Starting phenix.real_space_refine on Sun Sep 13 09:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kro_23008/09_2026/7kro_23008.cif" } resolution = 3.6 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= 0.004 sd= 0.091 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 86 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13642 2.51 5 N 3707 2.21 5 O 4383 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21988 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 30, 'TRANS': 896} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "F" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNAv2': 43} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 73.888 58.971 122.812 1.00 38.24 S ATOM 2495 SG CYS A 306 74.634 60.042 126.547 1.00 31.54 S ATOM 2527 SG CYS A 310 75.110 56.427 125.385 1.00 44.33 S ATOM 3935 SG CYS A 487 76.891 72.859 108.537 1.00 38.63 S ATOM 5188 SG CYS A 645 77.165 75.182 111.520 1.00 45.39 S ATOM 5194 SG CYS A 646 75.483 71.788 112.024 1.00 43.78 S ATOM 10924 SG CYS E 5 116.902 64.767 51.873 1.00 53.22 S ATOM 10945 SG CYS E 8 120.444 64.603 52.931 1.00 57.87 S ATOM 11083 SG CYS E 26 119.149 68.046 52.383 1.00 57.27 S ATOM 11104 SG CYS E 29 119.574 66.254 49.466 1.00 62.73 S ATOM 11269 SG CYS E 50 101.114 86.502 49.723 1.00 97.32 S ATOM 11299 SG CYS E 55 99.863 86.541 46.164 1.00111.12 S ATOM 11432 SG CYS E 72 102.870 88.588 47.064 1.00106.78 S ATOM 11006 SG CYS E 16 109.047 68.612 45.257 1.00 52.87 S ATOM 11021 SG CYS E 19 108.372 64.927 44.093 1.00 62.83 S ATOM 15526 SG CYS F 5 66.643 74.883 62.030 1.00 81.43 S ATOM 15547 SG CYS F 8 68.614 74.900 58.897 1.00 81.50 S ATOM 15685 SG CYS F 26 68.910 78.000 60.930 1.00 83.74 S ATOM 15706 SG CYS F 29 65.837 77.641 59.405 1.00 92.86 S ATOM 15871 SG CYS F 50 67.340 92.652 82.281 1.00125.84 S ATOM 15901 SG CYS F 55 63.809 93.919 82.685 1.00143.39 S ATOM 16034 SG CYS F 72 66.234 95.897 80.623 1.00127.64 S ATOM 15608 SG CYS F 16 59.677 79.704 68.992 1.00 68.26 S ATOM 15623 SG CYS F 19 57.173 76.750 68.365 1.00 86.69 S Time building chain proxies: 4.41, per 1000 atoms: 0.20 Number of scatterers: 21988 At special positions: 0 Unit cell: (143.775, 160.815, 184.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 86 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4383 8.00 N 3707 7.00 C 13642 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: 1.74 Conformation dependent library (CDL) restraints added in 866.3 milliseconds 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 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 28 sheets defined 43.5% alpha, 12.9% beta 33 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.511A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (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 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.580A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.647A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.943A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.746A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.680A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 318 removed outlier: 3.529A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.544A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.679A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 468 through 480 removed outlier: 5.061A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.758A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.457A pdb=" N LYS A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.929A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.895A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.310A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.762A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.863A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.607A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 4.003A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.532A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.614A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 902 removed outlier: 3.641A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 924 removed outlier: 4.208A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.646A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.610A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.768A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.608A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.729A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.574A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.854A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 82 removed outlier: 4.373A pdb=" N LYS D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.735A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.802A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.793A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 59 through 62 removed outlier: 3.667A pdb=" N GLN E 62 " --> pdb=" O ASP E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 59 through 62' Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.924A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.596A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 123 removed outlier: 4.002A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 376 through 379 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 433 Processing helix chain 'E' and resid 445 through 455 Processing helix chain 'E' and resid 489 through 500 removed outlier: 3.601A pdb=" N LEU E 500 " --> pdb=" O VAL E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 509 removed outlier: 4.048A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 526 removed outlier: 3.658A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 584 Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 59 through 62 removed outlier: 3.667A pdb=" N GLN F 62 " --> pdb=" O ASP F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 59 through 62' Processing helix chain 'F' and resid 93 through 97 removed outlier: 3.924A pdb=" N CYS F 97 " --> pdb=" O LYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.595A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 removed outlier: 4.003A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 311 through 325 Processing helix chain 'F' and resid 376 through 379 Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 445 through 455 Processing helix chain 'F' and resid 489 through 500 removed outlier: 3.601A pdb=" N LEU F 500 " --> pdb=" O VAL F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 509 removed outlier: 