdbres="ASN G 1 " Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 82.675 50.470 64.055 1.00 64.63 S ATOM 2487 SG CYS A 306 82.697 51.796 60.462 1.00 64.60 S ATOM 2519 SG CYS A 310 81.174 48.347 61.284 1.00 63.72 S ATOM 3927 SG CYS A 487 81.031 65.168 79.302 1.00 84.90 S ATOM 5180 SG CYS A 645 82.124 66.659 75.944 1.00102.92 S ATOM 5186 SG CYS A 646 83.731 63.408 77.227 1.00 97.68 S ATOM 12035 SG CYS F 16 52.929 63.017 134.833 1.00191.23 S ATOM 12050 SG CYS F 19 51.962 59.704 136.711 1.00207.65 S ATOM 11953 SG CYS F 5 40.570 66.188 132.135 1.00172.78 S ATOM 11974 SG CYS F 8 39.911 68.612 134.884 1.00193.87 S ATOM 12112 SG CYS F 26 41.858 69.862 132.030 1.00177.26 S ATOM 12129 SG CYS F 29 43.657 67.586 134.176 1.00184.44 S ATOM 12294 SG CYS F 50 66.174 72.667 121.669 1.00225.07 S ATOM 12324 SG CYS F 55 68.111 70.331 123.915 1.00221.22 S ATOM 12457 SG CYS F 72 67.786 74.162 124.908 1.00223.77 S ATOM 16548 SG CYS E 16 97.549 68.183 120.864 1.00141.25 S ATOM 16563 SG CYS E 19 99.383 65.136 122.370 1.00152.92 S ATOM 16466 SG CYS E 5 87.046 64.410 128.196 1.00145.34 S ATOM 16487 SG CYS E 8 87.101 66.377 131.444 1.00162.65 S ATOM 16625 SG CYS E 26 85.394 67.908 128.423 1.00163.75 S ATOM 16642 SG CYS E 29 89.242 67.644 128.841 1.00171.71 S ATOM 16807 SG CYS E 50 93.717 82.204 106.944 1.00209.10 S ATOM 16837 SG CYS E 55 97.251 83.057 105.932 1.00236.60 S ATOM 16970 SG CYS E 72 95.613 84.985 108.798 1.00208.87 S Time building chain proxies: 19.93, per 1000 atoms: 0.91 Number of scatterers: 21880 At special positions: 0 Unit cell: (154.16, 134.48, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 157 16.00 P 56 15.00 O 4288 8.00 N 3682 7.00 C 13689 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 - 3.00 Amino acid : True - 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: 5.54 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 27 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 39.2% alpha, 11.1% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.906A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.638A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.562A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.515A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.621A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.631A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.657A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.781A pdb=" N ALA A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.727A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.549A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 468 through 480 removed outlier: 4.815A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.899A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.621A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.545A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 4.017A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.629A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.077A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.591A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 767 through 772 removed outlier: 3.802A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 865 removed outlier: 3.555A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 removed outlier: 3.955A pdb=" N LEU A 869 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.178A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.856A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 926 removed outlier: 3.509A pdb=" N THR A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.188A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.699A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.020A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.944A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.537A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.862A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.788A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 71' Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.510A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 41 removed outlier: 4.267A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 80 removed outlier: 3.926A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.393A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.796A pdb=" N GLU D 171 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 172' Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.975A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.537A pdb=" N THR F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.641A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 removed outlier: 3.620A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 271 removed outlier: 4.376A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.808A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 297 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 4.421A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.425A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.576A pdb=" N ARG F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 removed outlier: 3.752A pdb=" N LEU