Starting phenix.real_space_refine on Fri Jul 3 21:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne6_49299/07_2026/9ne6_49299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne6_49299/07_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_49299/07_2026/9ne6_49299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne6_49299/07_2026/9ne6_49299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ne6_49299/07_2026/9ne6_49299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne6_49299/07_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-dev-6108/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: 3.23, per 1000 atoms: 0.20 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: 1.14 Conformation dependent library (CDL) restraints added in 557.9 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: 1.71 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: 3.38 Time building geometry restraints manager: 1.53 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: 21403 1.70 - 3.39: 1232 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: 2.820 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.130 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- 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 : 0.912 20.824 22891 Z= 0.518 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 0.88294 / 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 : 0.548 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: 0.1376 time to fit residues: 67.0753 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 : 0.412 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.4756 r_free = 0.4756 target = 0.234585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.188081 restraints weight = 19105.358| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 3.13 r_work: 0.3927 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16776 Z= 0.130 Angle : 0.652 18.722 22891 Z= 0.328 Chirality : 0.044 0.220 2551 Planarity : 0.004 0.047 2772 Dihedral : 17.175 154.447 2648 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -0.75 (0.19), residues: 1911 helix: 0.18 (0.21), residues: 591 sheet: -0.04 (0.22), residues: 543 loop : -1.27 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 91 TYR 0.024 0.001 TYR C 211 PHE 0.019 0.002 PHE A 815 TRP 0.018 0.001 TRP D 28 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (16772) covalent geometry : angle 0.61441 / 0.33 (22879) hydrogen bonds : bond 0.04154 / 2.79 ( 813) hydrogen bonds : angle 5.55000 / 3.81 ( 2213) metal coordination : bond 0.00687 / 0.34 ( 4) metal coordination : angle 9.54370 / 5.20 ( 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 269 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7936 (mmtm) REVERT: A 405 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: A 1050 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7148 (mtpp) REVERT: A 1077 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7651 (ttm-80) REVERT: A 1197 MET cc_start: 0.1662 (tpt) cc_final: -0.0049 (ttp) REVERT: B 80 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6502 (ttpt) REVERT: B 102 VAL cc_start: 0.8024 (t) cc_final: 0.7812 (t) REVERT: B 108 GLN cc_start: 0.6998 (mm-40) cc_final: 0.6327 (mp10) REVERT: B 160 ILE cc_start: 0.7004 (mm) cc_final: 0.6575 (mm) REVERT: B 165 ASP cc_start: 0.7518 (p0) cc_final: 0.6563 (t0) REVERT: B 199 MET cc_start: 0.7345 (tpp) cc_final: 0.6600 (tpp) REVERT: C 40 MET cc_start: 0.6298 (tpp) cc_final: 0.5894 (tpp) REVERT: C 61 ARG cc_start: 0.6999 (tmt170) cc_final: 0.6694 (tmt-80) REVERT: C 91 ARG cc_start: 0.6944 (ttm110) cc_final: 0.6700 (ttp-110) REVERT: C 199 MET cc_start: 0.2630 (mtt) cc_final: 0.1070 (ttt) REVERT: D 36 ASN cc_start: 0.8039 (t0) cc_final: 0.7831 (t0) outliers start: 26 outliers final: 20 residues processed: 257 average time/residue: 0.1319 time to fit residues: 48.8057 Evaluate side-chains 244 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 155 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.230953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.183247 restraints weight = 19632.746| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.20 r_work: 0.3877 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16776 Z= 0.172 Angle : 0.655 19.732 22891 Z= 0.328 Chirality : 0.045 0.223 2551 Planarity : 0.004 