Starting phenix.real_space_refine on Thu Aug 6 16:52:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne6_49299/08_2026/9ne6_49299.map" } resolution = 3.11 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= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 51 5.49 5 S 102 5.16 5 C 10195 2.51 5 N 2754 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16349 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9271 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1081} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4824 SG CYS A 651 44.568 87.350 85.851 1.00 62.20 S ATOM 4840 SG CYS A 654 42.637 88.894 90.761 1.00 73.65 S ATOM 4906 SG CYS A 663 48.893 90.130 89.142 1.00 68.06 S ATOM 5630 SG CYS A 747 47.477 84.259 91.186 1.00 41.10 S Time building chain proxies: 3.59, per 1000 atoms: 0.22 Number of scatterers: 16349 At special positions: 0 Unit cell: (103.5, 111.78, 139.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 102 16.00 P 51 15.00 O 3243 8.00 N 2754 7.00 C 10195 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: 1.33 Conformation dependent library (CDL) restraints added in 733.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " Number of angles added : 12 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 34.3% alpha, 23.8% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 159 through 181 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.601A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.761A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.509A pdb=" N ASP A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYS A 445 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 446 " --> pdb=" O ASP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 473 removed outlier: 3.502A pdb=" N TYR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.522A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.596A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.945A pdb=" N GLU A 584 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 610 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.636A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 Processing helix chain 'A' and resid 788 through 821 removed outlier: 4.413A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 821 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 3.844A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 905 removed outlier: 3.656A pdb=" N LEU A 897 " --> pdb=" O PRO A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 993 removed outlier: 4.096A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 removed outlier: 4.227A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1051 through 1064 Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 4.117A pdb=" N MET A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1093 removed outlier: 3.501A pdb=" N ARG A1092 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A1093 " --> pdb=" O THR A1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1089 through 1093' Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 3.645A pdb=" N GLN A1100 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.546A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.644A pdb=" N ILE A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.866A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1151 Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 4.186A pdb=" N LEU A1172 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 removed outlier: 3.802A pdb=" N LEU A1186 " --> pdb=" O LYS A1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.526A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.305A pdb=" N MET B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.560A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.906A pdb=" N LYS B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.642A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 removed outlier: 4.536A pdb=" N LYS C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.666A pdb=" N LYS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 removed outlier: 4.364A pdb=" N LEU D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 4.084A pdb=" N HIS D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.797A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 81 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP A 83 " --> pdb=" O MET A 66 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 66 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR A 85 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TRP A 243 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136 removed outlier: 3.782A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 removed outlier: 6.761A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.972A pdb=" N THR A 745 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA8, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AA9, first strand: chain 'A' and resid 907 through 915 removed