F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.755A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 515 through 523 removed outlier: 4.065A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 3.801A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 4.147A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.327A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.677A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 273 removed outlier: 3.787A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.600A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 removed outlier: 4.135A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 429 Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.586A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'E' and resid 515 through 524 removed outlier: 4.226A pdb=" N ASN E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.230A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 removed outlier: 3.596A pdb=" N ARG G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.828A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.642A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.791A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.564A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.564A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.788A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 560 removed outlier: 7.178A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 614 through 615 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 757 removed outlier: 3.749A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.690A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.532A pdb=" N GLY F 3 " --> pdb=" O THR F 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.996A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.911A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 153 through 157 removed outlier: 6.870A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 182 through 187 removed outlier: 6.706A pdb=" N PHE F 182 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU F 197 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY F 184 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'F' and resid 304 through 307 removed outlier: 5.309A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 330 through 332 removed outlier: 5.796A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 472 through 474 removed outlier: 3.727A pdb=" N LEU F 573 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 575 " --> pdb=" O PHE F 546 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 481 through 482 removed outlier: 4.016A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 511 through 512 removed outlier: 6.097A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC8, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC9, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=AD1, first strand: chain 'E' and resid 154 through 159 removed outlier: 4.004A pdb=" N GLU E 156 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU E 158 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 186 through 187 Processing sheet with id=AD3, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AD4, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.446A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 366 through 367 removed outlier: 6.941A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AD7, first strand: chain 'E' and resid 530 through 531 removed outlier: 6.113A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'G' and resid 15 through 17 removed outlier: 4.509A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 43 through 46 724 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 8.37 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 16 1.22 - 1.37: 7276 1.37 - 1.52: 10601 1.52 - 1.67: 4336 1.67 - 1.82: 226 Bond restraints: 22455 Sorted by residual: bond pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 1.424 1.075 0.349 1.50e-02 4.44e+03 5.43e+02 bond pdb=" P U G 0 " pdb=" OP1 U G 0 " ideal model delta sigma weight residual 1.485 1.813 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P U G 0 " pdb=" OP2 U G 0 " ideal model delta sigma weight residual 1.485 1.781 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4 U I 13 " pdb=" O4 U I 13 " ideal model delta sigma weight residual 1.232 1.426 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C4 U I 16 " pdb=" O4 U I 16 " ideal model delta sigma weight residual 1.232 1.426 -0.194 2.00e-02 2.50e+03 9.37e+01 ... (remaining 22450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 30538 3.65 - 7.30: 228 7.30 - 10.95: 14 10.95 - 14.60: 3 14.60 - 18.26: 1 Bond angle restraints: 30784 Sorted by residual: angle pdb=" N PRO F 254 " pdb=" CD PRO F 254 " pdb=" CG PRO F 254 " ideal model delta sigma weight residual 103.20 84.94 18.26 1.50e+00 4.44e-01 1.48e+02 angle pdb=" CA PRO F 254 " pdb=" N PRO F 254 " pdb=" CD PRO F 254 " ideal model delta sigma weight residual 112.00 99.64 12.36 1.40e+00 5.10e-01 7.79e+01 angle pdb=" CA PRO F 254 " pdb=" CB PRO F 254 " pdb=" CG PRO F 254 " ideal model delta sigma weight residual 104.50 91.88 