Starting phenix.real_space_refine on Fri Aug 7 14:30:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwo_34318/08_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_34318/08_2026/8gwo_34318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwo_34318/08_2026/8gwo_34318.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 5.97, per 1000 atoms: 0.27 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: 1.68 Conformation dependent library (CDL) restraints added in 1.3 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: 2.42 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: 4.43 Time building geometry restraints manager: 2.26 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 1.427 1.075 0.352 2.00e-02 2.50e+03 3.10e+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: 30534 3.65 - 7.30: 233 7.30 - 10.95: 13 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=" OP1 U G 0 " pdb=" P U G 0 " pdb=" OP2 U G 0 " ideal model delta sigma weight residual 119.60 105.17 14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 12400 25.26 - 50.51: 821 50.51 - 75.77: 76 75.77 - 101.02: 12 101.02 - 126.28: 1 Dihedral angle restraints: 13310 sinusoidal: 5454 harmonic: 7856 Sorted by residual: dihedral pdb=" C4' U G 0 " pdb=" C3' U G 0 " pdb=" C2' U G 0 " pdb=" C1' U G 0 " ideal model delta sinusoidal sigma weight residual 36.34 -39.46 75.80 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " pdb=" C1' G I 33 " ideal model delta sinusoidal sigma weight residual 36.35 -36.14 72.48 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' G J 25 " pdb=" C3' G J 25 " pdb=" C2' G J 25 " pdb=" C1' G J 25 " ideal model delta sinusoidal sigma weight residual 36.34 -34.45 70.80 1 3.10e+00 1.04e-01 6.70e+02 ... (remaining 13307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 3560 0.311 - 0.622: 9 0.622 - 0.932: 0 0.932 - 1.243: 0 1.243 - 1.554: 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 2.17 -3.73 -1.55 2.00e-01 2.50e+01 6.04e+01 chirality pdb=" P U J 24 " pdb=" OP1 U J 24 " pdb=" OP2 U J 24 " pdb=" O5' U J 24 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" P U I 13 " pdb=" OP1 U I 13 " pdb=" OP2 U I 13 " pdb=" O5' U I 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (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: 12.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- 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 0.352 22487 Z= 0.376 Angle : 0.853 18.255 30811 Z= 0.464 Chirality : 0.059 1.554 3570 Planarity : 0.005 0.127 3732 Dihedral : 15.757 126.279 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 0.00760 / 0.37 (22455) covalent geometry : angle 0.84395 / 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 : 0.759 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: 0.1490 time to fit residues: 41.5046 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 : 0.788 ------------------------------------------------------------------------------- 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 = 0.125970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081860 restraints weight = 102801.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080654 restraints weight = 55607.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080571 restraints weight = 44224.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081432 restraints weight = 33247.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081806 restraints weight = 26868.941| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 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 = 0.3281 r_free = 0.3281 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: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22487 Z= 0.183 Angle : 0.706 12.711 30811 Z= 0.352 Chirality : 0.046 0.278 3570 Planarity : 0.005 0.078 3732 Dihedral : 8.655 121.050 3544 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.84 % Favored : 90.09 % Rotamer: Outliers : 3.35 % Allowed : 17.07 % Favored : 79.58 % 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: -0.33 (0.17), residues: 946 sheet: -2.15 (0.33), residues: 226 loop : -2.58 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 443 TYR 0.019 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 0.00416 / 0.18 (22455) covalent geometry : angle 0.69570 / 0.35 (30784) hydrogen bonds : bond 0.05628 / 3.81 ( 757) hydrogen bonds : angle 5.57868 / 3.86 ( 2092) metal coordination : bond 0.01799 / 1.11 ( 32) metal coordination : angle 4.08509 / 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 244 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 0.780 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: 0.8506 (mmm) cc_final: 0.7917 (mmm) REVERT: A 131 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 51 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8572 (mpt90) REVERT: B 77 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 94 MET cc_start: 0.8968 (tmm) cc_final: 0.8758 (tmm) REVERT: F 112 CYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6136 (t) REVERT: F 495 VAL cc_start: -0.1115 (t) cc_final: -0.1645 (t) REVERT: E 274 MET cc_start: 0.8002 (ttm) cc_final: 0.7491 (mmt) REVERT: E 458 ASP cc_start: 0.6707 (p0) cc_final: 0.5728 (t0) outliers start: 74 outliers final: 37 residues processed: 231 average time/residue: 0.1447 time to fit residues: 53.4816 Evaluate side-chains 201 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 586 THR 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 759 SER 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 499 PHE Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.125758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081424 restraints weight = 105686.