outlier: 5.651A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR A 920 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1035 through 1038 Processing sheet with id=AB2, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 3.898A pdb=" N ARG A1193 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 123 " --> pdb=" O ARG A1193 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A1195 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 121 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.575A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.902A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 203 through 208 removed outlier: 5.560A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 177 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 111 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 3 " --> pdb=" O ARG D 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 61 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 62 removed outlier: 4.155A pdb=" N VAL C 111 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 181 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN D 177 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.510A pdb=" N VAL C 70 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 51 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS C 246 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 66 through 68 removed outlier: 5.495A pdb=" N SER D 230 " --> pdb=" O PRO D 234 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 7024 1.43 - 1.64: 9578 1.64 - 1.85: 158 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 16772 Sorted by residual: bond pdb=" C3' DT P 28 " pdb=" C2' DT P 28 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.85e+01 bond pdb=" C1' DT P 28 " pdb=" N1 DT P 28 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" C3' DT P 19 " pdb=" C2' DT P 19 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C1' DC T 22 " pdb=" N1 DC T 22 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.14e+01 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21402 1.70 - 3.39: 1233 3.39 - 5.09: 179 5.09 - 6.79: 47 6.79 - 8.48: 18 Bond angle restraints: 22879 Sorted by residual: angle pdb=" O4' DA P 12 " pdb=" C4' DA P 12 " pdb=" C3' DA P 12 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" C PHE A 366 " pdb=" CA PHE A 366 " pdb=" CB PHE A 366 " ideal model delta sigma weight residual 109.03 116.74 -7.71 1.62e+00 3.81e-01 2.26e+01 angle pdb=" N ILE A 734 " pdb=" CA ILE A 734 " pdb=" C ILE A 734 " ideal model delta sigma weight residual 111.81 107.81 4.00 8.60e-01 1.35e+00 2.16e+01 angle pdb=" N3 DT P 32 " pdb=" C4 DT P 32 " pdb=" O4 DT P 32 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT T 23 " pdb=" C4 DT T 23 " pdb=" O4 DT T 23 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 22874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 9550 30.21 - 60.42: 527 60.42 - 90.63: 50 90.63 - 120.84: 1 120.84 - 151.05: 2 Dihedral angle restraints: 10130 sinusoidal: 4484 harmonic: 5646 Sorted by residual: dihedral pdb=" CA ASN A 751 " pdb=" C ASN A 751 " pdb=" N SER A 752 " pdb=" CA SER A 752 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLU A 450 " pdb=" C GLU A 450 " pdb=" N GLN A 451 " pdb=" CA GLN A 451 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE C 197 " pdb=" C ILE C 197 " pdb=" N GLU C 198 " pdb=" CA GLU C 198 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 10127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2389 0.104 - 0.209: 155 0.209 - 0.313: 5 0.313 - 0.418: 0 0.418 - 0.522: 2 Chirality restraints: 2551 Sorted by residual: chirality pdb=" P DG T 27 " pdb=" OP1 DG T 27 " pdb=" OP2 DG T 27 " pdb=" O5' DG T 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P DC T 28 " pdb=" OP1 DC T 28 " pdb=" OP2 DC T 28 " pdb=" O5' DC T 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" P DA T 32 " pdb=" OP1 DA T 32 " pdb=" OP2 DA T 32 " pdb=" O5' DA T 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.61 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2548 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 33 " -0.008 2.00e-02 2.50e+03 2.01e-02 9.09e+00 pdb=" N1 DC T 33 " 0.045 2.00e-02 2.50e+03 pdb=" C2 DC T 33 " -0.035 2.00e-02 2.50e+03 pdb=" O2 DC T 33 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC T 33 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC T 33 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC T 33 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC T 33 " -0.012 2.00e-02 2.50e+03 pdb=" C6 DC T 33 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 815 " 0.013 2.00e-02 2.50e+03 1.74e-02 5.28e+00 pdb=" CG PHE A 815 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 815 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 815 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 815 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 815 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 815 