12.62 1.90e+00 2.77e-01 4.41e+01 angle pdb=" C HIS A 898 " pdb=" N MET A 899 " pdb=" CA MET A 899 " ideal model delta sigma weight residual 122.73 113.56 9.17 1.61e+00 3.86e-01 3.25e+01 angle pdb=" P U G 0 " pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 120.90 128.54 -7.64 1.50e+00 4.44e-01 2.59e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 12553 25.26 - 50.51: 825 50.51 - 75.77: 148 75.77 - 101.02: 11 101.02 - 126.28: 1 Dihedral angle restraints: 13538 sinusoidal: 5682 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA VAL A 848 " pdb=" C VAL A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG E 502 " pdb=" C ARG E 502 " pdb=" N ASN E 503 " pdb=" CA ASN E 503 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 13535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 3569 0.263 - 0.527: 0 0.527 - 0.790: 0 0.790 - 1.054: 0 1.054 - 1.317: 1 Chirality restraints: 3570 Sorted by residual: chirality pdb=" P U G 0 " pdb=" OP1 U G 0 " pdb=" OP2 U G 0 " pdb=" O5' U G 0 " both_signs ideal model delta sigma weight residual True 2.41 -3.73 -1.32 2.00e-01 2.50e+01 4.34e+01 chirality pdb=" CB ILE F 592 " pdb=" CA ILE F 592 " pdb=" CG1 ILE F 592 " pdb=" CG2 ILE F 592 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB VAL E 449 " pdb=" CA VAL E 449 " pdb=" CG1 VAL E 449 " pdb=" CG2 VAL E 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 3567 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 253 " 0.090 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO F 254 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO F 254 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 254 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 71 " 0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO G 72 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 22 " -0.013 2.00e-02 2.50e+03 2.09e-02 8.77e+00 pdb=" CG TYR D 22 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 22 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 22 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 22 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 22 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 22 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 22 " 0.004 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 91 2.38 - 3.01: 12515 3.01 - 3.64: 33005 3.64 - 4.27: 47684 4.27 - 4.90: 77308 Nonbonded interactions: 170603 Sorted by model distance: nonbonded pdb=" P U G 0 " pdb=" N ASN G 1 " model vdw 1.755 3.480 nonbonded pdb=" NE2 HIS A 295 " pdb="ZN ZN A1001 " model vdw 2.075 1.848 nonbonded pdb=" OP2 U G 0 " pdb=" O3G GNP A1003 " model vdw 2.092 3.040 nonbonded pdb=" OD1 ASP B 50 " pdb=" O2' A I 14 " model vdw 2.132 3.040 nonbonded pdb=" N ASN E 116 " pdb=" OD2 ASP E 119 " model vdw 2.138 3.120 ... (remaining 170598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 68.840 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.008 0.349 22487 Z= 0.389 Angle : 0.834 18.255 30811 Z= 0.461 Chirality : 0.048 1.317 3570 Planarity : 0.005 0.127 3732 Dihedral : 16.542 126.279 8470 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.81 % Favored : 91.11 % Rotamer: Outliers : 0.66 % Allowed : 18.26 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.55 (0.16), residues: 2639 helix: -0.52 (0.17), residues: 934 sheet: -2.15 (0.33), residues: 224 loop : -2.50 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 114 HIS 0.006 0.001 HIS E 464 PHE 0.035 0.001 PHE A 396 TYR 0.049 0.001 TYR D 22 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.20233 ( 757) hydrogen bonds : angle 7.26002 ( 2092) metal coordination : bond 0.05074 ( 32) metal coordination : angle 4.16521 ( 27) covalent geometry : bond 0.00757 (22455) covalent geometry : angle 0.82469 (30784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 2.265 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: A 855 MET cc_start: 0.8599 (mmt) cc_final: 0.8397 (mmt) REVERT: A 899 MET cc_start: 0.7853 (ttp) cc_final: 0.7368 (ttp) REVERT: B 51 ARG cc_start: 0.8811 (mtp85) cc_final: 0.8494 (mtt90) REVERT: B 79 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8834 (mtpt) REVERT: F 299 TYR cc_start: 0.4654 (m-80) cc_final: 0.4451 (m-80) REVERT: E 274 MET cc_start: 0.8125 (ttm) cc_final: 0.7609 (mmt) REVERT: E 458 ASP cc_start: 0.6756 (p0) cc_final: 0.5721 (t0) REVERT: G 52 LYS cc_start: 0.7291 (mttm) cc_final: 0.7088 (mmmt) outliers start: 13 outliers final: 9 residues processed: 176 average time/residue: 0.3329 time to fit residues: 91.7097 Evaluate side-chains 164 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.0870 chunk 201 optimal weight: 0.0060 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN B 88 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN F 404 GLN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.128458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.084078 restraints weight = 95578.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083926 restraints weight = 48054.