4.049A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.658A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.036A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.507A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.499A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.555A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 132 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.197A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 815 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.452A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.805A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'E' and resid 152 through 157 removed outlier: 7.341A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 347 through 348 removed outlier: 7.134A pdb=" N CYS E 330 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 366 through 367 removed outlier: 6.808A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 474 removed outlier: 6.227A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.805A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.342A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL F 157 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU F 162 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 347 through 348 removed outlier: 7.133A pdb=" N CYS F 330 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N MET F 436 " --> pdb=" O TYR F 277 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR F 279 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 366 through 367 removed outlier: 6.808A pdb=" N THR F 366 " --> pdb=" O ARG F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 471 through 474 removed outlier: 6.227A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR F 541 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLY F 571 " --> pdb=" O TYR F 541 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR F 543 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU F 573 " --> pdb=" O TYR F 543 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE F 545 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE F 575 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR F 547 " --> pdb=" O ILE F 575 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 843 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5398 1.33 - 1.45: 4823 1.45 - 1.57: 11962 1.57 - 1.69: 219 1.69 - 1.81: 220 Bond restraints: 22622 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 22617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 30299 2.23 - 4.47: 694 4.47 - 6.70: 101 6.70 - 8.93: 23 8.93 - 11.17: 5 Bond angle restraints: 31122 Sorted by residual: angle pdb=" N ILE A 856 " pdb=" CA ILE A 856 " pdb=" C ILE A 856 " ideal model delta sigma weight residual 112.96 105.97 6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" C3' C P 25 " pdb=" O3' C P 25 " pdb=" P U P 26 " ideal model delta sigma weight residual 119.70 124.82 -5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 118.59 -8.78 2.21e+00 2.05e-01 1.58e+01 angle pdb=" C PHE F 499 " pdb=" N LEU F 500 " pdb=" CA LEU F 500 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 ... (remaining 31117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 12894 33.68 - 67.37: 419 67.37 - 101.05: 24 101.05 - 134.74: 5 134.74 - 168.42: 2 Dihedral angle restraints: 13344 sinusoidal: 5785 harmonic: 7559 Sorted by residual: dihedral pdb=" C4' C T 8 " pdb=" C3' C T 8 " pdb=" C2' C T 8 " pdb=" C1' C T 8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.29 73.64 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' C T 6 " pdb=" C3' C T 6 " pdb=" C2' C T 6 " pdb=" C1' C T 6 " ideal model delta sinusoidal sigma weight residual 36.34 -36.43 72.77 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' C T 7 " pdb=" C3' C T 7 " pdb=" C2' C T 7 " pdb=" C1' C T 7 " ideal model delta sinusoidal sigma weight residual 36.35 -35.06 71.40 1 3.10e+00 1.04e-01 6.80e+02 ... (remaining 13341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 3614 1.029 - 2.059: 0 2.059 - 3.088: 0 3.088 - 4.118: 0 4.118 - 5.147: 2 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.72 -5.15 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.54 5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" C15 1N7 A1005 " pdb=" C14 1N7 A1005 " pdb=" C16 1N7 A1005 " pdb=" C2 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.47 -2.88 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 3613 not shown) Planarity restraints: 3649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 183 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 927 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 94 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.028 5.00e-02 4.00e+02 ... (remaining 3646 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 39 2.27 - 2.93: 9589 2.93 - 3.59: 32344 3.59 - 4.24: 51457 4.24 - 4.90: 84654 Nonbonded interactions: 178083 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.614 2.170 nonbonded pdb=" O1B ADP A1004 " pdb=" O2A ADP A1004 " model vdw 1.807 3.040 nonbonded pdb=" O3B ADP F1003 " pdb="MG MG F1004 " model vdw 1.841 2.170 nonbonded pdb=" O3B ADP E 704 " pdb="MG MG E 705 " model vdw 1.841 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb=" O2A ADP A1004 " model vdw 1.845 3.040 ... (remaining 178078 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 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 191)) } ncs_group { reference = (chain 'E' and resid 1 through 706) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.810 Find NCS groups from input model: 0.260 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.009 0.204 22654 Z= 0.389 Angle : 0.833 13.316 31148 Z= 0.414 Chirality : 0.136 5.147 3616 Planarity : 0.005 0.104 3649 Dihedral : 15.619 168.423 8470 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 9.40 % Allowed : 10.