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 325 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A 326 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.031 5.00e-02 4.00e+02 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 6086 2.93 - 3.42: 15983 3.42 - 3.91: 26971 3.91 - 4.41: 29673 4.41 - 4.90: 50402 Nonbonded interactions: 129115 Sorted by model distance: nonbonded pdb=" O5' DT P 29 " pdb=" O4' DT P 29 " model vdw 2.433 2.432 nonbonded pdb=" N1 DG T 37 " pdb=" C4 DG T 37 " model vdw 2.594 2.672 nonbonded pdb=" N1 DG T 15 " pdb=" C4 DG T 15 " model vdw 2.599 2.672 nonbonded pdb=" N1 DG P 15 " pdb=" C4 DG P 15 " model vdw 2.600 2.672 nonbonded pdb=" N1 DG P 14 " pdb=" C4 DG P 14 " model vdw 2.602 2.672 ... (remaining 129110 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' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.940 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 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 : 0.005 0.055 16776 Z= 0.291 Angle : 0.913 20.824 22891 Z= 0.521 Chirality : 0.056 0.522 2551 Planarity : 0.005 0.056 2772 Dihedral : 17.445 151.051 6470 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1911 helix: -0.39 (0.21), residues: 575 sheet: -0.18 (0.22), residues: 537 loop : -1.41 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 154 TYR 0.020 0.002 TYR C 211 PHE 0.040 0.002 PHE A 815 TRP 0.026 0.002 TRP D 28 HIS 0.009 0.001 HIS A 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.29 (16772) covalent geometry : angle 0.88433 / 0.52 (22879) hydrogen bonds : bond 0.11787 / 7.34 ( 813) hydrogen bonds : angle 6.45030 / 4.36 ( 2213) metal coordination : bond 0.00874 / 0.43 ( 4) metal coordination : angle 9.99503 / 5.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8387 (mttm) cc_final: 0.8185 (pttm) REVERT: A 237 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7883 (mmtm) REVERT: A 462 ASP cc_start: 0.7326 (t70) cc_final: 0.6637 (m-30) REVERT: A 612 ASP cc_start: 0.8162 (m-30) cc_final: 0.7861 (p0) REVERT: A 733 LYS cc_start: 0.6607 (mttm) cc_final: 0.6216 (mttt) REVERT: A 943 PRO cc_start: 0.7855 (Cg_endo) cc_final: 0.7631 (Cg_exo) REVERT: A 967 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6665 (mt-10) REVERT: A 1018 TYR cc_start: 0.7302 (m-10) cc_final: 0.7046 (m-10) REVERT: A 1036 ASN cc_start: 0.8157 (m-40) cc_final: 0.7944 (m-40) REVERT: A 1050 LYS cc_start: 0.7640 (mmpt) cc_final: 0.6945 (mtpp) REVERT: A 1111 ARG cc_start: 0.5648 (mmt180) cc_final: 0.4815 (ttm-80) REVERT: A 1197 MET cc_start: 0.1425 (tpt) cc_final: -0.0156 (ttp) REVERT: B 17 GLU cc_start: 0.7175 (tp30) cc_final: 0.6952 (mt-10) REVERT: B 80 LYS cc_start: 0.7457 (mmtt) cc_final: 0.6655 (ttpt) REVERT: B 94 ASP cc_start: 0.7175 (m-30) cc_final: 0.6533 (p0) REVERT: B 102 VAL cc_start: 0.8009 (t) cc_final: 0.7798 (t) REVERT: B 108 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6307 (mp10) REVERT: B 165 ASP cc_start: 0.7327 (p0) cc_final: 0.6514 (t0) REVERT: C 199 MET cc_start: 0.2245 (mtt) cc_final: 0.0783 (ttt) REVERT: D 40 MET cc_start: 0.4187 (tpp) cc_final: 0.3558 (tpt) REVERT: D 164 LYS cc_start: 0.5160 (mmpt) cc_final: 0.4515 (mmmm) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1559 time to fit residues: 76.3770 Evaluate side-chains 229 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0020 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D 24 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.236101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.190469 restraints weight = 19480.044| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.07 r_work: 0.3947 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16776 Z= 0.130 Angle : 0.663 18.882 22891 Z= 0.333 Chirality : 0.045 0.241 2551 Planarity : 0.004 0.048 2772 Dihedral : 17.157 153.132 2648 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.54 % Allowed : 7.03 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1911 helix: 0.15 (0.21), residues: 591 sheet: -0.05 (0.22), residues: 543 loop : -1.28 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 91 TYR 0.024 0.001 TYR C 211 PHE 0.020 0.002 PHE A 815 TRP 0.019 0.001 TRP D 28 HIS 0.003 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16772) covalent geometry : angle 0.62627 / 0.33 (22879) hydrogen bonds : bond 0.04229 / 2.84 ( 813) hydrogen bonds : angle 5.57272 / 3.83 ( 2213) metal coordination : bond 0.00683 / 0.34 ( 4) metal coordination : angle 9.57647 / 5.