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079714 restraints weight = 55676.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080368 restraints weight = 42263.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080853 restraints weight = 30998.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081074 restraints weight = 26467.965| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22487 Z= 0.179 Angle : 0.675 10.067 30811 Z= 0.336 Chirality : 0.045 0.284 3570 Planarity : 0.004 0.052 3732 Dihedral : 8.245 120.281 3530 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.19 % Favored : 90.73 % Rotamer: Outliers : 3.48 % Allowed : 19.10 % Favored : 77.42 % 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: -2.40 (0.16), residues: 2639 helix: -0.23 (0.17), residues: 950 sheet: -1.98 (0.33), residues: 227 loop : -2.57 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.022 0.001 TYR F 298 PHE 0.015 0.001 PHE A 396 TRP 0.015 0.001 TRP E 114 HIS 0.004 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (22455) covalent geometry : angle 0.66340 / 0.34 (30784) hydrogen bonds : bond 0.05302 / 3.60 ( 757) hydrogen bonds : angle 5.34162 / 3.69 ( 2092) metal coordination : bond 0.01700 / 1.02 ( 32) metal coordination : angle 4.25021 / 2.69 ( 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 247 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8509 (mmm) cc_final: 0.7917 (mmm) REVERT: A 131 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 235 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: B 51 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8508 (mtt90) REVERT: B 77 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7978 (tm-30) REVERT: B 94 MET cc_start: 0.9021 (tmm) cc_final: 0.8772 (tmm) REVERT: C 28 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8264 (tp) REVERT: F 112 CYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6173 (t) REVERT: F 495 VAL cc_start: -0.1355 (t) cc_final: -0.1829 (t) REVERT: E 274 MET cc_start: 0.8106 (ttm) cc_final: 0.7571 (mmt) REVERT: E 458 ASP cc_start: 0.6598 (p0) cc_final: 0.5609 (t0) REVERT: G 92 LYS cc_start: 0.8295 (mmmm) cc_final: 0.7973 (mmmt) outliers start: 77 outliers final: 49 residues processed: 235 average time/residue: 0.1447 time to fit residues: 54.5473 Evaluate side-chains 208 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 189 THR 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 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 410 VAL 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 476 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 758 LEU Chi-restraints excluded: chain A residue 759 SER 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 845 ASP Chi-restraints excluded: chain A residue 888 ILE 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 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 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 E residue 574 CYS Chi-restraints excluded: chain G residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 56 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 chunk 161 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.204 > 50:) chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.130245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085321 restraints weight = 107476.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085864 restraints weight = 53556.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085577 restraints weight = 37339.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086028 restraints weight = 39534.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086809 restraints weight = 31257.210| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 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 = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1739 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= 0.119 Angle : 0.621 8.557 30811 Z= 0.310 Chirality : 0.044 0.274 3570 Planarity : 0.004 0.055 3732 Dihedral : 7.950 119.617 3528 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 2.56 % Allowed : 20.20 % Favored : 77.24 % 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: -2.16 (0.16), residues: 2639 helix: -0.05 (0.17), residues: 957 sheet: -1.76 (0.35), residues: 204 loop : -2.45 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 390 TYR 0.019 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 A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22455) covalent