Starting phenix.real_space_refine on Sat Jul 4 16:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwo_34318/07_2026/8gwo_34318.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} 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, 'GLN:plan1': 1, 'ASN: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: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU: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: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU: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: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU: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: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU: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: 5.41, per 1000 atoms: 0.25 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 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: 2.43 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: 4.54 Time building geometry restraints manager: 2.20 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: 12463 25.26 - 50.51: 778 50.51 - 75.77: 57 75.77 - 101.02: 11 101.02 - 126.28: 1 Dihedral angle restraints: 13310 sinusoidal: 5454 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 13307 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 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 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: 12.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.320 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 15.177 126.279 8242 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 15.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG G 99 TYR 0.049 0.001 TYR D 22 PHE 0.035 0.001 PHE A 396 TRP 0.020 0.002 TRP F 114 HIS 0.006 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.39 (22455) covalent geometry : angle 0.82469 / 0.46 (30784) hydrogen bonds : bond 0.20233 / 13.32 ( 757) hydrogen bonds : angle 7.26002 / 5.09 ( 2092) metal coordination : bond 0.05074 / 2.72 ( 32) metal coordination : angle 4.16521 / 2.65 ( 27) *********************** 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 : 0.514 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: 0.1372 time to fit residues: 37.8005 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 : 0.497 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.0870 chunk 111 optimal weight: 0.7980 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN D 157 GLN 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 = 0.4103 r_free = 0.4103 target = 0.125977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081750 restraints weight = 102859.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080548 restraints weight = 55613.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080369 restraints weight = 45837.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081372 restraints weight = 33528.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081584 restraints weight = 26745.433| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22487 Z= 0.180 Angle : 0.663 8.903 30811 Z= 0.343 Chirality : 0.043 0.225 3570 Planarity : 0.005 0.080 3732 Dihedral : 7.354 123.048 3544 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.03 % Favored : 89.90 % Rotamer: Outliers : 3.31 % Allowed : 17.16 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.16), residues: 2639 helix: -0.34 (0.17), residues: 947 sheet: -2.06 (0.32), residues: 234 loop : -2.59 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.018 0.001 TYR E 306 PHE 0.018 0.001 PHE E 357 TRP 0.017 0.002 TRP E 506 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (22455) covalent geometry : angle 0.65221 / 0.34 (30784) hydrogen bonds : bond 0.05629 / 3.81 ( 757) hydrogen bonds : angle 5.54001 / 3.83 ( 2092) metal coordination : bond 0.01797 / 1.11 ( 32) metal coordination : angle 4.09184 / 2.57 ( 27) *********************** 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 245 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 172 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8502 (mmm) cc_final: 0.7905 (mmm) REVERT: A 131 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 51 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8573 (mpt90) REVERT: B 77 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 94 MET cc_start: 0.8980 (tmm) cc_final: 0.8760 (tmm) REVERT: F 112 CYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6148 (t) REVERT: F 495 VAL cc_start: -0.1073 (t) cc_final: -0.1607 (t) REVERT: E 274 MET cc_start: 0.8022 (ttm) cc_final: 0.7496 (mmt) REVERT: E 355 TYR cc_start: 0.1994 (OUTLIER) cc_final: 0.0607 (m-80) REVERT: E 458 ASP cc_start: 0.6709 (p0) cc_final: 0.5736 (t0) outliers start: 73 outliers final: 34 residues processed: 232 average time/residue: 0.1286 time to fit residues: 47.7949 Evaluate side-chains 200 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 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 231 VAL Chi-restraints excluded: chain A residue 295 HIS 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 463 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 669 CYS 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 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 D residue 160 VAL Chi-restraints excluded: chain F residue 60 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 Chi-restraints excluded: chain E residue 574 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 190 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.128740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085936 restraints weight = 104896.