0.043 2772 Dihedral : 17.175 156.042 2648 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.77 % Allowed : 9.57 % Favored : 88.66 % 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: -0.67 (0.19), residues: 1911 helix: 0.23 (0.21), residues: 597 sheet: 0.04 (0.22), residues: 536 loop : -1.25 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 413 TYR 0.029 0.002 TYR C 211 PHE 0.021 0.002 PHE C 215 TRP 0.014 0.002 TRP D 28 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (16772) covalent geometry : angle 0.61404 / 0.33 (22879) hydrogen bonds : bond 0.04096 / 2.79 ( 813) hydrogen bonds : angle 5.36028 / 3.69 ( 2213) metal coordination : bond 0.01835 / 0.90 ( 4) metal coordination : angle 10.01375 / 5.55 ( 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: 30 poor density : 231 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8013 (mtpp) REVERT: A 462 ASP cc_start: 0.7437 (t70) cc_final: 0.6874 (m-30) REVERT: A 487 MET cc_start: 0.8294 (mtp) cc_final: 0.8041 (mtp) REVERT: A 684 HIS cc_start: 0.7529 (m-70) cc_final: 0.7208 (m170) REVERT: A 1050 LYS cc_start: 0.7846 (mmpt) cc_final: 0.7196 (mtpp) REVERT: A 1197 MET cc_start: 0.1806 (tpt) cc_final: 0.0075 (ttp) REVERT: B 1 MET cc_start: 0.5024 (tpp) cc_final: 0.3938 (tpt) REVERT: B 80 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6535 (ttpt) REVERT: B 102 VAL cc_start: 0.8082 (t) cc_final: 0.7881 (t) REVERT: B 108 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6373 (mp10) REVERT: B 165 ASP cc_start: 0.7648 (p0) cc_final: 0.6649 (t0) REVERT: C 1 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.4166 (ttt) REVERT: C 61 ARG cc_start: 0.7306 (tmt170) cc_final: 0.6940 (tmt170) REVERT: C 91 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6897 (ttm110) REVERT: C 199 MET cc_start: 0.2407 (mtt) cc_final: 0.0996 (ttt) REVERT: C 229 MET cc_start: 0.4570 (OUTLIER) cc_final: 0.3604 (pmm) REVERT: D 36 ASN cc_start: 0.7994 (t0) cc_final: 0.7750 (t0) REVERT: D 40 MET cc_start: 0.4471 (tpt) cc_final: 0.3713 (tpt) REVERT: D 75 MET cc_start: 0.7260 (tpp) cc_final: 0.7042 (tpp) REVERT: D 139 MET cc_start: 0.6967 (pmm) cc_final: 0.6248 (pmm) outliers start: 30 outliers final: 20 residues processed: 248 average time/residue: 0.1308 time to fit residues: 46.4338 Evaluate side-chains 243 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 930 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 1 MET 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 137 VAL 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: 0.8980 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 ** 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 = 0.4718 r_free = 0.4718 target = 0.231333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.184081 restraints weight = 19494.959| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 3.02 r_work: 0.3890 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16776 Z= 0.140 Angle : 0.627 19.715 22891 Z= 0.314 Chirality : 0.044 0.224 2551 Planarity : 0.004 0.071 2772 Dihedral : 17.164 155.537 2648 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.07 % Allowed : 11.16 % Favored : 86.77 % 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: -0.55 (0.19), residues: 1911 helix: 0.35 (0.21), residues: 600 sheet: 0.07 (0.22), residues: 535 loop : -1.16 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 722 TYR 0.027 0.001 TYR C 211 PHE 0.038 0.002 PHE C 215 TRP 0.012 0.001 TRP A 669 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16772) covalent geometry : angle 0.58749 / 0.31 (22879) hydrogen bonds : bond 0.03787 / 2.60 ( 813) hydrogen bonds : angle 5.23420 / 3.60 ( 2213) metal coordination : bond 0.01281 / 0.63 ( 4) metal coordination : angle 9.56936 / 5.28 ( 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 260 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8342 (mtmm) cc_final: 0.8021 (mtpp) REVERT: A 462 ASP cc_start: 0.7364 (t70) cc_final: 0.6814 (m-30) REVERT: A 487 MET cc_start: 0.8353 (mtp) cc_final: 0.8088 (mtp) REVERT: A 684 HIS cc_start: 0.7545 (m-70) cc_final: 0.7222 (m170) REVERT: A 1050 LYS cc_start: 0.7827 (mmpt) cc_final: 0.7192 (mtpp) REVERT: A 1197 MET cc_start: 0.1825 (tpt) cc_final: 0.0098 (ttp) REVERT: B 1 MET cc_start: 0.5283 (tpp) cc_final: 0.4283 (tpt) REVERT: B 80 LYS cc_start: 0.7429 (mmtt) cc_final: 0.6510 (ttpt) REVERT: B 102 VAL cc_start: 0.8066 (t) cc_final: 0.7850 (t) REVERT: B 108 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6353 (mp10) REVERT: B 110 LYS cc_start: 0.8102 (tptp) cc_final: 0.7836 (mmtm) REVERT: B 165 ASP cc_start: 0.7667 (p0) cc_final: 0.6697 (t0) REVERT: B 199 MET cc_start: 0.7155 (tpp) cc_final: 0.6582 (tpp) REVERT: C 91 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6903 (ttm110) REVERT: C 199 MET cc_start: 0.2105 (mtt) cc_final: 0.0745 (ttt) REVERT: C 244 MET cc_start: 0.5076 (tpt) cc_final: 0.3493 (tmm) REVERT: D 36 ASN cc_start: 0.8016 (t0) cc_final: 0.7758 (t0) REVERT: D 75 MET cc_start: 0.7177 (tpp) cc_final: 0.6883 (tpp) REVERT: D 139 MET cc_start: 0.7251 (pmm) cc_final: 0.6530 (pmm) outliers start: 35 outliers final: 27 residues processed: 249 average time/residue: 0.1146 time to fit residues: 41.2887 Evaluate side-chains 241 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 258 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 360 VAL 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 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 47 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU 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: 3.9990 chunk 135 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** B 71 ASN ** C 49 GLN ** 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 = 0.4711 r_free = 0.4711 target = 0.230546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.182857 restraints weight = 19456.323| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.28 r_work: 0.3869 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16776 Z= 0.147 Angle : 0.629 19.681 22891 Z= 0.312 Chirality : 0.044 0.220 2551 Planarity : 0.004 0.057 2772 Dihedral : 17.153 156.144 2648 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.48 % Allowed : 12.17 % Favored : 85.35 % 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: -0.51 (0.19), residues: 1911 helix: 0.37 (0.21), residues: 604 sheet: 0.06 (0.22), residues: 539 loop : -1.12 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 728 TYR 0.023 0.001 TYR C 211 PHE 0.033 0.002 PHE C 215 TRP 0.014 0.002 TRP D 28 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16772) covalent geometry : angle 0.58954 / 0.31 (22879) hydrogen bonds : bond 0.03764 / 2.57 ( 813) hydrogen bonds : angle 5.14546 / 3.53 ( 2213) metal coordination : bond 0.01405 / 0.69 ( 4) metal coordination : angle 9.55206 / 5.29 ( 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 262 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8030 (mtpp) REVERT: A 462 ASP cc_start: 0.7411 (t70) cc_final: 0.6873 (m-30) REVERT: A 487 MET cc_start: 0.8358 (mtp) cc_final: 0.8101 (mtp) REVERT: A 562 MET cc_start: 0.7479 (mtm) cc_final: 0.7255 (ptp) REVERT: A 684 HIS cc_start: 0.7572 (m-70) cc_final: 0.7248 (m170) REVERT: A 1050 LYS cc_start: 0.7859 (mmpt) cc_final: 0.7209 (mtpp) REVERT: A 1197 MET cc_start: 0.1874 (tpt) cc_final: 0.0142 (ttp) REVERT: B 1 MET cc_start: 0.5275 (tpp) cc_final: 0.4392 (tpt) REVERT: B 80 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6511 (ttpt) REVERT: B 102 VAL cc_start: 0.8101 (t) cc_final: 0.7880 (t) REVERT: B 108 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6286 (mp10) REVERT: B 110 LYS cc_start: 0.8058 (tptp) cc_final: 0.7833 (mmtm) REVERT: B 165 ASP cc_start: 0.7691 (p0) cc_final: 0.6702 (t0) REVERT: C 199 MET cc_start: 0.2163 (mtt) cc_final: 0.0791 (ttt) REVERT: C 229 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.3787 (pmm) REVERT: D 40 MET cc_start: 0.4435 (tpt) cc_final: 0.3704 (tpt) REVERT: D 75 MET cc_start: 0.7266 (tpp) cc_final: 0.6875 (tpp) REVERT: D 139 MET cc_start: 0.7464 (pmm) cc_final: 0.6756 (pmm) outliers start: 42 outliers final: 30 residues processed: 251 average time/residue: 0.1365 time to fit residues: 49.6173 Evaluate side-chains 242 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 262 ASP 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 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=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: 0.0470 chunk 130 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.9838 ------------------------------------------------------------------------------- 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 = 0.4712 r_free = 0.4712 target = 0.230630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.183264 restraints weight = 19470.198| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.20 r_work: 0.3889 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16776 Z= 0.143 Angle : 0.629 19.731 22891 Z= 0.312 Chirality : 0.044 0.220 2551 Planarity : 0.004 0.040 2772 Dihedral : 17.151 156.082 2648 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.19 % Allowed : 13.35 % Favored : 84.47 % 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: 606 sheet: 0.08 (0.22), residues: 539 loop : -1.08 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 91 TYR 0.013 0.001 TYR C 250 PHE 0.021 0.002 PHE A 761 TRP 0.012 0.001 TRP A 669 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16772) covalent geometry : angle 0.59106 / 0.31 (22879) hydrogen bonds : bond 0.03721 / 2.54 ( 813) hydrogen bonds : angle 5.08442 / 3.49 ( 2213) metal coordination : bond 0.01230 / 0.60 ( 4) metal coordination : angle 9.45096 / 5.22 ( 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 255 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8011 (mtpp) REVERT: A 462 ASP cc_start: 0.7362 (t70) cc_final: 0.6841 (m-30) REVERT: A 487 MET cc_start: 0.8361 (mtp) cc_final: 0.8066 (mtp) REVERT: A 684 HIS cc_start: 0.7502 (m-70) cc_final: 0.7191 (m170) REVERT: A 728 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7481 (ptp-170) REVERT: A 848 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: A 1050 LYS cc_start: 0.7796 (mmpt) cc_final: 0.7163 (mtpp) REVERT: A 1197 MET cc_start: 0.1921 (tpt) cc_final: 0.0174 (ttp) REVERT: B 80 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6502 (ttpt) REVERT: B 102 VAL cc_start: 0.8160 (t) cc_final: 0.7936 (t) REVERT: B 108 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6291 (mp10) REVERT: B 165 ASP cc_start: 0.7598 (p0) cc_final: 0.6601 (t0) REVERT: C 61 ARG cc_start: 0.7443 (tmt170) cc_final: 0.7141 (tmt170) REVERT: C 199 MET cc_start: 0.2334 (mtt) cc_final: 0.0969 (ttt) REVERT: C 229 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.3794 (pmm) REVERT: D 75 MET cc_start: 0.7143 (tpp) cc_final: 0.6794 (tpp) REVERT: D 139 MET cc_start: 0.7452 (pmm) cc_final: 0.6737 (pmm) outliers start: 37 outliers final: 32 residues processed: 245 average time/residue: 0.1569 time to fit residues: 55.4269 Evaluate side-chains 244 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 258 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 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 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 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: 0.9990 chunk 172 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.230904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183317 restraints weight = 19444.024| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.13 r_work: 0.3900 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16776 Z= 0.136 Angle : 0.633 19.617 22891 Z= 0.313 Chirality : 0.044 0.282 2551 Planarity : 0.004 0.055 2772 Dihedral : 17.146 156.067 2648 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.78 % Allowed : 12.88 % 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: -0.41 (0.19), residues: 1911 helix: 0.47 (0.21), residues: 600 sheet: 0.07 (0.22), residues: 540 loop : -1.03 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 91 TYR 0.012 0.001 TYR C 250 PHE 0.020 0.001 PHE A 761 TRP 0.021 0.002 TRP D 28 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16772) covalent geometry : angle 0.59637 / 0.31 (22879) hydrogen bonds : bond 0.03671 / 2.49 ( 813) hydrogen bonds : angle 5.04335 / 3.46 ( 2213) metal coordination : bond 0.01060 / 0.52 ( 4) metal coordination : angle 9.28090 / 5.12 ( 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 276 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7991 (mtpp) REVERT: A 462 ASP cc_start: 0.7348 (t70) cc_final: 0.6816 (m-30) REVERT: A 487 MET cc_start: 0.8316 (mtp) cc_final: 0.8050 (mtp) REVERT: A 684 HIS cc_start: 0.7494 (m-70) cc_final: 0.7194 (m170) REVERT: A 728 ARG cc_start: 0.8016 (ptp-110) cc_final: 0.7512 (ptp-170) REVERT: A 848 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.5993 (mp0) REVERT: A 1050 LYS cc_start: 0.7826 (mmpt) cc_final: 0.7157 (mtpp) REVERT: A 1197 MET cc_start: 0.1827 (tpt) cc_final: 0.0099 (ttp) REVERT: B 1 MET cc_start: 0.4744 (tpp) cc_final: 0.3822 (tpp) REVERT: B 80 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6458 (ttpt) REVERT: B 102 VAL cc_start: 0.8148 (t) cc_final: 0.7921 (t) REVERT: B 108 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6292 (mp10) REVERT: B 165 ASP cc_start: 0.7645 (p0) cc_final: 0.6631 (t0) REVERT: B 199 MET cc_start: 0.6634 (tpp) cc_final: 0.6290 (tpp) REVERT: C 61 ARG cc_start: 0.7594 (tmt170) cc_final: 0.7293 (tmt170) REVERT: C 199 MET cc_start: 0.2355 (mtt) cc_final: 0.1004 (ttt) REVERT: C 229 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.3747 (pmm) REVERT: C 244 MET cc_start: 0.5456 (tpt) cc_final: 0.4067 (tmm) REVERT: D 40 MET cc_start: 0.4469 (tpt) cc_final: 0.3795 (tpt) REVERT: D 75 MET cc_start: 0.7071 (tpp) cc_final: 0.6701 (tpp) REVERT: D 139 MET cc_start: 0.7415 (pmm) cc_final: 0.6743 (pmm) REVERT: D 248 LYS cc_start: 0.7601 (mttt) cc_final: 0.7123 (mtpt) outliers start: 47 outliers final: 36 residues processed: 259 average time/residue: 0.1543 time to fit residues: 57.6397 Evaluate side-chains 257 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 258 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 334 VAL Chi-restraints excluded: chain A residue 359 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 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 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 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 37 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 213 ASN ** 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 = 0.4706 r_free = 0.4706 target = 0.229933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.182344 restraints weight = 19442.348| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 3.15 r_work: 0.3861 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16776 Z= 0.150 Angle : 0.652 19.838 22891 Z= 0.320 Chirality : 0.045 0.221 2551 Planarity : 0.004 0.066 2772 Dihedral : 17.137 156.480 2648 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.36 % Allowed : 14.12 % 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: -0.45 (0.19), residues: 1911 helix: 0.38 (0.21), residues: 604 sheet: 0.09 (0.22), residues: 543 loop : -1.03 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 91 TYR 0.014 0.001 TYR A 726 PHE 0.021 0.002 PHE A 761 TRP 0.016 0.002 TRP D 28 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16772) covalent geometry : angle 0.61476 / 0.32 (22879) hydrogen bonds : bond 0.03764 / 2.56 ( 813) hydrogen bonds : angle 5.04509 / 3.46 ( 2213) metal coordination : bond 0.01366 / 0.67 ( 4) metal coordination : angle 9.46064 / 5.24 ( 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 257 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8008 (mtpp) REVERT: A 462 ASP cc_start: 0.7409 (t70) cc_final: 0.6869 (m-30) REVERT: A 487 MET cc_start: 0.8351 (mtp) cc_final: 0.8091 (mtp) REVERT: A 684 HIS cc_start: 0.7568 (m-70) cc_final: 0.7301 (m170) REVERT: A 728 ARG cc_start: 0.8031 (ptp-110) cc_final: 0.7471 (ptp-170) REVERT: A 848 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: A 1050 LYS cc_start: 0.7922 (mmpt) cc_final: 0.7231 (mtpp) REVERT: A 1197 MET cc_start: 0.1796 (tpt) cc_final: 0.0080 (ttp) REVERT: B 1 MET cc_start: 0.4879 (tpp) cc_final: 0.3985 (tpp) REVERT: B 80 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6436 (ttpt) REVERT: B 102 VAL cc_start: 0.8111 (t) cc_final: 0.7887 (t) REVERT: B 108 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6334 (mp10) REVERT: B 164 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7862 (mmmm) REVERT: B 165 ASP cc_start: 0.7731 (p0) cc_final: 0.6728 (t0) REVERT: C 199 MET cc_start: 0.2486 (mtt) cc_final: 0.1099 (ttt) REVERT: C 210 ARG cc_start: 0.6215 (ppt170) cc_final: 0.5593 (ptm-80) REVERT: C 229 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.3821 (pmm) REVERT: C 244 MET cc_start: 0.5633 (tpt) cc_final: 0.3889 (tmm) REVERT: D 1 MET cc_start: 0.3788 (tpt) cc_final: 0.3411 (tpt) REVERT: D 40 MET cc_start: 0.4390 (tpt) cc_final: 0.3694 (tpt) REVERT: D 75 MET cc_start: 0.7135 (tpp) cc_final: 0.6737 (tpp) REVERT: D 139 MET cc_start: 0.7432 (pmm) cc_final: 0.6719 (pmm) outliers start: 40 outliers final: 33 residues processed: 244 average time/residue: 0.1472 time to fit residues: 52.3377 Evaluate side-chains 247 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 258 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 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 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 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 C residue 229 MET Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 228 SER 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: 2.