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -1.73 (0.16), residues: 2541 helix: -0.55 (0.16), residues: 1012 sheet: -1.05 (0.29), residues: 331 loop : -1.64 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 51 TYR 0.023 0.002 TYR A 748 PHE 0.021 0.002 PHE A 920 TRP 0.029 0.002 TRP D 182 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.39 (22622) covalent geometry : angle 0.81768 / 0.41 (31122) hydrogen bonds : bond 0.14522 / 9.94 ( 924) hydrogen bonds : angle 6.21300 / 4.42 ( 2499) metal coordination : bond 0.04120 / 2.36 ( 32) metal coordination : angle 5.56738 / 3.86 ( 26) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 311 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7982 (tp40) REVERT: A 105 ARG cc_start: 0.7475 (tpp80) cc_final: 0.7176 (tpp-160) REVERT: A 131 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8193 (tt) REVERT: A 231 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 280 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 349 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7746 (ttm-80) REVERT: A 542 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7719 (mtt) REVERT: A 610 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: A 633 MET cc_start: 0.8363 (tmm) cc_final: 0.7874 (tmm) REVERT: A 658 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6517 (mt-10) REVERT: A 682 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 807 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7566 (tptp) REVERT: A 855 MET cc_start: 0.7330 (mmt) cc_final: 0.7098 (mmt) REVERT: A 911 ASN cc_start: 0.8238 (t0) cc_final: 0.7862 (t0) REVERT: B 39 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8201 (tppt) REVERT: B 50 ASP cc_start: 0.8418 (t0) cc_final: 0.8092 (t70) REVERT: B 60 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: B 69 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 78 ASP cc_start: 0.7697 (t0) cc_final: 0.7467 (t0) REVERT: B 127 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: D 97 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8222 (ttpt) REVERT: E 62 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: E 122 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8014 (tt) REVERT: E 168 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: E 187 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6936 (p) REVERT: E 194 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: E 261 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: E 319 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7617 (tt0) REVERT: E 327 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (mp) REVERT: E 347 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (ptmm) REVERT: E 350 SER cc_start: 0.7166 (t) cc_final: 0.6821 (t) REVERT: E 465 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.5300 (mptt) REVERT: E 471 CYS cc_start: 0.6925 (m) cc_final: 0.5995 (m) REVERT: E 493 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7786 (tt) REVERT: E 526 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8679 (pp) REVERT: E 543 TYR cc_start: 0.7075 (m-80) cc_final: 0.6593 (m-80) REVERT: F 62 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6584 (pp30) REVERT: F 161 ARG cc_start: 0.5478 (ttp-110) cc_final: 0.4626 (mmm160) REVERT: F 211 TYR cc_start: 0.1296 (p90) cc_final: 0.0823 (p90) REVERT: F 227 LEU cc_start: 0.0908 (OUTLIER) cc_final: 0.0555 (tt) REVERT: F 261 GLU cc_start: 0.3738 (OUTLIER) cc_final: 0.3518 (pm20) REVERT: F 324 TYR cc_start: 0.7395 (m-10) cc_final: 0.7194 (m-10) REVERT: F 378 MET cc_start: 0.7691 (mmm) cc_final: 0.7261 (mmm) REVERT: F 426 CYS cc_start: 0.7415 (m) cc_final: 0.6796 (t) REVERT: F 447 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4754 (tp30) REVERT: F 467 LYS cc_start: 0.5400 (mttt) cc_final: 0.4543 (tptt) REVERT: F 562 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.6629 (t0) outliers start: 209 outliers final: 74 residues processed: 507 average time/residue: 0.1439 time to fit residues: 114.5758 Evaluate side-chains 304 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 202 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 9.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 724 GLN D 65 GLN D 179 ASN F 265 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 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 = 0.3927 r_free = 0.3927 target = 0.149788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107080 restraints weight = 32260.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104506 restraints weight = 37312.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106114 restraints weight = 40688.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106941 restraints weight = 22670.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108347 restraints weight = 19426.753| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22654 Z= 0.154 Angle : 0.739 18.118 31148 Z= 0.341 Chirality : 0.050 0.649 3616 Planarity : 0.004 0.089 3649 Dihedral : 13.086 172.121 3993 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.79 % Favored : 93.90 % Rotamer: Outliers : 5.67 % Allowed : 15.34 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -1.27 (0.16), residues: 2541 helix: 0.02 (0.16), residues: 1036 sheet: -0.91 (0.29), residues: 326 loop : -1.58 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 567 TYR 0.019 0.001 TYR F 224 PHE 0.029 0.001 PHE E 475 TRP 0.027 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (22622) covalent geometry : angle 0.73017 / 0.34 (31122) hydrogen bonds : bond 0.04024 / 2.71 ( 924) hydrogen bonds : angle 4.76403 / 3.39 ( 2499) metal coordination : bond 0.01108 / 0.76 ( 32) metal coordination : angle 3.92328 / 2.45 ( 26) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 229 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7058 (tpp-160) REVERT: A 131 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 610 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: A 613 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7772 (m170) REVERT: A 633 MET cc_start: 0.8552 (tmm) cc_final: 0.7974 (tmm) REVERT: A 658 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6455 (mt-10) REVERT: A 666 MET cc_start: 0.8291 (mmm) cc_final: 0.7982 (mmm) REVERT: A 724 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 791 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (m110) REVERT: A 807 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7275 (tptp) REVERT: A 855 MET cc_start: 0.7256 (mmt) cc_final: 0.7051 (mmt) REVERT: A 911 ASN cc_start: 0.8273 (t0) cc_final: 0.7891 (t0) REVERT: A 928 HIS cc_start: 0.7896 (t70) cc_final: 0.7690 (t-90) REVERT: B 39 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8603 (tptt) REVERT: B 50 ASP cc_start: 0.8209 (t0) cc_final: 0.7841 (t70) REVERT: B 60 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: B 69 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 78 ASP cc_start: 0.7508 (t0) cc_final: 0.7188 (t0) REVERT: B 90 MET cc_start: 0.7906 (ttp) cc_final: 0.7678 (ttp) REVERT: B 127 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (mtpt) REVERT: D 43 ASN cc_start: 0.8678 (m-40) cc_final: 0.8404 (t0) REVERT: D 97 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8312 (ttpt) REVERT: E 62 