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085463 restraints weight = 51891.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085448 restraints weight = 38852.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.086085 restraints weight = 32696.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086736 restraints weight = 28340.132| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22487 Z= 0.133 Angle : 0.615 10.324 30811 Z= 0.314 Chirality : 0.042 0.232 3570 Planarity : 0.004 0.053 3732 Dihedral : 6.704 121.905 3530 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.91 % Rotamer: Outliers : 2.87 % Allowed : 19.32 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2639 helix: -0.14 (0.17), residues: 952 sheet: -2.01 (0.33), residues: 220 loop : -2.50 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.020 0.001 TYR F 298 PHE 0.016 0.001 PHE A 396 TRP 0.016 0.001 TRP E 506 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22455) covalent geometry : angle 0.60303 / 0.31 (30784) hydrogen bonds : bond 0.04877 / 3.33 ( 757) hydrogen bonds : angle 5.12557 / 3.55 ( 2092) metal coordination : bond 0.01550 / 0.94 ( 32) metal coordination : angle 4.14219 / 2.64 ( 27) *********************** 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 243 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8530 (mmm) cc_final: 0.7903 (mmm) REVERT: A 131 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 51 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8465 (mtt90) REVERT: B 77 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 94 MET cc_start: 0.9014 (tmm) cc_final: 0.8797 (tmm) REVERT: C 28 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8200 (tp) REVERT: F 112 CYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6060 (t) REVERT: F 495 VAL cc_start: -0.1557 (t) cc_final: -0.2188 (t) REVERT: E 274 MET cc_start: 0.8108 (ttm) cc_final: 0.7539 (mmt) REVERT: E 458 ASP cc_start: 0.6514 (p0) cc_final: 0.5438 (t0) outliers start: 63 outliers final: 38 residues processed: 233 average time/residue: 0.1311 time to fit residues: 47.9261 Evaluate side-chains 203 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 224 GLN 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 463 MET 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 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain B residue 83 VAL 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 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 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 G residue 62 THR 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 56 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 161 optimal weight: 0.0370 chunk 38 optimal weight: 0.0980 chunk 85 optimal weight: 0.0470 chunk 125 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN ** A 295 HIS ** 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** E 290 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.131257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086147 restraints weight = 107053.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086777 restraints weight = 53411.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086566 restraints weight = 36858.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087129 restraints weight = 38260.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088253 restraints weight = 30114.820| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 22487 Z= 0.108 Angle : 0.583 8.458 30811 Z= 0.297 Chirality : 0.041 0.215 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.295 121.008 3528 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.44 % Rotamer: Outliers : 2.07 % Allowed : 19.98 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2639 helix: 0.05 (0.17), residues: 958 sheet: -1.69 (0.34), residues: 209 loop : -2.37 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 733 TYR 0.018 0.001 TYR F 298 PHE 0.011 0.001 PHE A 422 TRP 0.015 0.001 TRP E 114 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (22455) covalent geometry : angle 0.57280 / 0.30 (30784) hydrogen bonds : bond 0.04296 / 2.97 ( 757) hydrogen bonds : angle 4.77144 / 3.32 ( 2092) metal coordination : bond 0.01369 / 0.85 ( 32) metal