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083865 restraints weight = 40424.108| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22487 Z= 0.123 Angle : 0.623 9.301 30811 Z= 0.321 Chirality : 0.042 0.219 3570 Planarity : 0.005 0.078 3732 Dihedral : 12.447 122.563 3772 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.43 % Favored : 91.53 % Rotamer: Outliers : 2.91 % Allowed : 16.45 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2639 helix: -0.22 (0.17), residues: 949 sheet: -1.93 (0.32), residues: 232 loop : -2.49 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 506 HIS 0.006 0.001 HIS E 464 PHE 0.020 0.001 PHE E 357 TYR 0.017 0.001 TYR E 306 ARG 0.003 0.000 ARG F 443 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 757) hydrogen bonds : angle 5.24470 ( 2092) metal coordination : bond 0.01638 ( 32) metal coordination : angle 4.02565 ( 27) covalent geometry : bond 0.00266 (22455) covalent geometry : angle 0.61164 (30784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 2.550 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: A 110 MET cc_start: 0.8447 (mmm) cc_final: 0.8082 (mmm) REVERT: A 131 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 77 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 79 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8724 (mtpt) REVERT: B 94 MET cc_start: 0.8936 (tmm) cc_final: 0.8726 (tmm) REVERT: F 112 CYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5881 (t) REVERT: F 495 VAL cc_start: -0.0938 (t) cc_final: -0.1523 (t) REVERT: E 194 GLN cc_start: 0.3724 (pt0) cc_final: 0.3359 (tp-100) REVERT: E 274 MET cc_start: 0.8126 (ttm) cc_final: 0.7554 (mmt) REVERT: E 355 TYR cc_start: 0.1935 (OUTLIER) cc_final: 0.0517 (m-80) REVERT: E 458 ASP cc_start: 0.6804 (p0) cc_final: 0.5834 (t0) outliers start: 64 outliers final: 27 residues processed: 237 average time/residue: 0.3372 time to fit residues: 126.1990 Evaluate side-chains 196 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 355 TYR Chi-restraints excluded: chain E residue 499 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 222 optimal weight: 0.0010 chunk 262 optimal weight: 2.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN F 492 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.128588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082834 restraints weight = 104297.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083710 restraints weight = 52186.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083824 restraints weight = 33806.745| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22487 Z= 0.148 Angle : 0.620 10.042 30811 Z= 0.316 Chirality : 0.042 0.220 3570 Planarity : 0.004 0.051 3732 Dihedral : 12.301 122.483 3756 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.13 % Favored : 91.83 % Rotamer: Outliers : 2.60 % Allowed : 19.32 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2639 helix: -0.09 (0.17), residues: 952 sheet: -1.85 (0.33), residues: 222 loop : -2.47 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 506 HIS 0.004 0.001 HIS E 464 PHE 0.013 0.001 PHE E 357 TYR 0.025 0.001 TYR F 298 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 757) hydrogen bonds : angle 5.08668 ( 2092) metal coordination : bond 0.01589 ( 32) metal coordination : angle 4.05769 ( 27) covalent geometry : bond 0.00329 (22455) covalent geometry : angle 0.60876 (30784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8503 (mmm) cc_final: 0.7802 (mmm) REVERT: A 131 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 608 ASP cc_start: 0.7992 (m-30) cc_final: 0.7719 (m-30) REVERT: B 77 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 28 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8296 (tp) REVERT: F 112 CYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5934 (t) REVERT: E 194 GLN cc_start: 0.3867 (pt0) cc_final: 0.3546 (tp-100) REVERT: E 274 MET cc_start: 0.8116 (ttm) cc_final: 0.7565 (mmt) REVERT: E 458 ASP cc_start: 0.6625 (p0) cc_final: 0.5530 (t0) outliers start: 57 outliers final: 39 residues processed: 224 average time/residue: 0.3171 time to fit residues: 114.0920 Evaluate side-chains 200 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 108 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 265 optimal weight: 0.5980 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 185 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.129959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085645 restraints weight = 121884.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084759 restraints weight = 52452.