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7459 (pp30) REVERT: E 235 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8436 (pp) REVERT: E 319 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7563 (tt0) REVERT: E 395 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7913 (m170) REVERT: E 465 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.5310 (mptt) REVERT: E 493 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7702 (tt) REVERT: E 526 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8724 (pp) REVERT: E 543 TYR cc_start: 0.7171 (m-80) cc_final: 0.6672 (m-80) REVERT: F 46 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7762 (p0) REVERT: F 62 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6493 (pp30) REVERT: F 68 MET cc_start: 0.7749 (pmm) cc_final: 0.6907 (mtp) REVERT: F 161 ARG cc_start: 0.5347 (ttp-110) cc_final: 0.4538 (mmm160) REVERT: F 211 TYR cc_start: 0.1623 (p90) cc_final: 0.1050 (p90) REVERT: F 329 LYS cc_start: 0.3725 (OUTLIER) cc_final: 0.2664 (mttt) REVERT: F 562 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6313 (t0) outliers start: 126 outliers final: 73 residues processed: 343 average time/residue: 0.1396 time to fit residues: 75.2442 Evaluate side-chains 284 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 191 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 164 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN D 179 ASN F 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086746 restraints weight = 34100.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090469 restraints weight = 17083.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092971 restraints weight = 11016.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094524 restraints weight = 8286.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095612 restraints weight = 6901.961| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22654 Z= 0.155 Angle : 0.668 10.328 31148 Z= 0.315 Chirality : 0.046 0.401 3616 Planarity : 0.004 0.087 3649 Dihedral : 12.019 176.784 3925 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.86 % Favored : 93.82 % Rotamer: Outliers : 5.31 % Allowed : 16.82 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.99 (0.17), residues: 2541 helix: 0.39 (0.17), residues: 1016 sheet: -0.88 (0.29), residues: 314 loop : -1.51 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.019 0.001 TYR F 224 PHE 0.016 0.001 PHE A 652 TRP 0.027 0.001 TRP D 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22622) covalent geometry : angle 0.65951 / 0.31 (31122) hydrogen bonds : bond 0.03660 / 2.45 ( 924) hydrogen bonds : angle 4.57281 / 3.25 ( 2499) metal coordination : bond 0.00980 / 0.69 ( 32) metal coordination : angle 3.69702 / 2.41 ( 26) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 213 time to evaluate : 0.824 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 5 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7546 (tp40) REVERT: A 110 MET cc_start: 0.8240 (mtp) cc_final: 0.7659 (mmt) REVERT: A 131 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 154 ASP cc_start: 0.8437 (t0) cc_final: 0.8215 (t0) REVERT: A 261 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 555 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7449 (ptp90) REVERT: A 610 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: A 613 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7734 (m170) REVERT: A 633 MET cc_start: 0.8346 (tmm) cc_final: 0.7721 (tmm) REVERT: A 658 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6354 (mt-10) REVERT: A 750 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: A 911 ASN cc_start: 0.8343 (t0) cc_final: 0.7687 (t0) REVERT: A 928 HIS cc_start: 0.8131 (t70) cc_final: 0.7909 (t-90) REVERT: B 19 GLN cc_start: 0.7435 (pt0) cc_final: 0.7228 (tm-30) REVERT: B 35 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6669 (mm) REVERT: B 50 ASP cc_start: 0.8663 (t0) cc_final: 0.8220 (t70) REVERT: B 60 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6090 (tm-30) REVERT: B 78 ASP cc_start: 0.7741 (t0) cc_final: 0.7267 (t0) REVERT: B 96 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: B 127 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7627 (mtpt) REVERT: C 73 GLU cc_start: 0.8242 (tp30) cc_final: 0.7942 (tp30) REVERT: D 43 ASN cc_start: 0.8157 (m-40) cc_final: 0.7561 (t0) REVERT: E 62 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7044 (pp30) REVERT: E 194 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7226 (mm-40) REVERT: E 235 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8179 (pp) REVERT: E 319 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6868 (tt0) REVERT: E 493 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7203 (tt) REVERT: E 526 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8475 (pp) REVERT: E 543 TYR cc_start: 0.7119 (m-80) cc_final: 0.6122 (m-80) REVERT: F 62 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6477 (pp30) REVERT: F 68 MET cc_start: 0.8009 (pmm) cc_final: 0.6803 (mtp) REVERT: F 161 ARG cc_start: 0.5599 (ttp-110) cc_final: 0.4743 (mmm160) REVERT: F 211 TYR cc_start: 0.0210 (p90) cc_final: -0.0300 (p90) REVERT: F 329 LYS cc_start: 0.3539 (OUTLIER) cc_final: 0.3027 (mttt) REVERT: F 395 HIS cc_start: 0.5993 (m90) cc_final: 0.5716 (m170) REVERT: F 436 MET cc_start: 0.6757 (mtm) cc_final: 0.6502 (mtm) REVERT: F 534 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5543 (t70) REVERT: F 562 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6869 (t0) outliers start: 118 outliers final: 74 residues processed: 319 average time/residue: 0.1441 time to fit residues: 73.8447 Evaluate side-chains 288 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 198 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 240 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 95 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN D 158 GLN D 179 ASN E 395 HIS E 516 ASN ** F 562 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 = 0.3945 r_free = 0.3945 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084802 restraints weight = 34289.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088390 restraints weight = 17505.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090799 restraints weight = 11409.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.092298 restraints weight = 8627.