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7923 (mmtm) REVERT: A 405 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: A 967 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 1050 LYS cc_start: 0.7757 (mmpt) cc_final: 0.7133 (mtpp) REVERT: A 1077 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7630 (ttm-80) REVERT: A 1197 MET cc_start: 0.1669 (tpt) cc_final: -0.0040 (ttp) REVERT: B 80 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6482 (ttpt) REVERT: B 102 VAL cc_start: 0.8003 (t) cc_final: 0.7791 (t) REVERT: B 108 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6320 (mp10) REVERT: B 160 ILE cc_start: 0.6975 (mm) cc_final: 0.6548 (mm) REVERT: B 165 ASP cc_start: 0.7499 (p0) cc_final: 0.6576 (t0) REVERT: C 40 MET cc_start: 0.6295 (tpp) cc_final: 0.5840 (tpp) REVERT: C 61 ARG cc_start: 0.7008 (tmt170) cc_final: 0.6711 (tmt-80) REVERT: C 91 ARG cc_start: 0.6926 (ttm110) cc_final: 0.6672 (ttp80) REVERT: C 199 MET cc_start: 0.2613 (mtt) cc_final: 0.1058 (ttt) REVERT: D 139 MET cc_start: 0.6596 (pmm) cc_final: 0.5953 (pmm) outliers start: 26 outliers final: 21 residues processed: 259 average time/residue: 0.1570 time to fit residues: 58.8957 Evaluate side-chains 244 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 1166 TRP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 195 optimal weight: 30.0000 chunk 74 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN B 71 ASN C 49 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.233841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186960 restraints weight = 19674.096| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.09 r_work: 0.3928 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16776 Z= 0.129 Angle : 0.621 18.607 22891 Z= 0.313 Chirality : 0.044 0.242 2551 Planarity : 0.004 0.043 2772 Dihedral : 17.113 154.219 2648 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.71 % Allowed : 8.98 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1911 helix: 0.39 (0.21), residues: 595 sheet: 0.01 (0.23), residues: 540 loop : -1.19 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.022 0.001 TYR C 211 PHE 0.026 0.001 PHE C 215 TRP 0.015 0.001 TRP D 28 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16772) covalent geometry : angle 0.58248 / 0.31 (22879) hydrogen bonds : bond 0.03808 / 2.59 ( 813) hydrogen bonds : angle 5.31765 / 3.65 ( 2213) metal coordination : bond 0.00954 / 0.47 ( 4) metal coordination : angle 9.42936 / 5.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.609 Fit side-chains REVERT: A 237 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7916 (mmtm) REVERT: A 487 MET cc_start: 0.8198 (mtp) cc_final: 0.7941 (mtp) REVERT: A 684 HIS cc_start: 0.7526 (m-70) cc_final: 0.7212 (m170) REVERT: A 1050 LYS cc_start: 0.7757 (mmpt) cc_final: 0.7148 (mtpp) REVERT: A 1077 ARG cc_start: 0.8126 (mtp-110) cc_final: 0.7508 (ttm-80) REVERT: A 1197 MET cc_start: 0.1774 (tpt) cc_final: 0.0036 (ttp) REVERT: B 1 MET cc_start: 0.5033 (tpp) cc_final: 0.4738 (tpp) REVERT: B 80 LYS cc_start: 0.7476 (mmtt) cc_final: 0.6574 (ttpt) REVERT: B 108 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6378 (mp10) REVERT: B 160 ILE cc_start: 0.6996 (mm) cc_final: 0.6584 (mm) REVERT: B 165 ASP cc_start: 0.7647 (p0) cc_final: 0.6658 (t0) REVERT: B 199 MET cc_start: 0.7199 (tpp) cc_final: 0.6597 (tpp) REVERT: C 61 ARG cc_start: 0.7268 (tmt170) cc_final: 0.6956 (tmt170) REVERT: C 91 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6845 (ttm110) REVERT: C 199 MET cc_start: 0.2372 (mtt) cc_final: 0.0980 (ttt) REVERT: C 229 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.3764 (pmm) REVERT: C 244 MET cc_start: 0.4773 (tpt) cc_final: 0.3332 (tmm) REVERT: D 28 TRP cc_start: 0.7380 (m100) cc_final: 0.6475 (m100) REVERT: D 36 ASN cc_start: 0.7964 (t0) cc_final: 0.7736 (t0) REVERT: D 40 MET cc_start: 0.4480 (tpt) cc_final: 0.3722 (tpt) REVERT: D 75 MET cc_start: 0.7155 (tpp) cc_final: 0.6948 (tpp) REVERT: D 139 MET cc_start: 0.6892 (pmm) cc_final: 0.6194 (pmm) outliers start: 29 outliers final: 19 residues processed: 249 average time/residue: 0.1576 time to fit residues: 56.2612 Evaluate side-chains 240 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.232441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185656 restraints weight = 19501.485| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.14 r_work: 0.3906 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16776 Z= 0.140 Angle : 0.621 19.070 22891 Z= 0.312 Chirality : 0.044 0.241 2551 Planarity : 0.004 0.087 2772 Dihedral : 17.115 154.542 2648 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.95 % Allowed : 11.05 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.19), residues: 1911 helix: 0.41 (0.21), residues: 601 sheet: 0.05 (0.22), residues: 536 loop : -1.14 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 722 TYR 0.027 0.001 TYR C 211 PHE 0.039 0.002 PHE C 215 TRP 0.012 0.001 TRP D 28 HIS 0.007 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16772) covalent geometry : angle 0.58279 / 0.31 (22879) hydrogen bonds : bond 0.03724 / 2.55 ( 813) hydrogen bonds : angle 5.21148 / 3.59 ( 2213) metal coordination : bond 0.01234 / 0.60 ( 4) metal coordination : angle 9.37749 / 5.