geometry : angle 0.61025 / 0.31 (30784) hydrogen bonds : bond 0.04617 / 3.18 ( 757) hydrogen bonds : angle 4.98074 / 3.45 ( 2092) metal coordination : bond 0.01427 / 0.87 ( 32) metal coordination : angle 3.89575 / 2.46 ( 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 233 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.801 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: 0.8558 (mmm) cc_final: 0.8052 (mmm) REVERT: A 131 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 608 ASP cc_start: 0.7889 (m-30) cc_final: 0.7627 (m-30) REVERT: A 892 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8387 (t-90) REVERT: B 51 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8450 (mtt90) REVERT: B 77 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 28 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8176 (tp) REVERT: F 112 CYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5985 (t) REVERT: F 495 VAL cc_start: -0.0797 (t) cc_final: -0.1134 (t) REVERT: E 274 MET cc_start: 0.8123 (ttm) cc_final: 0.7559 (mmt) REVERT: E 291 PHE cc_start: 0.4803 (m-10) cc_final: 0.4591 (m-10) REVERT: E 458 ASP cc_start: 0.6462 (p0) cc_final: 0.5408 (t0) REVERT: G 19 THR cc_start: 0.6302 (OUTLIER) cc_final: 0.6087 (m) outliers start: 56 outliers final: 39 residues processed: 226 average time/residue: 0.1454 time to fit residues: 52.5730 Evaluate side-chains 204 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 463 MET 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 759 SER Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 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 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 499 PHE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 62 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: 5.9990 chunk 222 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 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 = 0.4184 r_free = 0.4184 target = 0.129512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085527 restraints weight = 126260.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084443 restraints weight = 54964.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085371 restraints weight = 40138.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085504 restraints weight = 31052.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086018 restraints weight = 29736.144| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22487 Z= 0.140 Angle : 0.624 8.074 30811 Z= 0.310 Chirality : 0.043 0.280 3570 Planarity : 0.004 0.055 3732 Dihedral : 7.836 119.893 3528 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.77 % Favored : 91.19 % Rotamer: Outliers : 3.40 % Allowed : 20.16 % Favored : 76.44 % 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: -2.05 (0.16), residues: 2639 helix: 0.05 (0.17), residues: 949 sheet: -1.67 (0.35), residues: 204 loop : -2.38 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 443 TYR 0.018 0.001 TYR F 298 PHE 0.017 0.001 PHE D 15 TRP 0.012 0.001 TRP E 114 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22455) covalent geometry : angle 0.61273 / 0.31 (30784) hydrogen bonds : bond 0.04716 / 3.24 ( 757) hydrogen bonds : angle 4.86925 / 3.38 ( 2092) metal coordination : bond 0.01526 / 0.93 ( 32) metal coordination : angle 4.02558 / 2.67 ( 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 244 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 169 time to evaluate : 0.752 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: 0.8534 (mmm) cc_final: 0.8066 (mmm) REVERT: A 131 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8581 (tt) REVERT: A 235 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: A 462 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 608 ASP cc_start: 0.7929 (m-30) cc_final: 0.7658 (m-30) REVERT: A 879 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7684 (t0) REVERT: A 892 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8396 (t-90) REVERT: B 77 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 28 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8261 (tp) REVERT: F 106 PHE cc_start: 0.6444 (t80) cc_final: 0.6241 (t80) REVERT: F 112 CYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6057 (t) REVERT: F 233 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7148 (ppp) REVERT: F 495 VAL cc_start: -0.1012 (t) cc_final: -0.1387 (t) REVERT: E 194 GLN cc_start: 0.3782 (pt0) cc_final: 0.3526 (tp-100) REVERT: E 274 MET cc_start: 0.8092 (ttm) cc_final: 0.7557 (mmt) REVERT: E 291 PHE cc_start: 0.4840 (m-10) cc_final: 0.4298 (m-10) REVERT: E 458 ASP cc_start: 0.6471 (p0) cc_final: 0.5391 (t0) REVERT: G 19 THR cc_start: 0.6307 (OUTLIER) cc_final: 0.6091 (m) REVERT: G 92 LYS cc_start: 0.8221 (mmmm) cc_final: 0.8018 (mmmt) outliers start: 75 outliers final: 54 residues processed: 236 average time/residue: 0.1346 time to fit residues: 51.1134 Evaluate side-chains 220 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 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 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 720 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 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 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain E residue 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 499 PHE Chi-restraints excluded: chain E residue 570 VAL 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: 0.9990 chunk 121 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 270 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 = 0.4162 r_free = 0.4162 target = 0.128073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084328 restraints weight = 124522.