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093377 restraints weight = 7215.506| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22654 Z= 0.216 Angle : 0.694 10.178 31148 Z= 0.329 Chirality : 0.047 0.357 3616 Planarity : 0.004 0.091 3649 Dihedral : 11.527 169.893 3893 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.61 % Favored : 93.07 % Rotamer: Outliers : 5.49 % Allowed : 17.81 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.03 (0.17), residues: 2541 helix: 0.37 (0.16), residues: 1021 sheet: -0.77 (0.29), residues: 313 loop : -1.58 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 57 TYR 0.019 0.002 TYR A 903 PHE 0.024 0.002 PHE E 475 TRP 0.024 0.001 TRP D 182 HIS 0.007 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (22622) covalent geometry : angle 0.68522 / 0.33 (31122) hydrogen bonds : bond 0.03892 / 2.60 ( 924) hydrogen bonds : angle 4.59393 / 3.26 ( 2499) metal coordination : bond 0.01299 / 0.96 ( 32) metal coordination : angle 3.94502 / 2.62 ( 26) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 204 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7608 (tp40) REVERT: A 110 MET cc_start: 0.8292 (mtp) cc_final: 0.7693 (mmt) REVERT: A 261 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7637 (tt) REVERT: A 610 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: A 615 MET cc_start: 0.7614 (tpp) cc_final: 0.7331 (tpp) REVERT: A 633 MET cc_start: 0.8343 (tmm) cc_final: 0.7709 (tmm) REVERT: A 658 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6438 (mt-10) REVERT: A 718 LYS cc_start: 0.8199 (tptp) cc_final: 0.7967 (tptt) REVERT: A 750 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7509 (mmm-85) REVERT: A 791 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (m110) REVERT: A 911 ASN cc_start: 0.8370 (t0) cc_final: 0.7699 (t0) REVERT: B 50 ASP cc_start: 0.8617 (t0) cc_final: 0.8238 (t70) REVERT: B 60 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6035 (tm-30) REVERT: B 69 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 78 ASP cc_start: 0.7707 (t0) cc_final: 0.7203 (t0) REVERT: B 96 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7518 (ttm-80) REVERT: B 127 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7645 (mtpt) REVERT: C 50 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7716 (mt-10) REVERT: C 73 GLU cc_start: 0.8324 (tp30) cc_final: 0.8017 (tp30) REVERT: D 43 ASN cc_start: 0.8122 (m-40) cc_final: 0.7470 (t0) REVERT: E 114 TRP cc_start: 0.8289 (m100) cc_final: 0.7937 (m100) REVERT: E 119 ASP cc_start: 0.7054 (t0) cc_final: 0.6846 (t0) REVERT: E 194 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7539 (mm-40) REVERT: E 235 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8345 (pp) REVERT: E 493 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7332 (tt) REVERT: E 526 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8469 (pp) REVERT: E 543 TYR cc_start: 0.7143 (m-80) cc_final: 0.6095 (m-80) REVERT: F 62 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.6390 (pp30) REVERT: F 68 MET cc_start: 0.8208 (pmm) cc_final: 0.7325 (mtp) REVERT: F 161 ARG cc_start: 0.5622 (ttp-110) cc_final: 0.4748 (mmm160) REVERT: F 211 TYR cc_start: 0.0286 (p90) cc_final: -0.0299 (p90) REVERT: F 329 LYS cc_start: 0.3407 (OUTLIER) cc_final: 0.2884 (mttt) REVERT: F 395 HIS cc_start: 0.6508 (m90) cc_final: 0.6192 (m-70) REVERT: F 436 MET cc_start: 0.6824 (mtm) cc_final: 0.6595 (mtm) REVERT: F 534 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6353 (t70) REVERT: F 562 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.6635 (t0) outliers start: 122 outliers final: 81 residues processed: 315 average time/residue: 0.1366 time to fit residues: 69.0827 Evaluate side-chains 279 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 185 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 156 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 241 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 215 optimal weight: 50.0000 chunk 190 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 724 GLN D 179 ASN ** E 404 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 = 0.3928 r_free = 0.3928 target = 0.149900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107027 restraints weight = 31939.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104321 restraints weight = 35260.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106510 restraints weight = 35421.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106565 restraints weight = 20983.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108389 restraints weight = 18810.241| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22654 Z= 0.120 Angle : 0.619 10.341 31148 Z= 0.291 Chirality : 0.044 0.335 3616 Planarity : 0.004 0.083 3649 Dihedral : 10.981 160.582 3885 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.12 % Favored : 94.57 % Rotamer: Outliers : 4.59 % Allowed : 19.25 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.71 (0.17), residues: 2541 helix: 0.68 (0.17), residues: 1011 sheet: -0.62 (0.30), residues: 302 loop : -1.43 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.016 0.001 TYR A 903 PHE 0.015 0.001 PHE A 652 TRP 0.024 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22622) covalent geometry : angle 0.61234 / 0.29 (31122) hydrogen bonds : bond 0.03248 / 2.16 ( 924) hydrogen bonds : angle 4.32501 / 3.08 ( 2499) metal coordination : bond 0.00770 / 0.54 ( 32) metal coordination : angle 3.26598 / 2.04 ( 26) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 209 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8026 (tp40) REVERT: A 466 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 610 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: A 613 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7821 (m170) REVERT: A 633 MET cc_start: 0.8475 (tmm) cc_final: 0.7779 (tmm) REVERT: A 750 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: A 911 ASN cc_start: 0.8249 (t0) cc_final: 0.7829 (t0) REVERT: B 50 ASP cc_start: 0.8168 (t0) cc_final: 0.7884 (t70) REVERT: B 60 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: B 78 ASP cc_start: 0.7364 (t0) cc_final: 0.7043 (t0) REVERT: B 186 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8594 (m) REVERT: C 73 GLU cc_start: 0.7697 (tp30) cc_final: 0.7455 (tp30) REVERT: E 62 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: E 109 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7586 (mp) REVERT: E 114 TRP cc_start: 0.8447 (m100) cc_final: 0.7969 (m100) REVERT: E 119 ASP cc_start: 0.7495 (t0) cc_final: 0.7258 (t0) REVERT: E 235 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8490 (pp) REVERT: E 248 ARG cc_start: 0.7281 (ptm-80) cc_final: 0.6960 (ptm-80) REVERT: E 369 ASP cc_start: 0.8183 (t70) cc_final: 