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7943 (mmtm) REVERT: A 487 MET cc_start: 0.8280 (mtp) cc_final: 0.8012 (mtp) REVERT: A 684 HIS cc_start: 0.7526 (m-70) cc_final: 0.7197 (m170) REVERT: A 1050 LYS cc_start: 0.7816 (mmpt) cc_final: 0.7184 (mtpp) REVERT: A 1077 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7623 (ttm-80) REVERT: A 1197 MET cc_start: 0.1787 (tpt) cc_final: 0.0054 (ttp) REVERT: B 1 MET cc_start: 0.5298 (tpp) cc_final: 0.4270 (tpt) REVERT: B 80 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6497 (ttpt) REVERT: B 108 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6366 (mp10) REVERT: B 110 LYS cc_start: 0.8126 (tptp) cc_final: 0.7825 (mmtm) REVERT: B 160 ILE cc_start: 0.7045 (mm) cc_final: 0.6639 (mm) REVERT: B 165 ASP cc_start: 0.7651 (p0) cc_final: 0.6674 (t0) REVERT: C 91 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6936 (ttm110) REVERT: C 199 MET cc_start: 0.2177 (mtt) cc_final: 0.0829 (ttt) REVERT: C 229 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.3728 (pmm) REVERT: D 36 ASN cc_start: 0.8005 (t0) cc_final: 0.7751 (t0) REVERT: D 75 MET cc_start: 0.7117 (tpp) cc_final: 0.6850 (tpp) REVERT: D 139 MET cc_start: 0.7310 (pmm) cc_final: 0.6595 (pmm) outliers start: 33 outliers final: 25 residues processed: 251 average time/residue: 0.1521 time to fit residues: 55.2645 Evaluate side-chains 246 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1166 TRP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 7 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.232568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185400 restraints weight = 19453.888| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 3.02 r_work: 0.3929 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16776 Z= 0.128 Angle : 0.609 18.867 22891 Z= 0.304 Chirality : 0.044 0.241 2551 Planarity : 0.004 0.087 2772 Dihedral : 17.102 154.421 2648 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.13 % Allowed : 11.81 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1911 helix: 0.50 (0.21), residues: 600 sheet: 0.06 (0.22), residues: 538 loop : -1.07 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 728 TYR 0.024 0.001 TYR C 211 PHE 0.034 0.001 PHE C 215 TRP 0.014 0.001 TRP D 28 HIS 0.007 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16772) covalent geometry : angle 0.57177 / 0.30 (22879) hydrogen bonds : bond 0.03621 / 2.47 ( 813) hydrogen bonds : angle 5.12245 / 3.52 ( 2213) metal coordination : bond 0.01002 / 0.49 ( 4) metal coordination : angle 9.16346 / 5.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7883 (mtpp) REVERT: A 462 ASP cc_start: 0.7313 (t70) cc_final: 0.6757 (m-30) REVERT: A 487 MET cc_start: 0.8293 (mtp) cc_final: 0.8038 (mtp) REVERT: A 684 HIS cc_start: 0.7517 (m-70) cc_final: 0.7205 (m170) REVERT: A 831 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.5399 (mtp) REVERT: A 1006 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 1050 LYS cc_start: 0.7767 (mmpt) cc_final: 0.7148 (mtpp) REVERT: A 1197 MET cc_start: 0.1827 (tpt) cc_final: 0.0092 (ttp) REVERT: B 1 MET cc_start: 0.5242 (tpp) cc_final: 0.4346 (tpt) REVERT: B 80 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6506 (ttpt) REVERT: B 108 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6253 (mp10) REVERT: B 165 ASP cc_start: 0.7558 (p0) cc_final: 0.6599 (t0) REVERT: B 199 MET cc_start: 0.7188 (tpp) cc_final: 0.6616 (tpp) REVERT: C 53 ARG cc_start: 0.6564 (mtm-85) cc_final: 0.5784 (mpp-170) REVERT: C 199 MET cc_start: 0.2064 (mtt) cc_final: 0.0698 (ttt) REVERT: C 229 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.3786 (pmm) REVERT: C 244 MET cc_start: 0.5191 (tpt) cc_final: 0.3969 (tmm) REVERT: D 40 MET cc_start: 0.4408 (tpt) cc_final: 0.3712 (tpt) REVERT: D 75 MET cc_start: 0.7173 (tpp) cc_final: 0.6828 (tpp) REVERT: D 139 MET cc_start: 0.7321 (pmm) cc_final: 0.6617 (pmm) outliers start: 36 outliers final: 24 residues processed: 252 average time/residue: 0.1490 time to fit residues: 54.3363 Evaluate side-chains 246 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.228436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180392 restraints weight = 19463.226| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 3.17 r_work: 0.3840 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16776 Z= 0.202 Angle : 0.675 19.962 22891 Z= 0.335 Chirality : 0.046 0.232 2551 Planarity : 0.004 0.047 2772 Dihedral : 17.167 155.687 2648 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.36 % Allowed : 12.64 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1911 helix: 0.23 (0.21), residues: 607 sheet: 0.04 (0.22), residues: 539 loop : -1.11 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 91 TYR 0.016 0.002 TYR A 754 PHE 0.024 0.002 PHE A 761 TRP 0.016 0.002 TRP A 669 HIS 0.006 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (16772) covalent geometry : angle 0.63355 / 0.33 (22879) hydrogen bonds : bond 0.04121 / 2.82 ( 813) hydrogen bonds : angle 5.15277 / 3.55 ( 2213) metal coordination : bond 0.02369 / 1.16 ( 4) metal coordination : angle 10.23694 / 5.