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082913 restraints weight = 55624.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084276 restraints weight = 40002.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084276 restraints weight = 29796.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084823 restraints weight = 28901.316| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22487 Z= 0.192 Angle : 0.674 15.883 30811 Z= 0.330 Chirality : 0.044 0.289 3570 Planarity : 0.004 0.056 3732 Dihedral : 7.910 120.245 3528 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.57 % Favored : 90.35 % Rotamer: Outliers : 4.15 % Allowed : 20.56 % Favored : 75.30 % 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: -2.07 (0.16), residues: 2639 helix: 0.02 (0.17), residues: 944 sheet: -1.61 (0.35), residues: 213 loop : -2.39 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 443 TYR 0.020 0.002 TYR E 269 PHE 0.014 0.001 PHE E 475 TRP 0.009 0.001 TRP E 114 HIS 0.004 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (22455) covalent geometry : angle 0.66203 / 0.33 (30784) hydrogen bonds : bond 0.05165 / 3.52 ( 757) hydrogen bonds : angle 5.01504 / 3.49 ( 2092) metal coordination : bond 0.01725 / 1.03 ( 32) metal coordination : angle 4.29935 / 2.86 ( 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 255 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 163 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8528 (mmm) cc_final: 0.8177 (mmm) REVERT: A 131 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8664 (tt) REVERT: A 235 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 462 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 608 ASP cc_start: 0.7904 (m-30) cc_final: 0.7642 (m-30) REVERT: A 879 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7791 (t0) REVERT: A 892 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8427 (t-90) REVERT: B 77 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 28 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8310 (tp) REVERT: F 106 PHE cc_start: 0.6552 (t80) cc_final: 0.6347 (t80) REVERT: F 112 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6428 (t) REVERT: F 130 LEU cc_start: 0.7646 (mt) cc_final: 0.7139 (tp) REVERT: F 147 LEU cc_start: 0.8467 (tp) cc_final: 0.7925 (mm) REVERT: F 299 TYR cc_start: 0.2900 (m-80) cc_final: 0.2692 (m-80) REVERT: F 495 VAL cc_start: -0.1390 (t) cc_final: -0.1762 (t) REVERT: E 274 MET cc_start: 0.7988 (ttm) cc_final: 0.7446 (mmt) REVERT: E 458 ASP cc_start: 0.6505 (p0) cc_final: 0.5352 (t0) REVERT: G 12 MET cc_start: 0.4808 (tmm) cc_final: 0.4591 (tmm) REVERT: G 19 THR cc_start: 0.6332 (OUTLIER) cc_final: 0.6105 (m) outliers start: 92 outliers final: 67 residues processed: 243 average time/residue: 0.1231 time to fit residues: 48.3631 Evaluate side-chains 230 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 155 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 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 544 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 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 759 SER 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 888 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 898 HIS 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 119 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 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 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 570 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 0 optimal weight: 4.9990 chunk 249 optimal weight: 0.0870 chunk 15 optimal weight: 0.0010 chunk 188 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 264 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN D 140 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.134305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088258 restraints weight = 107224.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089076 restraints weight = 52127.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088590 restraints weight = 37891.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089191 restraints weight = 38722.