coordination : angle 3.75431 / 2.38 ( 27) *********************** 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 235 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8514 (mmm) cc_final: 0.7835 (mmm) REVERT: A 131 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 235 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: A 608 ASP cc_start: 0.7809 (m-30) cc_final: 0.7546 (m-30) REVERT: A 626 MET cc_start: 0.8617 (mmm) cc_final: 0.8280 (tpt) REVERT: A 633 MET cc_start: 0.8941 (tmm) cc_final: 0.8673 (tmm) REVERT: A 684 ASP cc_start: 0.7857 (p0) cc_final: 0.7653 (p0) REVERT: A 892 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8371 (t-90) REVERT: A 899 MET cc_start: 0.7582 (ttm) cc_final: 0.7290 (ttp) REVERT: B 77 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7969 (tm-30) REVERT: D 114 CYS cc_start: 0.7950 (m) cc_final: 0.7472 (m) REVERT: F 112 CYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5786 (t) REVERT: F 254 PRO cc_start: 0.4210 (Cg_exo) cc_final: 0.3905 (Cg_endo) REVERT: F 495 VAL cc_start: -0.1361 (t) cc_final: -0.1757 (t) REVERT: E 274 MET cc_start: 0.8074 (ttm) cc_final: 0.7509 (mmt) REVERT: E 291 PHE cc_start: 0.4594 (m-10) cc_final: 0.4370 (m-10) REVERT: E 458 ASP cc_start: 0.6523 (p0) cc_final: 0.5423 (t0) REVERT: E 511 PHE cc_start: 0.3521 (OUTLIER) cc_final: 0.3306 (t80) REVERT: G 19 THR cc_start: 0.6285 (OUTLIER) cc_final: 0.6064 (m) outliers start: 45 outliers final: 30 residues processed: 228 average time/residue: 0.1372 time to fit residues: 49.8433 Evaluate side-chains 199 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 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 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 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 892 HIS 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 56 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 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 274 MET 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 366 THR Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 19 THR 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 215 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.124232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079266 restraints weight = 126780.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.078372 restraints weight = 55348.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079196 restraints weight = 40760.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079396 restraints weight = 31514.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079775 restraints weight = 29483.832| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 22487 Z= 0.368 Angle : 0.795 10.962 30811 Z= 0.405 Chirality : 0.047 0.234 3570 Planarity : 0.005 0.054 3732 Dihedral : 7.002 123.125 3528 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.17 % Favored : 88.76 % Rotamer: Outliers : 4.19 % Allowed : 20.03 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.16), residues: 2639 helix: -0.40 (0.17), residues: 958 sheet: -1.69 (0.35), residues: 203 loop : -2.58 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 75 TYR 0.030 0.002 TYR F 298 PHE 0.024 0.002 PHE E 475 TRP 0.011 0.002 TRP A 290 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.37 (22455) covalent geometry : angle 0.78048 / 0.40 (30784) hydrogen bonds : bond 0.06364 / 4.27 ( 757) hydrogen bonds : angle 5.58171 / 3.87 ( 2092) metal coordination : bond 0.02362 / 1.38 ( 32) metal coordination : angle 5.17878 / 3.44 ( 27) *********************** 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 252 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 159 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8596 (mmm) cc_final: 0.8252 (mmm) REVERT: A 124 MET cc_start: 0.8770 (ttm) cc_final: 0.8368 (ttt) REVERT: A 235 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: A 462 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 608 ASP cc_start: 0.8109 (m-30) cc_final: 0.7854 (m-30) REVERT: A 879 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (t0) REVERT: A 899 MET cc_start: 0.7013 (ttm) cc_final: 0.6673 (ttm) REVERT: B 51 ARG cc_start: 0.8843 (mtp85) cc_final: 0.8540 (mtt90) REVERT: B 77 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 28 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 129 MET cc_start: 0.8271 (mpp) cc_final: 0.7963 (mpp) REVERT: F 112 CYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6729 (t) REVERT: E 274 MET cc_start: 0.8072 (ttm) cc_final: 0.7494 (mmt) REVERT: E 291 PHE cc_start: 0.5012 (m-10) cc_final: 0.4449 (m-10) REVERT: E 295 LEU cc_start: 0.8281 (mt) cc_final: 0.8074 (mt) REVERT: E 458 ASP cc_start: 0.6548 (p0) cc_final: 0.5509 (t0) REVERT: E 511 PHE cc_start: 0.3401 (OUTLIER) cc_final: 0.3125 (t80) REVERT: G 19 THR cc_start: 0.6235 (OUTLIER) cc_final: 0.6016 (m) outliers start: 93 outliers final: 65 residues processed: 241 