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 24 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 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 = 0.4701 r_free = 0.4701 target = 0.229293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181417 restraints weight = 19595.220| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 3.12 r_work: 0.3881 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16776 Z= 0.156 Angle : 0.666 20.075 22891 Z= 0.326 Chirality : 0.045 0.224 2551 Planarity : 0.004 0.058 2772 Dihedral : 17.124 156.578 2648 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 14.59 % Favored : 82.93 % 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: -0.48 (0.19), residues: 1911 helix: 0.36 (0.21), residues: 601 sheet: 0.05 (0.22), residues: 542 loop : -1.04 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 91 TYR 0.016 0.001 TYR C 249 PHE 0.024 0.002 PHE A 285 TRP 0.016 0.002 TRP D 28 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16772) covalent geometry : angle 0.62834 / 0.33 (22879) hydrogen bonds : bond 0.03831 / 2.61 ( 813) hydrogen bonds : angle 5.05622 / 3.47 ( 2213) metal coordination : bond 0.01457 / 0.71 ( 4) metal coordination : angle 9.60072 / 5.33 ( 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 264 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8002 (mtpp) REVERT: A 462 ASP cc_start: 0.7350 (t70) cc_final: 0.6834 (m-30) REVERT: A 487 MET cc_start: 0.8363 (mtp) cc_final: 0.8085 (mtp) REVERT: A 684 HIS cc_start: 0.7502 (m-70) cc_final: 0.7231 (m170) REVERT: A 728 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7559 (ptp-170) REVERT: A 848 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: A 1050 LYS cc_start: 0.7874 (mmpt) cc_final: 0.7194 (mtpp) REVERT: A 1197 MET cc_start: 0.1851 (tpt) cc_final: 0.0115 (ttp) REVERT: B 1 MET cc_start: 0.4917 (tpp) cc_final: 0.4124 (tpp) REVERT: B 80 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6454 (ttpt) REVERT: B 102 VAL cc_start: 0.8187 (t) cc_final: 0.7963 (t) REVERT: B 108 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6294 (mp10) REVERT: B 164 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7827 (mmmm) REVERT: B 165 ASP cc_start: 0.7619 (p0) cc_final: 0.6635 (t0) REVERT: B 199 MET cc_start: 0.6621 (tpp) cc_final: 0.6263 (tpp) REVERT: C 199 MET cc_start: 0.2477 (mtt) cc_final: 0.1165 (ttt) REVERT: C 229 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.3740 (pmm) REVERT: C 244 MET cc_start: 0.5743 (tpt) cc_final: 0.4041 (tmm) REVERT: D 28 TRP cc_start: 0.7420 (m100) cc_final: 0.6455 (m100) REVERT: D 75 MET cc_start: 0.7158 (tpp) cc_final: 0.6758 (tpp) REVERT: D 104 GLU cc_start: 0.6979 (tp30) cc_final: 0.6680 (tp30) REVERT: D 139 MET cc_start: 0.7441 (pmm) cc_final: 0.6544 (pmm) REVERT: D 248 LYS cc_start: 0.7790 (mttt) cc_final: 0.7275 (mtpt) outliers start: 42 outliers final: 35 residues processed: 248 average time/residue: 0.1518 time to fit residues: 54.5063 Evaluate side-chains 249 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 258 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 334 VAL Chi-restraints excluded: chain A residue 359 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 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 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 C residue 215 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 192 optimal weight: 50.0000 chunk 39 optimal weight: 0.3980 chunk 147 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 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 = 0.4703 r_free = 0.4703 target = 0.229514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.181820 restraints weight = 19490.213| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.14 r_work: 0.3868 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 