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086053 restraints weight = 36989.760| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22487 Z= 0.135 Angle : 0.596 8.495 30811 Z= 0.304 Chirality : 0.041 0.220 3570 Planarity : 0.004 0.053 3732 Dihedral : 12.184 121.727 3756 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.43 % Favored : 91.53 % Rotamer: Outliers : 2.82 % Allowed : 19.36 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2639 helix: 0.00 (0.17), residues: 956 sheet: -1.67 (0.34), residues: 219 loop : -2.40 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 114 HIS 0.004 0.001 HIS E 464 PHE 0.013 0.001 PHE A 396 TYR 0.021 0.001 TYR F 298 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 757) hydrogen bonds : angle 4.90386 ( 2092) metal coordination : bond 0.01483 ( 32) metal coordination : angle 3.95446 ( 27) covalent geometry : bond 0.00306 (22455) covalent geometry : angle 0.58456 (30784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8527 (mmm) cc_final: 0.8057 (mmm) REVERT: A 131 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 608 ASP cc_start: 0.7916 (m-30) cc_final: 0.7663 (m-30) REVERT: A 892 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: B 77 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 106 PHE cc_start: 0.6384 (t80) cc_final: 0.6155 (t80) REVERT: F 112 CYS cc_start: 0.6584 (OUTLIER) cc_final: 0.5950 (t) REVERT: F 495 VAL cc_start: -0.0920 (t) cc_final: -0.1260 (t) REVERT: E 194 GLN cc_start: 0.3802 (pt0) cc_final: 0.3539 (tp-100) REVERT: E 274 MET cc_start: 0.8057 (ttm) cc_final: 0.7487 (mmt) REVERT: E 458 ASP cc_start: 0.6545 (p0) cc_final: 0.5480 (t0) REVERT: E 511 PHE cc_start: 0.3560 (OUTLIER) cc_final: 0.3331 (t80) outliers start: 62 outliers final: 43 residues processed: 221 average time/residue: 0.3341 time to fit residues: 117.1531 Evaluate side-chains 206 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 108 optimal weight: 0.0970 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 214 optimal weight: 0.0010 chunk 126 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.130276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084498 restraints weight = 102730.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085306 restraints weight = 50536.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085730 restraints weight = 33767.401| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22487 Z= 0.123 Angle : 0.588 11.128 30811 Z= 0.297 Chirality : 0.040 0.219 3570 Planarity : 0.004 0.053 3732 Dihedral : 12.076 121.476 3756 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.13 % Favored : 91.83 % Rotamer: Outliers : 2.60 % Allowed : 19.98 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.90 (0.16), residues: 2639 helix: 0.14 (0.17), residues: 953 sheet: -1.38 (0.36), residues: 199 loop : -2.30 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 114 HIS 0.005 0.001 HIS E 464 PHE 0.010 0.001 PHE E 291 TYR 0.017 0.001 TYR F 298 ARG 0.008 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 757) hydrogen bonds : angle 4.70037 ( 2092) metal coordination : bond 0.01451 ( 32) metal coordination : angle 3.83035 ( 27) covalent geometry : bond 0.00279 (22455) covalent geometry : angle 0.57678 (30784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8507 (mmm) cc_final: 0.7959 (mmm) REVERT: A 131 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 235 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: A 608 ASP cc_start: 0.7872 (m-30) cc_final: 0.7619 (m-30) REVERT: A 892 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8365 (t-90) REVERT: A 899 MET cc_start: 0.7356 (ttm) cc_final: 0.7111 (ttm) REVERT: B 77 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7932 (tm-30) REVERT: C 28 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8259 (tp) REVERT: F 106 PHE cc_start: 0.6394 (t80) cc_final: 0.6190 (t80) REVERT: F 112 CYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5869 (t) REVERT: F 130 LEU cc_start: 0.7564 (mt) cc_final: 0.7068 (tp) REVERT: F 233 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7119 (ppp) REVERT: F 495 VAL cc_start: -0.1282 (t) cc_final: -0.1654 (t) REVERT: E 177 ASN cc_start: 0.3039 (OUTLIER) cc_final: 0.2270 (p0) REVERT: E 270 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6755 (tp40) REVERT: E 274 MET cc_start: 0.8072 (ttm) cc_final: 0.7489 (mmt) REVERT: E 458 ASP cc_start: 0.6509 (p0) cc_final: 0.5416 (t0) REVERT: E 511 PHE cc_start: 0.3433 (OUTLIER) cc_final: 0.3228 (t80) REVERT: G 12 MET cc_start: 0.4725 (tmm) cc_final: 0.4501 (tmm) outliers start: 57 outliers final: 42 residues processed: 217 average time/residue: 0.3284 time to fit residues: 113.4322 Evaluate side-chains 206 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 141 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 111 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 265 ASN ** 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 = 0.4193 r_free = 0.4193 target = 0.130143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085788 restraints weight = 110022.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085780 restraints weight = 51721.