0.7888 (t0) REVERT: E 543 TYR cc_start: 0.7083 (m-80) cc_final: 0.6565 (m-80) REVERT: F 62 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7829 (pp30) REVERT: F 68 MET cc_start: 0.7963 (pmm) cc_final: 0.7447 (mtp) REVERT: F 161 ARG cc_start: 0.5560 (ttp-110) cc_final: 0.4702 (mmm160) REVERT: F 211 TYR cc_start: 0.1533 (p90) cc_final: 0.1218 (p90) REVERT: F 274 MET cc_start: 0.7362 (mmt) cc_final: 0.7079 (mmp) REVERT: F 329 LYS cc_start: 0.3776 (OUTLIER) cc_final: 0.3385 (mttt) REVERT: F 447 GLU cc_start: 0.4820 (OUTLIER) cc_final: 0.3600 (pm20) REVERT: F 534 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6563 (t70) REVERT: F 562 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6180 (t0) outliers start: 102 outliers final: 66 residues processed: 299 average time/residue: 0.1412 time to fit residues: 67.2796 Evaluate side-chains 272 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 34 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 191 optimal weight: 0.0770 chunk 197 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 255 optimal weight: 8.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105188 restraints weight = 32238.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103830 restraints weight = 34654.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104978 restraints weight = 35946.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105782 restraints weight = 20602.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107103 restraints weight = 17740.513| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22654 Z= 0.163 Angle : 0.649 9.087 31148 Z= 0.305 Chirality : 0.045 0.339 3616 Planarity : 0.004 0.086 3649 Dihedral : 10.769 159.631 3871 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 4.77 % Allowed : 19.21 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -0.72 (0.17), residues: 2541 helix: 0.65 (0.17), residues: 1019 sheet: -0.63 (0.30), residues: 315 loop : -1.41 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.001 TYR A 903 PHE 0.037 0.002 PHE E 475 TRP 0.037 0.001 TRP D 182 HIS 0.008 0.001 HIS F 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22622) covalent geometry : angle 0.64167 / 0.30 (31122) hydrogen bonds : bond 0.03494 / 2.32 ( 924) hydrogen bonds : angle 4.33907 / 3.08 ( 2499) metal coordination : bond 0.01013 / 0.75 ( 32) metal coordination : angle 3.38540 / 2.23 ( 26) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 195 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8072 (tp40) REVERT: A 261 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 610 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: A 633 MET cc_start: 0.8524 (tmm) cc_final: 0.7880 (tmm) REVERT: A 724 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 750 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7624 (mmm-85) REVERT: A 911 ASN cc_start: 0.8255 (t0) cc_final: 0.7834 (t0) REVERT: B 50 ASP cc_start: 0.8183 (t0) cc_final: 0.7888 (t70) REVERT: B 60 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: B 62 MET cc_start: 0.7732 (tmm) cc_final: 0.7531 (ttp) REVERT: B 69 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 78 ASP cc_start: 0.7399 (t0) cc_final: 0.7041 (t0) REVERT: B 186 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8601 (m) REVERT: C 73 GLU cc_start: 0.7739 (tp30) cc_final: 0.7509 (tp30) REVERT: E 62 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7361 (pp30) REVERT: E 109 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (mt) REVERT: E 114 TRP cc_start: 0.8485 (m100) cc_final: 0.8063 (m100) REVERT: E 119 ASP cc_start: 0.7491 (t0) cc_final: 0.7287 (t0) REVERT: E 235 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 248 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.7155 (ptm-80) REVERT: E 440 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8313 (t) REVERT: E 543 TYR cc_start: 0.7203 (m-80) cc_final: 0.6620 (m-80) REVERT: F 62 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7816 (pp30) REVERT: F 68 MET cc_start: 0.7969 (pmm) cc_final: 0.7603 (mtp) REVERT: F 161 ARG cc_start: 0.5527 (ttp-110) cc_final: 0.4833 (mmm160) REVERT: F 274 MET cc_start: 0.7334 (mmt) cc_final: 0.7050 (mmp) REVERT: F 329 LYS cc_start: 0.3847 (OUTLIER) cc_final: 0.3249 (mttt) REVERT: F 447 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4156 (pm20) REVERT: F 534 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.6695 (t70) outliers start: 106 outliers final: 80 residues processed: 287 average time/residue: 0.1277 time to fit residues: 59.6401 Evaluate side-chains 277 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 184 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105653 restraints weight = 32172.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103069 restraints weight = 34815.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104484 restraints weight = 39189.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105395 restraints weight = 22266.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106689 restraints weight = 18800.531| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22654 Z= 0.155 Angle : 0.637 9.442 31148 Z= 0.300 Chirality : 0.045 0.339 3616 Planarity : 0.004 0.085 3649 Dihedral : 10.615 157.112 3868 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.59 % Favored : 94.10 % Rotamer: Outliers : 4.63 % Allowed : 19.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.62 (0.17), residues: 2541 helix: 0.75 (0.17), residues: 1006 sheet: -0.56 (0.30), residues: 315 loop : -1.37 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 57 TYR 0.028 0.001 TYR B 22 PHE 0.016 0.001 PHE A 652 TRP 0.029 0.001 TRP D 182 HIS 0.006 0.001 HIS F 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (22622) covalent geometry : angle 0.63017 / 0.30 (31122) hydrogen bonds : bond 0.03390 / 2.25 ( 924) hydrogen bonds : angle 4.28415 / 3.05 ( 2499) metal coordination : bond 0.00934 / 0.68 ( 32) metal coordination : angle 3.27757 / 2.12 ( 26) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 194 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8043 (tp40) REVERT: A 610 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: A 633 MET cc_start: 0.8471 (tmm) cc_final: 0.7882 (tmm) REVERT: A 724 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 911 ASN cc_start: 0.8247 (t0) cc_final: 0.7869 (t0) REVERT: B 50 ASP cc_start: 0.8161 (t0) cc_final: 0.7840 (t70) REVERT: B 60 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: B 78 ASP cc_start: 0.7378 (t0) cc_final: 0.7041 (t0) REVERT: B 186 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8638 (m) REVERT: C 50 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7626 (mt-10) REVERT: E 62 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: E 109 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7768 (mm) REVERT: E 235 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8527 (pp) REVERT: E 248 ARG cc_start: 0.7515 (ptm-80) cc_final: 0.7271 (ptm-80) REVERT: E 440 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8339 (t) REVERT: E 543 TYR cc_start: 0.7245 (m-80) cc_final: 0.6675 (m-80) REVERT: F 62 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.6718 (pp30) REVERT: F 68 MET cc_start: 0.8035 (pmm) cc_final: 0.7730 (mtp) REVERT: F 70 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: F 161 ARG cc_start: 0.5474 (ttp-110) cc_final: 0.4878 (mmm160) REVERT: F 329 LYS cc_start: 0.3860 (OUTLIER) cc_final: 0.3658 (mttt) REVERT: F 394 LYS cc_start: 0.7892 (mptt) cc_final: 0.7123 (tppt) REVERT: F 447 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4236 (pm20) REVERT: F 534 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.6776 (t70) outliers start: 103 outliers final: 81 residues processed: 285 average time/residue: 0.1366 time to fit residues: 62.6762 Evaluate side-chains 278 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 184 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 253 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 214 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105637 restraints weight = 32257.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104183 restraints weight = 34315.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105560 restraints weight = 36383.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106120 restraints weight = 21080.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107514 restraints weight = 18257.685| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22654 Z= 0.134 Angle : 0.633 10.898 31148 Z= 0.298 Chirality : 0.044 0.333 3616 Planarity : 0.004 0.084 3649 Dihedral : 10.449 153.940 3867 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 4.54 % Allowed : 19.97 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.56 (0.17), residues: 2541 helix: 0.83 (0.17), residues: 1013 sheet: -0.46 (0.30), residues: 309 loop : -1.39 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 57 TYR 0.019 0.001 TYR B 138 PHE 0.028 0.001 PHE E 475 TRP 0.030 0.001 TRP D 182 HIS 0.005 0.001 HIS F 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22622) covalent geometry : angle 0.62669 / 0.30 (31122) hydrogen bonds : bond 0.03293 / 2.19 ( 924) hydrogen bonds : angle 4.23995 / 3.02 ( 2499) metal coordination : bond 0.00778 / 0.56 ( 32) metal coordination : angle 3.14612 / 2.01 ( 26) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 192 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8000 (tp40) REVERT: A 261 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7745 (tt) REVERT: A 610 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: A 633 MET cc_start: 0.8533 (tmm) cc_final: 0.7874 (tmm) REVERT: A 724 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: A 911 ASN cc_start: 0.8239 (t0) cc_final: 0.7862 (t0) REVERT: B 50 ASP cc_start: 0.8156 (t0) cc_final: 0.7835 (t70) REVERT: B 60 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: B 78 ASP cc_start: 0.7364 (t0) cc_final: 0.7027 (t0) REVERT: B 186 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8622 (m) REVERT: E 62 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: E 109 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7753 (mm) REVERT: E 235 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8493 (pp) REVERT: E 248 ARG cc_start: 0.7416 (ptm-80) cc_final: 0.7175 (ptm-80) REVERT: E 448 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7786 (mt) REVERT: E 543 TYR cc_start: 0.7215 (m-80) cc_final: 0.6905 (m-80) REVERT: F 62 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.6679 (pp30) REVERT: F 161 ARG cc_start: 0.5463 (ttp-110) cc_final: 0.4811 (mmm160) REVERT: F 211 TYR cc_start: 0.1363 (p90) cc_final: 0.1111 (p90) REVERT: F 274 MET cc_start: 0.7407 (mmt) cc_final: 0.7180 (mmp) REVERT: F 394 LYS cc_start: 0.7921 (mptt) cc_final: 0.7177 (tppt) REVERT: F 447 GLU cc_start: 0.4980 (OUTLIER) cc_final: 0.4241 (pm20) REVERT: F 534 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.6819 (t70) outliers start: 101 outliers final: 77 residues processed: 277 average time/residue: 0.1310 time to fit residues: 58.8864 Evaluate side-chains 274 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 185 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 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 = 0.3890 r_free = 0.3890 target = 0.146208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102812 restraints weight = 32481.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101422 restraints weight = 33911.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102468 restraints weight = 37230.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103212 restraints weight = 21143.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104449 restraints weight = 18237.312| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22654 Z= 0.202 Angle : 0.678 10.473 31148 Z= 0.321 Chirality : 0.046 0.346 3616 Planarity : 0.004 0.089 3649 Dihedral : 10.435 156.433 3862 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.45 % Favored : 93.23 % Rotamer: Outliers : 4.23 % Allowed : 20.20 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.74 (0.17), residues: 2541 helix: 0.70 (0.17), residues: 1010 sheet: -0.81 (0.29), residues: 317 loop : -1.43 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 57 TYR 0.039 0.001 TYR B 22 PHE 0.016 0.002 PHE A 741 TRP 0.029 0.001 TRP D 182 HIS 0.006 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (22622) covalent geometry : angle 0.67072 / 0.32 (31122) hydrogen bonds : bond 0.03723 / 2.47 ( 924) hydrogen bonds : angle 4.37934 / 3.12 ( 2499) metal coordination : bond 0.01199 / 0.88 ( 32) metal coordination : angle 3.54528 / 2.37 ( 26) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 189 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8264 (tp40) REVERT: A 64 ASN cc_start: 0.7505 (m110) cc_final: 0.7304 (m-40) REVERT: A 261 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 570 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: A 610 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: A 633 MET cc_start: 0.8501 (tmm) cc_final: 0.7879 (tmm) REVERT: A 724 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: A 