average time/residue: 0.1327 time to fit residues: 50.8156 Evaluate side-chains 222 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 373 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 720 VAL 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 856 ILE Chi-restraints excluded: chain A residue 879 ASP 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 70 MET 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 120 ILE 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 274 MET Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 466 ASP 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 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 437 PHE 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 19 THR Chi-restraints excluded: chain G residue 25 ASP 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 245 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082622 restraints weight = 123802.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082080 restraints weight = 52914.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082714 restraints weight = 38939.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082897 restraints weight = 30517.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083178 restraints weight = 28846.425| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22487 Z= 0.163 Angle : 0.635 14.390 30811 Z= 0.321 Chirality : 0.042 0.222 3570 Planarity : 0.004 0.057 3732 Dihedral : 6.619 121.944 3528 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.70 % Favored : 91.26 % Rotamer: Outliers : 3.48 % Allowed : 21.48 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.16), residues: 2639 helix: -0.09 (0.17), residues: 946 sheet: -1.66 (0.35), residues: 213 loop : -2.44 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 390 TYR 0.019 0.001 TYR F 298 PHE 0.017 0.001 PHE F 106 TRP 0.015 0.001 TRP F 114 HIS 0.004 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (22455) covalent geometry : angle 0.62043 / 0.32 (30784) hydrogen bonds : bond 0.05026 / 3.41 ( 757) hydrogen bonds : angle 5.00910 / 3.48 ( 2092) metal coordination : bond 0.01655 / 1.00 ( 32) metal coordination : angle 4.54265 / 3.02 ( 27) *********************** 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 233 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 156 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8556 (mmm) cc_final: 0.8182 (mmm) REVERT: A 124 MET cc_start: 0.8565 (ttm) cc_final: 0.8164 (ttt) REVERT: A 235 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: A 608 ASP cc_start: 0.8002 (m-30) cc_final: 0.7733 (m-30) REVERT: A 666 MET cc_start: 0.8872 (mmm) cc_final: 0.8641 (mtp) REVERT: A 879 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7769 (t0) REVERT: A 892 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8382 (t-90) REVERT: B 77 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 28 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (tp) REVERT: D 129 MET cc_start: 0.8098 (mpp) cc_final: 0.7851 (mpp) REVERT: F 112 CYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6464 (t) REVERT: F 130 LEU cc_start: 0.7629 (mt) cc_final: 0.7119 (tp) REVERT: F 147 LEU cc_start: 0.8508 (tp) cc_final: 0.7948 (mm) REVERT: F 293 ILE cc_start: 0.5036 (mt) cc_final: 0.4685 (mm) REVERT: F 299 TYR cc_start: 0.3114 (m-80) cc_final: 0.2882 (m-80) REVERT: F 495 VAL cc_start: -0.1490 (t) cc_final: -0.2141 (t) REVERT: E 274 MET cc_start: 0.8041 (ttm) cc_final: 0.7578 (mmt) REVERT: E 291 PHE cc_start: 0.5009 (m-10) cc_final: 0.4404 (m-10) REVERT: E 295 LEU cc_start: 0.8212 (mt) cc_final: 0.7993 (mt) REVERT: E 458 ASP cc_start: 0.6531 (p0) cc_final: 0.5473 (t0) REVERT: E 511 PHE cc_start: 0.3377 (OUTLIER) cc_final: 0.3121 (t80) outliers start: 77 outliers final: 50 residues processed: 225 average time/residue: 0.1369 time to fit residues: 48.8118 Evaluate side-chains 208 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 120 THR 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 366 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 669 CYS 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 A residue 879 ASP 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 50 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 28 LEU 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 2 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 372 VAL 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 272 VAL 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 Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 0 optimal weight: 5.9990 chunk 249 optimal weight: 0.0060 chunk 15 optimal weight: 0.0470 chunk 188 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 102 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 264 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 overall best weight: 0.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.133158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088730 restraints weight = 106754.