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090011 restraints weight = 30672.839| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22487 Z= 0.109 Angle : 0.606 13.575 30811 Z= 0.297 Chirality : 0.042 0.269 3570 Planarity : 0.004 0.057 3732 Dihedral : 7.681 119.023 3528 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.59 % Rotamer: Outliers : 2.38 % Allowed : 22.45 % Favored : 75.17 % 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: -1.77 (0.16), residues: 2639 helix: 0.29 (0.18), residues: 931 sheet: -1.35 (0.36), residues: 214 loop : -2.21 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 507 TYR 0.017 0.001 TYR E 269 PHE 0.018 0.001 PHE A 396 TRP 0.020 0.001 TRP F 114 HIS 0.006 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (22455) covalent geometry : angle 0.59633 / 0.30 (30784) hydrogen bonds : bond 0.04223 / 2.94 ( 757) hydrogen bonds : angle 4.55855 / 3.17 ( 2092) metal coordination : bond 0.01344 / 0.83 ( 32) metal coordination : angle 3.78180 / 2.53 ( 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 225 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8539 (mmm) cc_final: 0.8042 (mmm) REVERT: A 131 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8336 (tt) REVERT: A 608 ASP cc_start: 0.7683 (m-30) cc_final: 0.7470 (m-30) REVERT: A 879 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7658 (t0) REVERT: A 892 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8359 (t-90) REVERT: B 77 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7959 (tm-30) REVERT: D 114 CYS cc_start: 0.7906 (m) cc_final: 0.7419 (m) REVERT: F 106 PHE cc_start: 0.6522 (t80) cc_final: 0.6162 (t80) REVERT: F 112 CYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5688 (t) REVERT: F 130 LEU cc_start: 0.7570 (mt) cc_final: 0.7063 (tp) REVERT: F 147 LEU cc_start: 0.8297 (tp) cc_final: 0.7762 (mm) REVERT: F 343 PHE cc_start: -0.0233 (OUTLIER) cc_final: -0.0484 (m-10) REVERT: F 495 VAL cc_start: -0.1151 (t) cc_final: -0.1518 (t) REVERT: E 177 ASN cc_start: 0.2856 (OUTLIER) cc_final: 0.2325 (p0) REVERT: E 274 MET cc_start: 0.8066 (ttm) cc_final: 0.7602 (mmt) REVERT: E 458 ASP cc_start: 0.6379 (p0) cc_final: 0.5284 (t0) REVERT: G 12 MET cc_start: 0.4580 (tmm) cc_final: 0.4370 (tmm) REVERT: G 19 THR cc_start: 0.6435 (OUTLIER) cc_final: 0.6226 (m) REVERT: G 92 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7414 (ttpt) outliers start: 52 outliers final: 34 residues processed: 223 average time/residue: 0.1303 time to fit residues: 46.7480 Evaluate side-chains 199 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 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 372 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 724 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 760 ASP 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 B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 66 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 343 PHE Chi-restraints excluded: chain F residue 372 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 570 VAL Chi-restraints excluded: chain G residue 19 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 151 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 146 optimal weight: 0.0020 overall best weight: 0.7968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 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 = 0.4235 r_free = 0.4235 target = 0.134184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088739 restraints weight = 134529.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088453 restraints weight = 63679.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089604 restraints weight = 44592.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088648 restraints weight = 38701.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089242 restraints weight = 35278.597| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22487 Z= 0.118 Angle : 0.615 13.259 30811 Z= 0.299 Chirality : 0.042 0.275 3570 Planarity : 0.004 0.057 3732 Dihedral : 7.619 119.256 3528 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 2.38 % Allowed : 22.67 % Favored : 74.94 % 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: -1.63 (0.16), residues: 2639 helix: 0.38 (0.18), residues: 929 sheet: -1.11 (0.37), residues: 207 loop : -2.14 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 427 TYR 0.021 0.001 TYR D 12 PHE 0.013 0.001 PHE A 422 TRP 0.014 0.001 TRP E 506 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 0.60522 / 0.30 (30784) hydrogen bonds : bond 0.04298 / 2.97 ( 757) hydrogen bonds : angle 4.56939 / 3.18 ( 2092) metal coordination : bond 0.01417 / 0.87 ( 32) metal coordination : angle 3.79880 / 2.52 ( 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 215 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8499 (mmm) cc_final: 0.8063 (mmm) REVERT: A 124 MET cc_start: 0.8253 (ttm) cc_final: 0.7952 (ttt) REVERT: A 131 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 608 ASP cc_start: 0.7791 (m-30) cc_final: 0.7533 (m-30) REVERT: A 879 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7746 (t0) REVERT: A 892 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: B 77 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 114 CYS cc_start: 0.7976 (m) cc_final: 0.7467 (m) REVERT: F 112 CYS cc_start: 0.6450 (OUTLIER) cc_final: 0.5895 (t) REVERT: F 130 LEU cc_start: 0.7579 (mt) cc_final: 0.7102 (tp) REVERT: F 147 LEU cc_start: 0.8364 (tp) cc_final: 0.7837 (mm) REVERT: F 495 VAL cc_start: -0.1154 (t) cc_final: -0.1510 (t) REVERT: E 274 MET cc_start: 0.8052 (ttm) cc_final: 0.7596 (mmt) REVERT: E 458 ASP cc_start: 0.6486 (p0) cc_final: 0.5376 (t0) REVERT: G 12 MET cc_start: 0.4524 (tmm) cc_final: 0.4323 (tmm) REVERT: G 19 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6277 (m) REVERT: G 92 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7650 (mmtp) outliers start: 52 outliers final: 38 residues processed: 210 average time/residue: 0.1350 time to fit residues: 45.0325 Evaluate side-chains 201 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 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 644 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 759 SER 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 B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 66 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 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 570 VAL Chi-restraints excluded: chain G residue 19 THR 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 172 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 overall best weight: 0.7978 ------------------------------------------------------------------------------- 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 ** E 270 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 = 0.4238 r_free = 0.4238 target = 0.134410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087034 restraints weight = 115165.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.087528 restraints weight = 62146.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087777 restraints weight = 39442.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088389 restraints weight = 32955.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088408 restraints weight = 28284.186| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22487 Z= 0.117 Angle : 0.614 12.844 30811 Z= 0.299 Chirality : 0.042 0.276 3570 Planarity : 0.004 0.056 3732 Dihedral : 7.566 119.177 3528 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 2.38 % Allowed : 22.41 % Favored : 75.21 % 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: -1.56 (0.16), residues: 2639 helix: 0.43 (0.18), residues: 930 sheet: -1.06 (0.36), residues: 207 loop : -2.09 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 507 TYR 0.021 0.001 TYR D 12 PHE 0.019 0.001 PHE A 396 TRP 0.018 0.001 TRP E 506 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 0.60326 / 0.30 (30784) hydrogen bonds : bond 0.04246 / 2.95 ( 757) hydrogen bonds : angle 4.49936 / 3.13 ( 2092) metal coordination : bond 0.01401 / 0.86 ( 32) metal coordination : angle 3.99620 / 2.61 ( 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 218 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8480 (mmm) cc_final: 0.8009 (mmm) REVERT: A 124 MET cc_start: 0.8198 (ttm) cc_final: 0.7843 (ttt) REVERT: A 131 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8566 (tt) REVERT: A 235 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: A 608 ASP cc_start: 0.7764 (m-30) cc_final: 0.7506 (m-30) REVERT: A 879 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (t0) REVERT: A 892 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8387 (t-90) REVERT: B 77 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 3 MET cc_start: 0.6619 (tmm) cc_final: 0.6197 (tmm) REVERT: D 67 MET cc_start: 0.7212 (ttm) cc_final: 0.6895 (tmm) REVERT: D 114 CYS cc_start: 0.7970 (m) cc_final: 0.7432 (m) REVERT: F 106 PHE cc_start: 0.6469 (t80) cc_final: 0.6152 (t80) REVERT: F 112 CYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5699 (t) REVERT: F 130 LEU cc_start: 0.7551 (mt) cc_final: 0.7060 (tp) REVERT: F 147 LEU cc_start: 0.8423 (tp) cc_final: 0.7853 (mm) REVERT: F 495 VAL cc_start: -0.1255 (t) cc_final: -0.1584 (t) REVERT: E 177 ASN cc_start: 0.3354 (OUTLIER) cc_final: 0.2978 (p0) REVERT: E 274 MET cc_start: 0.8051 (ttm) cc_final: 0.7628 (mmt) REVERT: E 458 ASP cc_start: 0.6368 (p0) cc_final: 0.5355 (t0) outliers start: 52 outliers final: 39 residues processed: 215 average time/residue: 0.1317 time to fit residues: 45.3196 Evaluate side-chains 202 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 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 644 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 759 SER 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 B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 66 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 372 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 499 PHE Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 234 optimal weight: 0.9990 chunk 241 optimal weight: 0.5980 chunk 205 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 134 optimal weight: 0.0670 chunk 119 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 270 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 = 0.4298 r_free = 0.4298 target = 0.135592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.091470 restraints weight = 105102.