911 ASN cc_start: 0.8282 (t0) cc_final: 0.7891 (t0) REVERT: B 50 ASP cc_start: 0.8194 (t0) cc_final: 0.7884 (t70) REVERT: B 60 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: B 78 ASP cc_start: 0.7408 (t0) cc_final: 0.7113 (t0) REVERT: B 186 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8665 (m) REVERT: C 50 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7611 (mt-10) REVERT: D 43 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8628 (t0) REVERT: E 62 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7403 (pp30) REVERT: E 109 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7864 (mm) REVERT: E 194 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: E 235 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8514 (pp) REVERT: E 248 ARG cc_start: 0.7427 (ptm-80) cc_final: 0.7215 (ptm-80) REVERT: E 543 TYR cc_start: 0.7290 (m-80) cc_final: 0.6917 (m-80) REVERT: F 62 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6624 (pp30) REVERT: F 161 ARG cc_start: 0.5228 (ttp-110) cc_final: 0.4683 (mmm160) REVERT: F 211 TYR cc_start: 0.1453 (p90) cc_final: 0.1171 (p90) REVERT: F 394 LYS cc_start: 0.8053 (mptt) cc_final: 0.7328 (tppt) REVERT: F 447 GLU cc_start: 0.5032 (OUTLIER) cc_final: 0.4246 (pm20) REVERT: F 534 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.6856 (t70) outliers start: 94 outliers final: 75 residues processed: 273 average time/residue: 0.1374 time to fit residues: 61.1946 Evaluate side-chains 272 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 183 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 16 optimal weight: 0.0670 chunk 158 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 127 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** E 404 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 = 0.3926 r_free = 0.3926 target = 0.149484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106442 restraints weight = 32121.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103848 restraints weight = 33049.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105436 restraints weight = 35953.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106097 restraints weight = 21266.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107422 restraints weight = 18460.694| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22654 Z= 0.114 Angle : 0.633 11.844 31148 Z= 0.297 Chirality : 0.044 0.330 3616 Planarity : 0.004 0.082 3649 Dihedral : 10.202 150.342 3862 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.04 % Favored : 94.65 % Rotamer: Outliers : 3.60 % Allowed : 21.05 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.49 (0.17), residues: 2541 helix: 0.87 (0.17), residues: 1018 sheet: -0.48 (0.30), residues: 298 loop : -1.32 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 497 TYR 0.043 0.001 TYR B 22 PHE 0.024 0.001 PHE E 475 TRP 0.028 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22622) covalent geometry : angle 0.62653 / 0.30 (31122) hydrogen bonds : bond 0.03255 / 2.16 ( 924) hydrogen bonds : angle 4.22398 / 3.01 ( 2499) metal coordination : bond 0.00662 / 0.46 ( 32) metal coordination : angle 3.13282 / 1.95 ( 26) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 198 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8443 (tp-100) cc_final: 0.7986 (tp40) REVERT: A 570 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: A 610 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: A 633 MET cc_start: 0.8324 (tmm) cc_final: 0.7697 (tmm) REVERT: A 724 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: A 911 ASN cc_start: 0.8223 (t0) cc_final: 0.7876 (t0) REVERT: B 50 ASP cc_start: 0.8184 (t0) cc_final: 0.7846 (t70) REVERT: B 60 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: B 78 ASP cc_start: 0.7326 (t0) cc_final: 0.7005 (t0) REVERT: B 186 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8626 (m) REVERT: E 62 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7393 (pp30) REVERT: E 109 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7782 (mm) REVERT: E 194 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: E 235 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8431 (pp) REVERT: E 448 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7803 (mt) REVERT: E 543 TYR cc_start: 0.7183 (m-80) cc_final: 0.6851 (m-80) REVERT: F 62 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.6551 (pp30) REVERT: F 161 ARG cc_start: 0.5441 (ttp-110) cc_final: 0.4816 (mmm160) REVERT: F 211 TYR cc_start: 0.1375 (p90) cc_final: 0.1062 (p90) REVERT: F 394 LYS cc_start: 0.8002 (mptt) cc_final: 0.7275 (tppt) REVERT: F 436 MET cc_start: 0.6815 (tpp) cc_final: 0.6532 (tpp) REVERT: F 447 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4241 (pm20) REVERT: F 534 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.6874 (t70) outliers start: 80 outliers final: 60 residues processed: 268 average time/residue: 0.1359 time to fit residues: 59.1485 Evaluate side-chains 259 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 214 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 57 optimal weight: 2.9990 chunk 222 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104403 restraints weight = 32214.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103261 restraints weight = 32645.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104192 restraints weight = 36167.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104853 restraints weight = 21036.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106180 restraints weight = 17743.572| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22654 Z= 0.169 Angle : 0.656 11.424 31148 Z= 0.309 Chirality : 0.045 0.336 3616 Planarity : 0.004 0.085 3649 Dihedral : 10.137 150.903 3859 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.98 % Favored : 93.70 % Rotamer: Outliers : 3.69 % Allowed : 21.10 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -0.61 (0.17), residues: 2541 helix: 0.77 (0.17), residues: 1017 sheet: -0.49 (0.30), residues: 299 loop : -1.40 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 497 TYR 0.053 0.001 TYR B 22 PHE 0.015 0.001 PHE A 652 TRP 0.038 0.001 TRP D 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (22622) covalent geometry : angle 0.64976 / 0.31 (31122) hydrogen bonds : bond 0.03525 / 2.34 ( 924) hydrogen bonds : angle 4.26570 / 3.03 ( 2499) metal coordination : bond 0.00974 / 0.72 ( 32) metal coordination : angle 3.28530 / 2.15 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.86 seconds wall clock time: 63 minutes 7.21 seconds (3787.21 seconds total)