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089839 restraints weight = 54960.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089553 restraints weight = 34191.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090220 restraints weight = 35873.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.091304 restraints weight = 28068.723| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22487 Z= 0.107 Angle : 0.592 13.794 30811 Z= 0.296 Chirality : 0.040 0.211 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.089 120.351 3528 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.79 % Favored : 92.18 % Rotamer: Outliers : 2.21 % Allowed : 22.98 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2639 helix: 0.30 (0.18), residues: 927 sheet: -1.31 (0.36), residues: 206 loop : -2.24 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 248 TYR 0.018 0.001 TYR D 138 PHE 0.019 0.001 PHE F 106 TRP 0.022 0.001 TRP D 182 HIS 0.006 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (22455) covalent geometry : angle 0.58134 / 0.30 (30784) hydrogen bonds : bond 0.04036 / 2.82 ( 757) hydrogen bonds : angle 4.51152 / 3.14 ( 2092) metal coordination : bond 0.01305 / 0.81 ( 32) metal coordination : angle 3.80370 / 2.56 ( 27) *********************** 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 221 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8563 (mmm) cc_final: 0.8078 (mmm) REVERT: A 124 MET cc_start: 0.8132 (ttm) cc_final: 0.7807 (ttt) REVERT: A 608 ASP cc_start: 0.7628 (m-30) cc_final: 0.7425 (m-30) REVERT: A 633 MET cc_start: 0.8796 (tmm) cc_final: 0.8580 (tmm) REVERT: A 892 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8370 (t-90) REVERT: A 906 MET cc_start: 0.4159 (mmm) cc_final: 0.3804 (mmm) REVERT: B 77 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 28 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8093 (tp) REVERT: D 67 MET cc_start: 0.7418 (ttm) cc_final: 0.7138 (tmm) REVERT: D 114 CYS cc_start: 0.7782 (m) cc_final: 0.7354 (m) REVERT: F 112 CYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5714 (t) REVERT: F 130 LEU cc_start: 0.7572 (mt) cc_final: 0.7112 (tp) REVERT: F 147 LEU cc_start: 0.8350 (tp) cc_final: 0.7812 (mm) REVERT: E 177 ASN cc_start: 0.2932 (OUTLIER) cc_final: 0.2350 (p0) REVERT: E 274 MET cc_start: 0.8040 (ttm) cc_final: 0.7531 (mmt) REVERT: E 291 PHE cc_start: 0.4826 (m-10) cc_final: 0.4200 (m-10) REVERT: E 295 LEU cc_start: 0.8100 (mt) cc_final: 0.7867 (mt) REVERT: E 458 ASP cc_start: 0.6429 (p0) cc_final: 0.5376 (t0) REVERT: E 511 PHE cc_start: 0.3319 (OUTLIER) cc_final: 0.3096 (t80) REVERT: G 92 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7295 (ttpt) outliers start: 48 outliers final: 36 residues processed: 217 average time/residue: 0.1318 time to fit residues: 45.3368 Evaluate side-chains 200 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 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 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 669 CYS 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 892 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 28 LEU 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 144 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 495 VAL 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 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 Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 49 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 156 optimal weight: 0.0040 chunk 241 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4225 r_free = 0.4225 target = 0.133380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087545 restraints weight = 133934.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087203 restraints weight = 57077.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088149 restraints weight = 40198.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088340 restraints weight = 31002.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088852 restraints weight = 29300.744| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22487 Z= 0.128 Angle : 0.609 13.118 30811 Z= 0.303 Chirality : 0.040 0.217 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.083 121.041 3528 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.86 % Favored : 92.10 % Rotamer: Outliers : 2.43 % Allowed : 22.89 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 2639 helix: 0.34 (0.18), residues: 929 sheet: -1.21 (0.36), residues: 205 loop : -2.18 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.022 0.001 TYR F 324 PHE 0.016 0.001 PHE F 343 TRP 0.014 0.001 TRP F 114 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22455) covalent geometry : angle 0.59755 / 0.30 (30784) hydrogen bonds : bond 0.04304 / 2.98 ( 757) hydrogen bonds : angle 4.56556 / 3.17 ( 2092) metal coordination : bond 0.01430 / 