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8057 (mtpp) REVERT: A 462 ASP cc_start: 0.7474 (t70) cc_final: 0.6936 (m-30) REVERT: A 487 MET cc_start: 0.8368 (mtp) cc_final: 0.8120 (mtp) REVERT: A 684 HIS cc_start: 0.7538 (m-70) cc_final: 0.7255 (m170) REVERT: A 728 ARG cc_start: 0.7890 (ptp-110) cc_final: 0.7260 (ptp-170) REVERT: A 831 MET cc_start: 0.5881 (mtm) cc_final: 0.5666 (mtp) REVERT: A 1050 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7235 (mtpp) REVERT: A 1197 MET cc_start: 0.1891 (tpt) cc_final: 0.0146 (ttp) REVERT: B 80 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6490 (ttpt) REVERT: B 108 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6332 (mp10) REVERT: B 165 ASP cc_start: 0.7653 (p0) cc_final: 0.6653 (t0) REVERT: B 199 MET cc_start: 0.7248 (tpp) cc_final: 0.6690 (tpp) REVERT: C 61 ARG cc_start: 0.7563 (tmt170) cc_final: 0.7263 (tmt170) REVERT: C 199 MET cc_start: 0.2371 (mtt) cc_final: 0.0956 (ttt) REVERT: C 229 MET cc_start: 0.4485 (OUTLIER) cc_final: 0.3585 (pmm) REVERT: C 244 MET cc_start: 0.5429 (tpt) cc_final: 0.3735 (tmm) REVERT: D 75 MET cc_start: 0.7253 (tpp) cc_final: 0.6905 (tpp) REVERT: D 139 MET cc_start: 0.7426 (pmm) cc_final: 0.6694 (pmm) outliers start: 40 outliers final: 33 residues processed: 247 average time/residue: 0.1438 time to fit residues: 52.0257 Evaluate side-chains 240 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 2 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 91 optimal weight: 0.0270 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 195 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.230858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.183269 restraints weight = 19412.679| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.15 r_work: 0.3873 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16776 Z= 0.131 Angle : 0.624 19.704 22891 Z= 0.310 Chirality : 0.044 0.271 2551 Planarity : 0.004 0.039 2772 Dihedral : 17.144 154.092 2648 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 13.11 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1911 helix: 0.45 (0.21), residues: 600 sheet: 0.06 (0.22), residues: 538 loop : -1.02 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 722 TYR 0.012 0.001 TYR C 250 PHE 0.023 0.002 PHE A 285 TRP 0.012 0.001 TRP A1013 HIS 0.011 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16772) covalent geometry : angle 0.58535 / 0.31 (22879) hydrogen bonds : bond 0.03673 / 2.51 ( 813) hydrogen bonds : angle 5.06161 / 3.49 ( 2213) metal coordination : bond 0.01037 / 0.51 ( 4) metal coordination : angle 9.48982 / 5.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.594 Fit side-chains REVERT: A 237 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8016 (mtpp) REVERT: A 462 ASP cc_start: 0.7399 (t70) cc_final: 0.6878 (m-30) REVERT: A 487 MET cc_start: 0.8377 (mtp) cc_final: 0.8106 (mtp) REVERT: A 684 HIS cc_start: 0.7505 (m-70) cc_final: 0.7206 (m170) REVERT: A 728 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7353 (ptp-170) REVERT: A 831 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5334 (ttt) REVERT: A 848 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: A 1050 LYS cc_start: 0.7847 (mmpt) cc_final: 0.7179 (mtpp) REVERT: A 1197 MET cc_start: 0.1883 (tpt) cc_final: 0.0125 (ttp) REVERT: B 1 MET cc_start: 0.4687 (tpp) cc_final: 0.3761 (tpp) REVERT: B 80 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6468 (ttpt) REVERT: B 108 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6320 (mp10) REVERT: B 165 ASP cc_start: 0.7649 (p0) cc_final: 0.6639 (t0) REVERT: B 199 MET cc_start: 0.7144 (tpp) cc_final: 0.6754 (tpp) REVERT: C 61 ARG cc_start: 0.7646 (tmt170) cc_final: 0.7340 (tmt170) REVERT: C 199 MET cc_start: 0.2452 (mtt) cc_final: 0.1036 (ttt) REVERT: C 229 MET cc_start: 0.4703 (OUTLIER) cc_final: 0.3756 (pmm) REVERT: C 244 MET cc_start: 0.5408 (tpt) cc_final: 0.3705 (tmm) REVERT: D 40 MET cc_start: 0.4502 (tpt) cc_final: 0.3854 (tpt) REVERT: D 75 MET cc_start: 0.7097 (tpp) cc_final: 0.6740 (tpp) REVERT: D 139 MET cc_start: 0.7429 (pmm) cc_final: 0.6711 (pmm) REVERT: D 248 LYS cc_start: 0.7282 (mttt) cc_final: 0.6926 (mtpt) outliers start: 43 outliers final: 28 residues processed: 254 average time/residue: 0.1519 time to fit residues: 56.0067 Evaluate side-chains 249 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 0.5980 chunk 162 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN D 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.229320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.181207 restraints weight = 19385.269| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.18 r_work: 0.3814 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16776 Z= 0.162 Angle : 0.676 21.962 22891 Z= 0.321 Chirality : 0.045 0.239 2551 Planarity : 0.004 0.039 2772 Dihedral : 17.125 154.971 2648 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.36 % Allowed : 13.70 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 1911 helix: 0.39 (0.21), residues: 601 sheet: 0.02 (0.22), residues: 545 loop : -1.03 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 91 TYR 0.013 0.001 TYR C 250 PHE 0.024 0.002 PHE A 285 TRP 0.025 0.002 TRP D 28 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (16772) covalent geometry : angle 0.61161 / 0.32 (22879) hydrogen bonds : bond 0.03859 / 2.62 ( 813) hydrogen bonds : angle 5.04462 / 3.47 ( 2213) metal coordination : bond 0.01844 / 0.88 ( 4) metal coordination : angle 12.56257 / 7.