16776 Z= 0.211 Angle : 0.843 59.198 22891 Z= 0.452 Chirality : 0.046 0.430 2551 Planarity : 0.004 0.055 2772 Dihedral : 17.123 156.520 2648 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.19 % Allowed : 14.94 % Favored : 82.87 % 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: -0.48 (0.19), residues: 1911 helix: 0.38 (0.21), residues: 601 sheet: 0.04 (0.22), residues: 542 loop : -1.05 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 91 TYR 0.013 0.001 TYR C 211 PHE 0.021 0.002 PHE A 285 TRP 0.014 0.002 TRP D 28 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (16772) covalent geometry : angle 0.80025 / 0.45 (22879) hydrogen bonds : bond 0.03804 / 2.59 ( 813) hydrogen bonds : angle 5.05389 / 3.47 ( 2213) metal coordination : bond 0.16947 / 8.47 ( 4) metal coordination : angle 11.67085 / 6.23 ( 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 250 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8012 (mtpp) REVERT: A 462 ASP cc_start: 0.7384 (t70) cc_final: 0.6863 (m-30) REVERT: A 487 MET cc_start: 0.8349 (mtp) cc_final: 0.8082 (mtp) REVERT: A 684 HIS cc_start: 0.7552 (m-70) cc_final: 0.7284 (m170) REVERT: A 728 ARG cc_start: 0.8107 (ptp-110) cc_final: 0.7525 (ptp-170) REVERT: A 848 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 1050 LYS cc_start: 0.7899 (mmpt) cc_final: 0.7234 (mtpp) REVERT: A 1197 MET cc_start: 0.1827 (tpt) cc_final: 0.0094 (ttp) REVERT: B 1 MET cc_start: 0.4994 (tpp) cc_final: 0.4151 (tpp) REVERT: B 80 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6436 (ttpt) REVERT: B 102 VAL cc_start: 0.8128 (t) cc_final: 0.7905 (t) REVERT: B 108 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6317 (mp10) REVERT: B 164 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7843 (mmmm) REVERT: B 165 ASP cc_start: 0.7653 (p0) cc_final: 0.6666 (t0) REVERT: B 199 MET cc_start: 0.6647 (tpp) cc_final: 0.6279 (tpp) REVERT: C 199 MET cc_start: 0.2496 (mtt) cc_final: 0.1185 (ttt) REVERT: C 229 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.3740 (pmm) REVERT: C 244 MET cc_start: 0.5706 (tpt) cc_final: 0.3995 (tmm) REVERT: D 28 TRP cc_start: 0.7393 (m100) cc_final: 0.6464 (m100) REVERT: D 75 MET cc_start: 0.7178 (tpp) cc_final: 0.6762 (tpp) REVERT: D 104 GLU cc_start: 0.6993 (tp30) cc_final: 0.6667 (tp30) REVERT: D 139 MET cc_start: 0.7327 (pmm) cc_final: 0.6614 (pmm) outliers start: 37 outliers final: 35 residues processed: 236 average time/residue: 0.1558 time to fit residues: 53.1517 Evaluate side-chains 249 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 258 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 334 VAL Chi-restraints excluded: chain A residue 359 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 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 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 112 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 137 VAL 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: 3.9990 chunk 172 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 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 = 0.4703 r_free = 0.4703 target = 0.229533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.181743 restraints weight = 19413.476| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 3.11 r_work: 0.3871 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 16776 Z= 0.211 Angle : 0.843 59.198 22891 Z= 0.452 Chirality : 0.046 0.430 2551 Planarity : 0.004 0.055 2772 Dihedral : 17.123 156.520 2648 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.19 % Allowed : 15.00 % Favored : 82.81 % 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: -0.48 (0.19), residues: 1911 helix: 0.38 (0.21), residues: 601 sheet: 0.04 (0.22), residues: 542 loop : -1.05 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 91 TYR 0.013 0.001 TYR C 211 PHE 0.021 0.002 PHE A 285 TRP 0.014 0.002 TRP D 28 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (16772) covalent geometry : angle 0.80025 / 0.45 (22879) hydrogen bonds : bond 0.03804 / 2.59 ( 813) hydrogen bonds : angle 5.05389 / 3.47 ( 2213) metal coordination : bond 0.16947 / 8.47 ( 4) metal coordination : angle 11.67085 / 6.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.89 seconds wall clock time: 69 minutes 31.77 seconds (4171.77 seconds total)