0.87 ( 32) metal coordination : angle 3.98126 / 2.62 ( 27) *********************** 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 212 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8515 (mmm) cc_final: 0.8089 (mmm) REVERT: A 124 MET cc_start: 0.8370 (ttm) cc_final: 0.8015 (ttt) REVERT: A 235 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: A 608 ASP cc_start: 0.7717 (m-30) cc_final: 0.7491 (m-30) REVERT: A 892 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8390 (t-90) REVERT: B 77 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7970 (tm-30) REVERT: C 28 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8227 (tp) REVERT: D 67 MET cc_start: 0.7414 (ttm) cc_final: 0.7165 (tmm) REVERT: F 112 CYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5848 (t) REVERT: F 130 LEU cc_start: 0.7576 (mt) cc_final: 0.7110 (tp) REVERT: F 147 LEU cc_start: 0.8365 (tp) cc_final: 0.7841 (mm) REVERT: E 274 MET cc_start: 0.8051 (ttm) cc_final: 0.7826 (tmm) REVERT: E 291 PHE cc_start: 0.4960 (m-10) cc_final: 0.4436 (m-10) REVERT: E 458 ASP cc_start: 0.6449 (p0) cc_final: 0.5431 (t0) REVERT: E 511 PHE cc_start: 0.3265 (OUTLIER) cc_final: 0.3025 (t80) outliers start: 53 outliers final: 43 residues processed: 206 average time/residue: 0.1355 time to fit residues: 44.4635 Evaluate side-chains 203 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 MET 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 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 669 CYS 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 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 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 F residue 2 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 495 VAL 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 272 VAL 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 Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.134043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087823 restraints weight = 113429.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087995 restraints weight = 51102.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088219 restraints weight = 37191.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088409 restraints weight = 37109.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088512 restraints weight = 29938.784| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22487 Z= 0.118 Angle : 0.602 12.501 30811 Z= 0.298 Chirality : 0.040 0.217 3570 Planarity : 0.004 0.056 3732 Dihedral : 6.011 120.929 3528 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.01 % Favored : 91.95 % Rotamer: Outliers : 2.56 % Allowed : 22.67 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2639 helix: 0.41 (0.18), residues: 930 sheet: -1.11 (0.37), residues: 206 loop : -2.12 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 443 TYR 0.022 0.001 TYR D 12 PHE 0.022 0.001 PHE F 106 TRP 0.015 0.001 TRP F 114 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22455) covalent geometry : angle 0.58959 / 0.30 (30784) hydrogen bonds : bond 0.04237 / 2.93 ( 757) hydrogen bonds : angle 4.52734 / 3.14 ( 2092) metal coordination : bond 0.01414 / 0.87 ( 32) metal coordination : angle 4.09065 / 2.67 ( 27) *********************** 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 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8543 (mmm) cc_final: 0.8110 (mmm) REVERT: A 124 MET cc_start: 0.8399 (ttm) cc_final: 0.8065 (ttt) REVERT: A 235 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: A 608 ASP cc_start: 0.7744 (m-30) cc_final: 0.7520 (m-30) REVERT: A 892 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8398 (t-90) REVERT: A 906 MET cc_start: 0.3910 (mmm) cc_final: 0.3657 (mmm) REVERT: B 77 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 3 MET cc_start: 0.6666 (tmm) cc_final: 0.6222 (tmm) REVERT: C 28 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8256 (tp) REVERT: D 67 MET cc_start: 0.7429 (ttm) cc_final: 0.7209 (tmm) REVERT: F 112 CYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6039 (t) REVERT: F 130 LEU cc_start: 0.7612 (mt) cc_final: 0.7145 (tp) REVERT: F 147 LEU cc_start: 0.8453 (tp) cc_final: 0.7894 (mm) REVERT: E 177 ASN cc_start: 0.3049 (OUTLIER) cc_final: 0.2502 (p0) REVERT: E 458 ASP cc_start: 0.6466 (p0) cc_final: 0.5442 (t0) outliers start: 56 outliers final: 42 residues processed: 204 average time/residue: 0.1316 time to fit residues: 43.0272 Evaluate side-chains 200 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 MET 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 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 669 CYS 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 50 ASP 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 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 F residue 2 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 495 VAL 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 272 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 234 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.133230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086384 restraints weight = 103300.