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8032 (mtpp) REVERT: A 462 ASP cc_start: 0.7463 (t70) cc_final: 0.6926 (m-30) REVERT: A 487 MET cc_start: 0.8335 (mtp) cc_final: 0.8068 (mtp) REVERT: A 684 HIS cc_start: 0.7543 (m-70) cc_final: 0.7248 (m170) REVERT: A 728 ARG cc_start: 0.7852 (ptp-110) cc_final: 0.7314 (ptp-170) REVERT: A 756 ASP cc_start: 0.6846 (p0) cc_final: 0.6643 (p0) REVERT: A 831 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5457 (ttt) REVERT: A 848 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 1050 LYS cc_start: 0.7924 (mmpt) cc_final: 0.7249 (mtpp) REVERT: A 1197 MET cc_start: 0.1860 (tpt) cc_final: 0.0084 (ttp) REVERT: B 1 MET cc_start: 0.4880 (tpp) cc_final: 0.4007 (tpp) REVERT: B 80 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6438 (ttpt) REVERT: B 108 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6303 (mp10) REVERT: B 164 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7822 (mmmm) REVERT: B 165 ASP cc_start: 0.7663 (p0) cc_final: 0.6665 (t0) REVERT: B 199 MET cc_start: 0.7125 (tpp) cc_final: 0.6750 (tpp) REVERT: C 61 ARG cc_start: 0.7703 (tmt170) cc_final: 0.7383 (tmt170) REVERT: C 199 MET cc_start: 0.2665 (mtt) cc_final: 0.1236 (ttt) REVERT: C 210 ARG cc_start: 0.6290 (ppt170) cc_final: 0.5648 (ptm-80) REVERT: C 229 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.3705 (pmm) REVERT: D 1 MET cc_start: 0.3773 (tpt) cc_final: 0.3376 (tpt) REVERT: D 40 MET cc_start: 0.4446 (tpt) cc_final: 0.3743 (tpt) REVERT: D 75 MET cc_start: 0.7104 (tpp) cc_final: 0.6719 (tpp) REVERT: D 139 MET cc_start: 0.7435 (pmm) cc_final: 0.6716 (pmm) REVERT: D 248 LYS cc_start: 0.7422 (mttt) cc_final: 0.7001 (mtpt) outliers start: 40 outliers final: 32 residues processed: 243 average time/residue: 0.1575 time to fit residues: 55.0089 Evaluate side-chains 245 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 148 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.230792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.182947 restraints weight = 19490.545| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.94 r_work: 0.3891 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16776 Z= 0.128 Angle : 0.656 22.309 22891 Z= 0.315 Chirality : 0.044 0.242 2551 Planarity : 0.004 0.057 2772 Dihedral : 17.082 154.175 2648 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1911 helix: 0.47 (0.21), residues: 603 sheet: 0.08 (0.22), residues: 539 loop : -0.98 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 91 TYR 0.015 0.001 TYR C 250 PHE 0.023 0.001 PHE A 285 TRP 0.019 0.002 TRP A1166 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16772) covalent geometry : angle 0.60108 / 0.31 (22879) hydrogen bonds : bond 0.03631 / 2.46 ( 813) hydrogen bonds : angle 4.99217 / 3.43 ( 2213) metal coordination : bond 0.01731 / 0.86 ( 4) metal coordination : angle 11.46909 / 6.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7988 (mtpp) REVERT: A 257 ILE cc_start: 0.7928 (tt) cc_final: 0.7724 (tt) REVERT: A 462 ASP cc_start: 0.7375 (t70) cc_final: 0.6832 (m-30) REVERT: A 487 MET cc_start: 0.8360 (mtp) cc_final: 0.8089 (mtp) REVERT: A 684 HIS cc_start: 0.7540 (m-70) cc_final: 0.7289 (m170) REVERT: A 728 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7299 (ptp-170) REVERT: A 831 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5351 (ttt) REVERT: A 848 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: A 1018 TYR cc_start: 0.7786 (m-10) cc_final: 0.7445 (m-10) REVERT: A 1050 LYS cc_start: 0.7896 (mmpt) cc_final: 0.7210 (mtpp) REVERT: A 1077 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7715 (ttm-80) REVERT: A 1197 MET cc_start: 0.1854 (tpt) cc_final: 0.0089 (ttp) REVERT: B 1 MET cc_start: 0.4959 (tpp) cc_final: 0.4128 (tpp) REVERT: B 80 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6413 (ttpt) REVERT: B 108 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6298 (mp10) REVERT: B 164 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7804 (mmmm) REVERT: B 165 ASP cc_start: 0.7662 (p0) cc_final: 0.6655 (t0) REVERT: C 40 MET cc_start: 0.6128 (tpp) cc_final: 0.5730 (tpp) REVERT: C 61 ARG cc_start: 0.7735 (tmt170) cc_final: 0.7410 (tmt170) REVERT: C 199 MET cc_start: 0.2693 (mtt) cc_final: 0.1266 (ttt) REVERT: C 210 ARG cc_start: 0.6238 (ppt170) cc_final: 0.5609 (ptm-80) REVERT: C 229 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.3754 (pmm) REVERT: C 244 MET cc_start: 0.5595 (tpt) cc_final: 0.4337 (tmm) REVERT: D 40 MET cc_start: 0.4407 (tpt) cc_final: 0.3731 (tpt) REVERT: D 75 MET cc_start: 0.7115 (tpp) cc_final: 0.6719 (tpp) REVERT: D 104 GLU cc_start: 0.6941 (tp30) cc_final: 0.6608 (tp30) REVERT: D 139 MET cc_start: 0.7416 (pmm) cc_final: 0.6700 (pmm) outliers start: 35 outliers final: 27 residues processed: 245 average time/residue: 0.1537 time to fit residues: 54.5043 Evaluate side-chains 243 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 chunk 114 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 39 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 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 = 0.4710 r_free = 0.4710 target = 0.230651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.182505 restraints weight = 19452.754| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.99 r_work: 0.3890 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16776 Z= 0.134 Angle : 0.661 22.602 22891 Z= 0.318 Chirality : 0.044 0.237 2551 Planarity : 0.004 0.058 2772 Dihedral : 17.035 154.590 2648 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.83 % Allowed : 14.65 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1911 helix: 0.48 (0.21), residues: 600 sheet: 0.09 (0.22), residues: 539 loop : -1.00 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 91 TYR 0.018 0.001 TYR C 211 PHE 0.023 0.001 PHE A 285 TRP 0.018 0.002 TRP D 28 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16772) covalent geometry : angle 0.60752 / 0.32 (22879) hydrogen bonds : bond 0.03651 / 2.47 ( 813) hydrogen bonds : angle 4.98027 / 3.42 ( 2213) metal coordination : bond 0.01603 / 0.79 ( 4) metal coordination : angle 11.41463 / 6.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7966 (mtpp) REVERT: A 257 ILE cc_start: 0.7929 (tt) cc_final: 0.7728 (tt) REVERT: A 462 ASP cc_start: 0.7366 (t70) cc_final: 0.6825 (m-30) REVERT: A 487 MET cc_start: 0.8332 (mtp) cc_final: 0.8052 (mtp) REVERT: A 684 HIS cc_start: 0.7552 (m-70) cc_final: 0.7301 (m170) REVERT: A 728 ARG cc_start: 0.7807 (ptp-110) cc_final: 0.7360 (ptp-170) REVERT: A 756 ASP cc_start: 0.7014 (p0) cc_final: 0.6699 (p0) REVERT: A 831 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5386 (ttt) REVERT: A 848 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: A 1039 MET cc_start: 0.7406 (tpp) cc_final: 0.7171 (mtp) REVERT: A 1050 LYS cc_start: 0.7893 (mmpt) cc_final: 0.7199 (mtpp) REVERT: A 1077 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7664 (ttm-80) REVERT: A 1197 MET cc_start: 0.1869 (tpt) cc_final: 0.0102 (ttp) REVERT: B 1 MET cc_start: 0.4943 (tpp) cc_final: 0.4144 (tpp) REVERT: B 80 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6403 (ttpt) REVERT: B 108 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6299 (mp10) REVERT: B 160 ILE cc_start: 0.7284 (mm) cc_final: 0.6903 (mm) REVERT: B 164 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7787 (mmmm) REVERT: B 165 ASP cc_start: 0.7658 (p0) cc_final: 0.6679 (t0) REVERT: B 199 MET cc_start: 0.7069 (tpp) cc_final: 0.6338 (tpp) REVERT: C 199 MET cc_start: 0.2816 (mtt) cc_final: 0.1346 (ttt) REVERT: D 1 MET cc_start: 0.3479 (tpt) cc_final: 0.3230 (tpt) REVERT: D 40 MET cc_start: 0.4376 (tpt) cc_final: 0.3666 (tpt) REVERT: D 75 MET cc_start: 0.7108 (tpp) cc_final: 0.6726 (tpp) REVERT: D 104 GLU cc_start: 0.6975 (tp30) cc_final: 0.6652 (tp30) REVERT: D 139 MET cc_start: 0.7434 (pmm) cc_final: 0.6746 (pmm) outliers start: 31 outliers final: 29 residues processed: 242 average time/residue: 0.1522 time to fit residues: 53.7213 Evaluate side-chains 248 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 59 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 128 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 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 = 0.4711 r_free = 0.4711 target = 0.230632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.182530 restraints weight = 19337.471| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.01 r_work: 0.3909 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 16776 Z= 0.211 Angle : 0.834 59.128 22891 Z= 0.456 Chirality : 0.045 0.342 2551 Planarity : 0.004 0.056 2772 Dihedral : 17.034 154.598 2648 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.83 % Allowed : 15.00 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1911 helix: 0.48 (0.21), residues: 600 sheet: 0.09 (0.22), residues: 539 loop : -1.00 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 91 TYR 0.030 0.001 TYR A 224 PHE 0.021 0.001 PHE A 285 TRP 0.016 0.002 TRP D 28 HIS 0.005 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (16772) covalent geometry : angle 0.79201 / 0.46 (22879) hydrogen bonds : bond 0.03655 / 2.48 ( 813) hydrogen bonds : angle 4.98010 / 3.42 ( 2213) metal coordination : bond 0.01571 / 0.77 ( 4) metal coordination : angle 11.40749 / 6.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.02 seconds wall clock time: 76 minutes 24.59 seconds (4584.59 seconds total)