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085652 restraints weight = 37556.538| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22487 Z= 0.132 Angle : 0.598 15.430 30811 Z= 0.298 Chirality : 0.041 0.220 3570 Planarity : 0.004 0.053 3732 Dihedral : 12.021 121.377 3756 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 3.09 % Allowed : 20.11 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.82 (0.16), residues: 2639 helix: 0.19 (0.17), residues: 950 sheet: -1.26 (0.36), residues: 212 loop : -2.26 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 114 HIS 0.004 0.001 HIS E 464 PHE 0.016 0.001 PHE D 15 TYR 0.017 0.001 TYR D 12 ARG 0.004 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 757) hydrogen bonds : angle 4.65114 ( 2092) metal coordination : bond 0.01468 ( 32) metal coordination : angle 3.94876 ( 27) covalent geometry : bond 0.00300 (22455) covalent geometry : angle 0.58641 (30784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8492 (mmm) cc_final: 0.7999 (mmm) REVERT: A 131 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 235 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: A 462 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8120 (p) REVERT: A 608 ASP cc_start: 0.7876 (m-30) cc_final: 0.7613 (m-30) REVERT: A 633 MET cc_start: 0.8659 (tmm) cc_final: 0.8448 (tmm) REVERT: A 892 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8298 (t-90) REVERT: A 899 MET cc_start: 0.6602 (ttm) cc_final: 0.6285 (ttm) REVERT: B 77 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 79 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8705 (mppt) REVERT: C 28 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 138 TYR cc_start: 0.8608 (t80) cc_final: 0.8379 (t80) REVERT: F 106 PHE cc_start: 0.6482 (t80) cc_final: 0.6273 (t80) REVERT: F 112 CYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5908 (t) REVERT: F 130 LEU cc_start: 0.7618 (mt) cc_final: 0.7119 (tp) REVERT: F 147 LEU cc_start: 0.8580 (tp) cc_final: 0.8019 (mm) REVERT: F 233 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7226 (ppp) REVERT: F 495 VAL cc_start: -0.1238 (t) cc_final: -0.1592 (t) REVERT: E 160 ASP cc_start: 0.7441 (m-30) cc_final: 0.6983 (p0) REVERT: E 177 ASN cc_start: 0.3005 (OUTLIER) cc_final: 0.2404 (p0) REVERT: E 270 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6885 (tp40) REVERT: E 274 MET cc_start: 0.8090 (ttm) cc_final: 0.7485 (mmm) REVERT: E 458 ASP cc_start: 0.6518 (p0) cc_final: 0.5459 (t0) REVERT: E 511 PHE cc_start: 0.3302 (OUTLIER) cc_final: 0.3056 (t80) REVERT: G 12 MET cc_start: 0.4583 (tmm) cc_final: 0.4364 (tmm) REVERT: G 92 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7241 (ttpt) outliers start: 68 outliers final: 46 residues processed: 219 average time/residue: 0.3263 time to fit residues: 113.9776 Evaluate side-chains 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 228 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.133118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085845 restraints weight = 98517.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086770 restraints weight = 51679.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086711 restraints weight = 33385.721| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22487 Z= 0.130 Angle : 0.590 13.163 30811 Z= 0.296 Chirality : 0.040 0.220 3570 Planarity : 0.004 0.052 3732 Dihedral : 11.993 121.213 3756 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 3.18 % Allowed : 20.47 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.72 (0.16), residues: 2639 helix: 0.29 (0.18), residues: 937 sheet: -1.27 (0.35), residues: 219 loop : -2.18 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 506 HIS 0.004 0.001 HIS E 464 PHE 0.014 0.001 PHE E 291 TYR 0.019 0.001 TYR D 12 ARG 0.003 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 757) hydrogen bonds : angle 4.59298 ( 2092) metal coordination : bond 0.01454 ( 32) metal coordination : angle 3.84719 ( 27) covalent geometry : bond 0.00297 (22455) covalent geometry : angle 0.57889 (30784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8487 (mmm) cc_final: 0.8056 (mmm) REVERT: A 131 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 235 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: A 462 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8128 (p) REVERT: A 608 ASP cc_start: 0.7770 (m-30) cc_final: 0.7527 (m-30) REVERT: A 892 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8326 (t-90) REVERT: A 899 MET cc_start: 0.6176 (ttm) cc_final: 0.5935 (ttm) REVERT: B 77 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 79 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8709 (mppt) REVERT: C 28 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8287 (tp) REVERT: D 138 TYR cc_start: 0.8656 (t80) cc_final: 0.8433 (t80) REVERT: F 106 PHE cc_start: 0.6505 (t80) cc_final: 0.6298 (t80) REVERT: F 112 CYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5850 (t) REVERT: F 130 LEU cc_start: 0.7623 (mt) cc_final: 0.7141 (tp) REVERT: F 147 LEU cc_start: 0.8427 (tp) cc_final: 0.7864 (mm) REVERT: F 495 VAL cc_start: -0.1189 (t) cc_final: -0.1541 (t) REVERT: E 270 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6923 (tp40) REVERT: E 274 MET cc_start: 0.8061 (ttm) cc_final: 0.7482 (mmm) REVERT: E 458 ASP cc_start: 0.6519 (p0) cc_final: 0.5483 (t0) REVERT: E 511 PHE cc_start: 0.3323 (OUTLIER) cc_final: 0.3117 (t80) REVERT: G 12 MET cc_start: 0.4573 (tmm) cc_final: 0.4350 (tmm) outliers start: 70 outliers final: 46 residues processed: 221 average time/residue: 0.3915 time to fit residues: 141.1910 Evaluate side-chains 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 103 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 265 ASN ** 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 = 0.4180 r_free = 0.4180 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084280 restraints weight = 105292.