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.087213 restraints weight = 52442.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086715 restraints weight = 36529.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087329 restraints weight = 35817.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.087467 restraints weight = 28923.245| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2782 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= 0.141 Angle : 0.622 12.553 30811 Z= 0.307 Chirality : 0.041 0.219 3570 Planarity : 0.004 0.057 3732 Dihedral : 6.055 121.224 3528 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.91 % Rotamer: Outliers : 2.34 % Allowed : 23.07 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2639 helix: 0.44 (0.18), residues: 933 sheet: -1.08 (0.34), residues: 229 loop : -2.19 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 443 TYR 0.024 0.001 TYR D 12 PHE 0.024 0.001 PHE F 106 TRP 0.010 0.001 TRP D 182 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22455) covalent geometry : angle 0.60901 / 0.31 (30784) hydrogen bonds : bond 0.04425 / 3.05 ( 757) hydrogen bonds : angle 4.57421 / 3.17 ( 2092) metal coordination : bond 0.01500 / 0.90 ( 32) metal coordination : angle 4.32979 / 2.79 ( 27) ********************** 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 210 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8497 (mmm) cc_final: 0.8074 (mmm) REVERT: A 124 MET cc_start: 0.8453 (ttm) cc_final: 0.8084 (ttt) REVERT: A 235 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: A 608 ASP cc_start: 0.7822 (m-30) cc_final: 0.7567 (m-30) REVERT: A 892 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8403 (t-90) REVERT: A 906 MET cc_start: 0.3991 (mmm) cc_final: 0.3734 (mmm) REVERT: B 77 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 3 MET cc_start: 0.6701 (tmm) cc_final: 0.6266 (tmm) REVERT: C 28 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8281 (tp) REVERT: D 67 MET cc_start: 0.7424 (ttm) cc_final: 0.7192 (tmm) REVERT: F 112 CYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6206 (t) REVERT: F 130 LEU cc_start: 0.7605 (mt) cc_final: 0.7133 (tp) REVERT: F 147 LEU cc_start: 0.8402 (tp) cc_final: 0.7824 (mm) REVERT: F 414 LYS cc_start: 0.6603 (tmmt) cc_final: 0.6319 (pttt) REVERT: E 458 ASP cc_start: 0.6476 (p0) cc_final: 0.5455 (t0) outliers start: 51 outliers final: 43 residues processed: 205 average time/residue: 0.1296 time to fit residues: 42.3609 Evaluate side-chains 203 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 196 MET 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 544 LEU Chi-restraints excluded: chain A residue 563 CYS 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 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 50 ASP 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 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 F residue 2 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 495 VAL 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 272 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 154 optimal weight: 0.0970 chunk 111 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 212 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.134191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089779 restraints weight = 125905.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088604 restraints weight = 55651.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089752 restraints weight = 40713.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089867 restraints weight = 30896.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090491 restraints weight = 29273.685| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2909 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= 0.117 Angle : 0.607 11.812 30811 Z= 0.299 Chirality : 0.040 0.216 3570 Planarity : 0.004 0.056 3732 Dihedral : 5.961 120.776 3528 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 2.21 % Allowed : 23.29 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2639 helix: 0.51 (0.18), residues: 932 sheet: -1.08 (0.35), residues: 226 loop : -2.10 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.022 0.001 TYR D 12 PHE 0.024 0.001 PHE F 106 TRP 0.013 0.001 TRP D 182 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22455) covalent geometry : angle 0.59532 / 0.30 (30784) hydrogen bonds : bond 0.04188 / 2.90 ( 757) hydrogen bonds : angle 4.46394 / 3.09 ( 2092) metal coordination : bond 0.01396 / 0.86 ( 32) metal coordination : angle 4.05585 / 2.63 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.53 seconds wall clock time: 71 minutes 17.25 seconds (4277.25 seconds total)