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093325 restraints weight = 53110.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093009 restraints weight = 31119.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.093636 restraints weight = 32527.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093951 restraints weight = 25994.053| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2907 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= 0.106 Angle : 0.620 12.641 30811 Z= 0.299 Chirality : 0.042 0.272 3570 Planarity : 0.004 0.056 3732 Dihedral : 7.493 118.859 3528 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.18 % Favored : 92.78 % Rotamer: Outliers : 2.25 % Allowed : 22.76 % Favored : 74.99 % 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: -1.47 (0.16), residues: 2639 helix: 0.53 (0.18), residues: 927 sheet: -0.94 (0.36), residues: 210 loop : -2.07 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.025 0.001 TYR E 180 PHE 0.017 0.001 PHE F 106 TRP 0.016 0.001 TRP F 114 HIS 0.006 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (22455) covalent geometry : angle 0.60753 / 0.30 (30784) hydrogen bonds : bond 0.04028 / 2.81 ( 757) hydrogen bonds : angle 4.40678 / 3.06 ( 2092) metal coordination : bond 0.01300 / 0.81 ( 32) metal coordination : angle 4.20121 / 2.71 ( 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 216 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8507 (mmm) cc_final: 0.8070 (mmm) REVERT: A 124 MET cc_start: 0.8298 (ttm) cc_final: 0.7980 (ttt) REVERT: A 131 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 235 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: A 608 ASP cc_start: 0.7606 (m-30) cc_final: 0.7378 (m-30) REVERT: A 879 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7618 (t0) REVERT: A 892 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8394 (t-90) REVERT: B 77 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 3 MET cc_start: 0.6556 (tmm) cc_final: 0.6121 (tmm) REVERT: D 67 MET cc_start: 0.7408 (ttm) cc_final: 0.7095 (tmm) REVERT: D 114 CYS cc_start: 0.7801 (m) cc_final: 0.7374 (m) REVERT: D 129 MET cc_start: 0.7649 (mpp) cc_final: 0.7228 (mmt) REVERT: F 106 PHE cc_start: 0.6524 (t80) cc_final: 0.6281 (t80) REVERT: F 112 CYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5856 (t) REVERT: F 130 LEU cc_start: 0.7610 (mt) cc_final: 0.7122 (tp) REVERT: F 147 LEU cc_start: 0.8375 (tp) cc_final: 0.7805 (mm) REVERT: F 495 VAL cc_start: -0.1152 (t) cc_final: -0.1499 (t) REVERT: E 274 MET cc_start: 0.8043 (ttm) cc_final: 0.7559 (mmt) REVERT: E 458 ASP cc_start: 0.6351 (p0) cc_final: 0.5294 (t0) outliers start: 49 outliers final: 40 residues processed: 212 average time/residue: 0.1296 time to fit residues: 44.2355 Evaluate side-chains 207 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 131 LEU 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 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 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 644 THR Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 SER 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 B residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 66 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 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 499 PHE Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** E 270 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 = 0.4277 r_free = 0.4277 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.094236 restraints weight = 127932.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091537 restraints weight = 58892.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.093481 restraints weight = 42905.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.093226 restraints weight = 32428.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093347 restraints weight = 31090.151| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2940 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= 0.134 Angle : 0.635 11.811 30811 Z= 0.308 Chirality : 0.042 0.279 3570 Planarity : 0.004 0.054 3732 Dihedral : 7.511 119.196 3528 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.86 % Favored : 92.10 % Rotamer: Outliers : 2.43 % Allowed : 22.94 % Favored : 74.64 % 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: -1.50 (0.16), residues: 2639 helix: 0.49 (0.18), residues: 935 sheet: -0.90 (0.35), residues: 230 loop : -2.10 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 443 TYR 0.023 0.001 TYR D 12 PHE 0.020 0.001 PHE A 396 TRP 0.022 0.001 TRP E 506 HIS 0.005 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (22455) covalent geometry : angle 0.62381 / 0.31 (30784) hydrogen bonds : bond 0.04310 / 2.97 ( 757) hydrogen bonds : angle 4.48090 / 3.11 ( 2092) metal coordination : bond 0.01441 / 0.87 ( 32) metal coordination : angle 4.03886 / 2.61 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4313.16 seconds wall clock time: 75 minutes 10.32 seconds (4510.32 seconds total)