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084843 restraints weight = 51584.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.084847 restraints weight = 34722.514| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22487 Z= 0.156 Angle : 0.606 13.228 30811 Z= 0.304 Chirality : 0.041 0.222 3570 Planarity : 0.004 0.052 3732 Dihedral : 11.986 121.435 3756 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.62 % Favored : 91.34 % Rotamer: Outliers : 3.04 % Allowed : 21.00 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.68 (0.16), residues: 2639 helix: 0.35 (0.18), residues: 920 sheet: -1.15 (0.36), residues: 217 loop : -2.16 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 506 HIS 0.004 0.001 HIS E 464 PHE 0.012 0.001 PHE A 694 TYR 0.019 0.001 TYR D 12 ARG 0.003 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 757) hydrogen bonds : angle 4.66781 ( 2092) metal coordination : bond 0.01542 ( 32) metal coordination : angle 3.88758 ( 27) covalent geometry : bond 0.00360 (22455) covalent geometry : angle 0.59565 (30784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8488 (mmm) cc_final: 0.8066 (mmm) REVERT: A 131 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 235 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: A 462 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 608 ASP cc_start: 0.7865 (m-30) cc_final: 0.7584 (m-30) REVERT: A 892 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8339 (t-90) REVERT: A 906 MET cc_start: 0.4550 (mmm) cc_final: 0.4200 (mmm) REVERT: B 77 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 79 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8693 (mppt) REVERT: C 28 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8337 (tp) REVERT: D 138 TYR cc_start: 0.8646 (t80) cc_final: 0.8445 (t80) REVERT: F 106 PHE cc_start: 0.6590 (t80) cc_final: 0.6377 (t80) REVERT: F 112 CYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6059 (t) REVERT: F 130 LEU cc_start: 0.7587 (mt) cc_final: 0.7098 (tp) REVERT: F 147 LEU cc_start: 0.8395 (tp) cc_final: 0.7873 (mm) REVERT: F 495 VAL cc_start: -0.1195 (t) cc_final: -0.1546 (t) REVERT: E 160 ASP cc_start: 0.7502 (m-30) cc_final: 0.6951 (p0) REVERT: E 177 ASN cc_start: 0.3200 (OUTLIER) cc_final: 0.2272 (p0) REVERT: E 270 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6721 (tp40) REVERT: E 274 MET cc_start: 0.8011 (ttm) cc_final: 0.7392 (mmm) REVERT: E 291 PHE cc_start: 0.4742 (m-10) cc_final: 0.4257 (m-10) REVERT: E 458 ASP cc_start: 0.6503 (p0) cc_final: 0.5411 (t0) REVERT: E 511 PHE cc_start: 0.3393 (OUTLIER) cc_final: 0.3134 (t80) REVERT: G 12 MET cc_start: 0.4642 (tmm) cc_final: 0.4416 (tmm) outliers start: 67 outliers final: 50 residues processed: 219 average time/residue: 0.4347 time to fit residues: 153.3447 Evaluate side-chains 213 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 228 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 196 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN D 140 ASN F 489 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.128418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081765 restraints weight = 115990.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081517 restraints weight = 50551.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082367 restraints weight = 37125.096| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22487 Z= 0.238 Angle : 0.694 13.749 30811 Z= 0.348 Chirality : 0.043 0.227 3570 Planarity : 0.004 0.053 3732 Dihedral : 12.157 122.404 3756 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.84 % Favored : 90.09 % Rotamer: Outliers : 3.31 % Allowed : 20.69 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.87 (0.16), residues: 2639 helix: 0.17 (0.17), residues: 924 sheet: -1.30 (0.36), residues: 206 loop : -2.26 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 506 HIS 0.004 0.001 HIS A 256 PHE 0.022 0.002 PHE D 15 TYR 0.024 0.002 TYR D 12 ARG 0.003 0.000 ARG F 443 Details of bonding type rmsd hydrogen bonds : bond 0.05494 ( 757) hydrogen bonds : angle 5.00665 ( 2092) metal coordination : bond 0.01915 ( 32) metal coordination : angle 4.40823 ( 27) covalent geometry : bond 0.00549 (22455) covalent geometry : angle 0.68148 (30784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8552 (mmm) cc_final: 0.8251 (mmm) REVERT: A 131 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8732 (tt) REVERT: A 235 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: A 608 ASP cc_start: 0.8045 (m-30) cc_final: 0.7744 (m-30) REVERT: A 626 MET cc_start: 0.8738 (tpt) cc_final: 0.8220 (tpt) REVERT: A 879 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7863 (t0) REVERT: A 892 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8353 (t-90) REVERT: A 906 MET cc_start: 0.4766 (mmm) cc_final: 0.4403 (mmm) REVERT: B 51 ARG cc_start: 0.8783 (mpt180) cc_final: 0.8498 (mpt180) REVERT: B 77 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 28 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (tp) REVERT: F 112 CYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6655 (t) REVERT: F 130 LEU cc_start: 0.7503 (mt) cc_final: 0.6987 (tp) REVERT: F 147 LEU cc_start: 0.8412 (tp) cc_final: 0.7852 (mm) REVERT: F 299 TYR cc_start: 0.2918 (m-80) cc_final: 0.2615 (m-80) REVERT: F 489 ASN cc_start: -0.2605 (OUTLIER) cc_final: -0.2851 (p0) REVERT: F 495 VAL cc_start: -0.1430 (t) cc_final: -0.1787 (t) REVERT: E 160 ASP cc_start: 0.7602 (m-30) cc_final: 0.7072 (p0) REVERT: E 270 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6868 (tp40) REVERT: E 274 MET cc_start: 0.8026 (ttm) cc_final: 0.7515 (mmt) REVERT: E 458 ASP cc_start: 0.6447 (p0) cc_final: 0.5377 (t0) REVERT: E 511 PHE cc_start: 0.3298 (OUTLIER) cc_final: 0.3020 (t80) outliers start: 73 outliers final: 54 residues processed: 228 average time/residue: 0.3283 time to fit residues: 119.5097 Evaluate side-chains 216 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 489 ASN Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 259 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 254 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.083546 restraints weight = 122975.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082742 restraints weight = 55749.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083796 restraints weight = 40360.865| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 22487 Z= 0.191 Angle : 0.818 59.194 30811 Z= 0.434 Chirality : 0.043 0.306 3570 Planarity : 0.005 0.080 3732 Dihedral : 12.157 122.533 3756 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.76 % Favored : 90.16 % Rotamer: Outliers : 2.91 % Allowed : 21.26 % Favored : 75.83 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.88 (0.16), residues: 2639 helix: 0.17 (0.17), residues: 930 sheet: -1.31 (0.36), residues: 206 loop : -2.27 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 800 HIS 0.003 0.001 HIS E 554 PHE 0.024 0.002 PHE E 291 TYR 0.021 0.001 TYR D 12 ARG 0.003 0.000 ARG F 443 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 757) hydrogen bonds : angle 4.97501 ( 2092) metal coordination : bond 0.01813 ( 32) metal coordination : angle 4.37603 ( 27) covalent geometry : bond 0.00440 (22455) covalent geometry : angle 0.80802 (30784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8583 (mmm) cc_final: 0.8255 (mmm) REVERT: A 131 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 235 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: A 462 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8251 (p) REVERT: A 608 ASP cc_start: 0.8010 (m-30) cc_final: 0.7715 (m-30) REVERT: A 626 MET cc_start: 0.8692 (tpt) cc_final: 0.8140 (tpt) REVERT: A 629 MET cc_start: 0.8470 (mmm) cc_final: 0.8250 (tpp) REVERT: A 892 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.8340 (t-90) REVERT: A 906 MET cc_start: 0.4487 (mmm) cc_final: 0.4048 (mmm) REVERT: B 51 ARG cc_start: 0.8735 (mpt180) cc_final: 0.8441 (mpt180) REVERT: B 77 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 28 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8378 (tp) REVERT: F 106 PHE cc_start: 0.6525 (t80) cc_final: 0.6305 (t80) REVERT: F 112 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6710 (t) REVERT: F 130 LEU cc_start: 0.7509 (mt) cc_final: 0.6998 (tp) REVERT: F 147 LEU cc_start: 0.8379 (tp) cc_final: 0.7845 (mm) REVERT: F 299 TYR cc_start: 0.2877 (m-80) cc_final: 0.2528 (m-80) REVERT: F 495 VAL cc_start: -0.1370 (t) cc_final: -0.1729 (t) REVERT: E 160 ASP cc_start: 0.7533 (m-30) cc_final: 0.7008 (p0) REVERT: E 270 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6743 (tp40) REVERT: E 274 MET cc_start: 0.7990 (ttm) cc_final: 0.7486 (mmt) REVERT: E 458 ASP cc_start: 0.6455 (p0) cc_final: 0.5337 (t0) REVERT: E 511 PHE cc_start: 0.3528 (OUTLIER) cc_final: 0.3237 (t80) outliers start: 64 outliers final: 52 residues processed: 211 average time/residue: 0.3585 time to fit residues: 120.2031 Evaluate side-chains 212 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 574 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080752 restraints weight = 89288.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082162 restraints weight = 51259.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081842 restraints weight = 33881.605| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 22487 Z= 0.191 Angle : 0.818 59.194 30811 Z= 0.434 Chirality : 0.043 0.306 3570 Planarity : 0.005 0.080 3732 Dihedral : 12.157 122.533 3756 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.76 % Favored : 90.16 % Rotamer: Outliers : 2.73 % Allowed : 21.44 % Favored : 75.83 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.88 (0.16), residues: 2639 helix: 0.17 (0.17), residues: 930 sheet: -1.31 (0.36), residues: 206 loop : -2.27 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 800 HIS 0.003 0.001 HIS E 554 PHE 0.024 0.002 PHE E 291 TYR 0.021 0.001 TYR D 12 ARG 0.003 0.000 ARG F 443 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 757) hydrogen bonds : angle 4.97501 ( 2092) metal coordination : bond 0.01813 ( 32) metal coordination : angle 4.37603 ( 27) covalent geometry : bond 0.00440 (22455) covalent geometry : angle 0.80802 (30784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10123.84 seconds wall clock time: 180 minutes 21.68 seconds (10821.68 seconds total)