Starting phenix.real_space_refine on Thu Sep 18 11:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_49299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_49299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_49299.map" model { file = "/net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_49299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne6_49299/09_2025/9ne6_49299.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16349 At special positions: 0 Unit cell: (103.5, 111.78, 139.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 102 16.00 P 51 15.00 O 3243 8.00 N 2754 7.00 C 10195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 494.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " Number of angles added : 12 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 34.3% alpha, 23.8% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.04 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: 3.89 Time building geometry restraints manager: 1.50 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=" 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 bond pdb=" N ILE A 734 " pdb=" CA ILE A 734 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.57e+00 bond pdb=" N ASP A 368 " pdb=" CA ASP A 368 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.72e+00 bond pdb=" N PHE A 366 " pdb=" CA PHE A 366 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.28e-02 6.10e+03 7.06e+00 bond pdb=" N PHE A 367 " pdb=" CA PHE A 367 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.95e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21531 1.70 - 3.39: 1107 3.39 - 5.09: 178 5.09 - 6.79: 45 6.79 - 8.48: 18 Bond angle restraints: 22879 Sorted by residual: 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=" N PHE A 366 " pdb=" CA PHE A 366 " pdb=" CB PHE A 366 " ideal model delta sigma weight residual 110.59 105.46 5.13 1.33e+00 5.65e-01 1.49e+01 angle pdb=" C PHE A 366 " pdb=" N PHE A 367 " pdb=" CA PHE A 367 " ideal model delta sigma weight residual 122.17 116.34 5.83 1.54e+00 4.22e-01 1.43e+01 angle pdb=" CA GLU A 132 " pdb=" CB GLU A 132 " pdb=" CG GLU A 132 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.13e+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 - 0.102: 2374 0.102 - 0.205: 170 0.205 - 0.307: 5 0.307 - 0.410: 0 0.410 - 0.512: 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 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.56e+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 2.35 -2.79 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB ILE A 257 " pdb=" CA ILE A 257 " pdb=" CG1 ILE A 257 " pdb=" CG2 ILE A 257 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.800 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 0.004 0.056 16776 Z= 0.210 Angle : 0.893 20.824 22891 Z= 0.458 Chirality : 0.055 0.512 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 aren 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 covalent geometry : bond 0.00434 (16772) covalent geometry : angle 0.86301 (22879) hydrogen bonds : bond 0.11787 ( 813) hydrogen bonds : angle 6.45030 ( 2213) metal coordination : bond 0.00874 ( 4) metal coordination : angle 9.99503 ( 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 : 0.630 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: 0.7047 (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: 0.1438 time to fit residues: 70.1150 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 : 0.574 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.236369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.190926 restraints weight = 19447.369| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.07 r_work: 0.3945 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16776 Z= 0.117 Angle : 0.615 18.370 22891 Z= 0.305 Chirality : 0.042 0.145 2551 Planarity : 0.004 0.046 2772 Dihedral : 17.039 152.142 2648 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.24 % Allowed : 7.27 % Favored : 91.49 % 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 aren not related in a simple way. whole: -0.63 (0.19), residues: 1911 helix: 0.25 (0.21), residues: 598 sheet: 0.10 (0.23), residues: 531 loop : -1.24 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 91 TYR 0.015 0.001 TYR C 250 PHE 0.019 0.001 PHE A 815 TRP 0.017 0.001 TRP D 28 HIS 0.003 0.001 HIS A1168 Details of bonding type rmsd covalent geometry : bond 0.00266 (16772) covalent geometry : angle 0.57373 (22879) hydrogen bonds : bond 0.03550 ( 813) hydrogen bonds : angle 5.25289 ( 2213) metal coordination : bond 0.00706 ( 4) metal coordination : angle 9.65097 ( 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 278 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.621 Fit side-chains REVERT: A 237 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7872 (mmtm) REVERT: A 257 ILE cc_start: 0.7836 (tt) cc_final: 0.7599 (tt) REVERT: A 368 ASP cc_start: 0.7688 (t0) cc_final: 0.7445 (m-30) REVERT: A 487 MET cc_start: 0.8198 (mtp) cc_final: 0.7958 (mtp) REVERT: A 684 HIS cc_start: 0.7588 (m-70) cc_final: 0.7223 (m170) REVERT: A 1050 LYS cc_start: 0.7772 (mmpt) cc_final: 0.7171 (mtpp) REVERT: A 1077 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7695 (ttm-80) REVERT: A 1197 MET cc_start: 0.1655 (tpt) cc_final: -0.0050 (ttp) REVERT: B 80 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6507 (ttpt) REVERT: B 108 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6338 (mp10) REVERT: B 114 TYR cc_start: 0.8084 (m-80) cc_final: 0.7580 (m-80) REVERT: B 160 ILE cc_start: 0.6984 (mm) cc_final: 0.6527 (mm) REVERT: B 165 ASP cc_start: 0.7650 (p0) cc_final: 0.6651 (t0) REVERT: B 199 MET cc_start: 0.7255 (tpp) cc_final: 0.6711 (tpp) REVERT: C 40 MET cc_start: 0.6220 (tpp) cc_final: 0.5779 (tpp) REVERT: C 61 ARG cc_start: 0.7270 (tmt170) cc_final: 0.6981 (tmt170) REVERT: C 91 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6856 (ttp-110) REVERT: C 199 MET cc_start: 0.2181 (mtt) cc_final: 0.0851 (ttt) REVERT: D 75 MET cc_start: 0.7135 (tpp) cc_final: 0.6928 (tpp) outliers start: 21 outliers final: 18 residues processed: 271 average time/residue: 0.1447 time to fit residues: 55.9499 Evaluate side-chains 243 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 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 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN C 49 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.233066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.187814 restraints weight = 19560.869| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.56 r_work: 0.3875 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16776 Z= 0.131 Angle : 0.607 19.164 22891 Z= 0.299 Chirality : 0.042 0.149 2551 Planarity : 0.004 0.043 2772 Dihedral : 16.997 151.600 2648 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.77 % Allowed : 10.10 % Favored : 88.13 % 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 aren not related in a simple way. whole: -0.42 (0.19), residues: 1911 helix: 0.47 (0.21), residues: 600 sheet: 0.11 (0.22), residues: 544 loop : -1.09 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 728 TYR 0.018 0.001 TYR C 250 PHE 0.018 0.001 PHE A 761 TRP 0.013 0.001 TRP D 28 HIS 0.009 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00303 (16772) covalent geometry : angle 0.56556 (22879) hydrogen bonds : bond 0.03503 ( 813) hydrogen bonds : angle 5.02012 ( 2213) metal coordination : bond 0.01083 ( 4) metal coordination : angle 9.69953 ( 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 270 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7886 (mtpp) REVERT: A 368 ASP cc_start: 0.7934 (t0) cc_final: 0.7549 (m-30) REVERT: A 487 MET cc_start: 0.8327 (mtp) cc_final: 0.8096 (mtp) REVERT: A 684 HIS cc_start: 0.7596 (m-70) cc_final: 0.7259 (m170) REVERT: A 719 GLU cc_start: 0.6710 (mt-10) cc_final: 0.5984 (mt-10) REVERT: A 728 ARG cc_start: 0.7321 (ttm110) cc_final: 0.6984 (ptp-170) REVERT: A 831 MET cc_start: 0.5647 (mtm) cc_final: 0.5321 (mtp) REVERT: A 1050 LYS cc_start: 0.7843 (mmpt) cc_final: 0.7219 (mtpp) REVERT: A 1077 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7775 (ttm-80) REVERT: A 1197 MET cc_start: 0.1824 (tpt) cc_final: 0.0099 (ttp) REVERT: B 1 MET cc_start: 0.4950 (tpp) cc_final: 0.4245 (tpp) REVERT: B 17 GLU cc_start: 0.7351 (tp30) cc_final: 0.6884 (mt-10) REVERT: B 80 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6530 (ttpt) REVERT: B 108 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6335 (mp10) REVERT: B 114 TYR cc_start: 0.8123 (m-80) cc_final: 0.7828 (m-80) REVERT: B 160 ILE cc_start: 0.7078 (mm) cc_final: 0.6646 (mm) REVERT: B 164 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7718 (mmmm) REVERT: B 165 ASP cc_start: 0.7725 (p0) cc_final: 0.6719 (t0) REVERT: C 1 MET cc_start: 0.4878 (OUTLIER) cc_final: 0.4369 (ttt) REVERT: C 61 ARG cc_start: 0.7327 (tmt170) cc_final: 0.6905 (ttt-90) REVERT: C 113 ASP cc_start: 0.6351 (p0) cc_final: 0.5782 (t0) REVERT: C 199 MET cc_start: 0.2415 (mtt) cc_final: 0.1010 (ttt) REVERT: C 229 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.3758 (pmm) REVERT: D 40 MET cc_start: 0.4269 (tpt) cc_final: 0.3515 (tpt) REVERT: D 75 MET cc_start: 0.7146 (tpp) cc_final: 0.6833 (tpp) REVERT: D 139 MET cc_start: 0.7331 (pmm) cc_final: 0.6664 (pmm) outliers start: 30 outliers final: 23 residues processed: 258 average time/residue: 0.1439 time to fit residues: 52.9968 Evaluate side-chains 251 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 378 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 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 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 20.0000 chunk 109 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 13 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.233108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.185488 restraints weight = 19461.361| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.98 r_work: 0.3945 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1908 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= 0.118 Angle : 0.590 19.004 22891 Z= 0.290 Chirality : 0.042 0.225 2551 Planarity : 0.004 0.042 2772 Dihedral : 16.941 151.224 2648 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.13 % Allowed : 11.34 % Favored : 86.53 % 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 aren not related in a simple way. whole: -0.28 (0.19), residues: 1911 helix: 0.62 (0.22), residues: 604 sheet: 0.18 (0.22), residues: 538 loop : -1.02 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 91 TYR 0.020 0.001 TYR C 250 PHE 0.020 0.001 PHE A 104 TRP 0.011 0.001 TRP A 62 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00271 (16772) covalent geometry : angle 0.55032 (22879) hydrogen bonds : bond 0.03314 ( 813) hydrogen bonds : angle 4.87898 ( 2213) metal coordination : bond 0.00830 ( 4) metal coordination : angle 9.33884 ( 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 277 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7807 (mtpp) REVERT: A 368 ASP cc_start: 0.7803 (t0) cc_final: 0.7316 (m-30) REVERT: A 487 MET cc_start: 0.8275 (mtp) cc_final: 0.8033 (mtp) REVERT: A 562 MET cc_start: 0.7506 (mtm) cc_final: 0.7244 (ptp) REVERT: A 684 HIS cc_start: 0.7508 (m-70) cc_final: 0.7221 (m170) REVERT: A 719 GLU cc_start: 0.6655 (mt-10) cc_final: 0.5933 (mt-10) REVERT: A 793 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7178 (ptt-90) REVERT: A 831 MET cc_start: 0.5597 (mtm) cc_final: 0.5077 (ttt) REVERT: A 1050 LYS cc_start: 0.7748 (mmpt) cc_final: 0.7088 (mtpp) REVERT: A 1077 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7625 (ttm-80) REVERT: A 1197 MET cc_start: 0.1793 (tpt) cc_final: 0.0096 (ttp) REVERT: B 1 MET cc_start: 0.5060 (tpp) cc_final: 0.3957 (tpp) REVERT: B 17 GLU cc_start: 0.7309 (tp30) cc_final: 0.6886 (mt-10) REVERT: B 80 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6541 (ttpt) REVERT: B 108 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6242 (mp10) REVERT: B 114 TYR cc_start: 0.8144 (m-80) cc_final: 0.7827 (m-80) REVERT: B 165 ASP cc_start: 0.7604 (p0) cc_final: 0.6616 (t0) REVERT: C 1 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4179 (ttt) REVERT: C 61 ARG cc_start: 0.7575 (tmt170) cc_final: 0.7241 (ttt-90) REVERT: C 113 ASP cc_start: 0.6291 (p0) cc_final: 0.5840 (t70) REVERT: C 199 MET cc_start: 0.2523 (mtt) cc_final: 0.1143 (ttt) REVERT: C 244 MET cc_start: 0.5434 (tpt) cc_final: 0.3897 (tmm) REVERT: D 75 MET cc_start: 0.6990 (tpp) cc_final: 0.6650 (tpp) REVERT: D 139 MET cc_start: 0.7483 (pmm) cc_final: 0.6922 (pmm) outliers start: 36 outliers final: 24 residues processed: 263 average time/residue: 0.1376 time to fit residues: 52.1786 Evaluate side-chains 245 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 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 993 PHE Chi-restraints excluded: chain A residue 1005 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 1 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 7 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** 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 = 0.4697 r_free = 0.4697 target = 0.228991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180643 restraints weight = 19411.697| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 3.17 r_work: 0.3816 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2231 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= 0.167 Angle : 0.637 20.378 22891 Z= 0.313 Chirality : 0.044 0.185 2551 Planarity : 0.004 0.045 2772 Dihedral : 17.001 151.888 2648 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.66 % Allowed : 11.99 % 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 aren not related in a simple way. whole: -0.36 (0.19), residues: 1911 helix: 0.47 (0.21), residues: 602 sheet: 0.16 (0.22), residues: 540 loop : -1.02 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 91 TYR 0.014 0.001 TYR C 211 PHE 0.022 0.002 PHE A 761 TRP 0.014 0.002 TRP A 669 HIS 0.005 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00395 (16772) covalent geometry : angle 0.59217 (22879) hydrogen bonds : bond 0.03783 ( 813) hydrogen bonds : angle 4.93362 ( 2213) metal coordination : bond 0.01843 ( 4) metal coordination : angle 10.25523 ( 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 284 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.615 Fit side-chains REVERT: A 237 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7997 (mtpp) REVERT: A 257 ILE cc_start: 0.7948 (tt) cc_final: 0.7720 (tt) REVERT: A 368 ASP cc_start: 0.8078 (t0) cc_final: 0.7657 (m-30) REVERT: A 462 ASP cc_start: 0.7381 (t70) cc_final: 0.6878 (m-30) REVERT: A 487 MET cc_start: 0.8396 (mtp) cc_final: 0.8140 (mtp) REVERT: A 793 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7231 (ptt-90) REVERT: A 831 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5567 (ttt) REVERT: A 1050 LYS cc_start: 0.7895 (mmpt) cc_final: 0.7212 (mtpp) REVERT: A 1077 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7754 (ttm-80) REVERT: A 1122 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.4531 (t80) REVERT: A 1197 MET cc_start: 0.1887 (tpt) cc_final: 0.0059 (ttp) REVERT: B 1 MET cc_start: 0.5244 (tpp) cc_final: 0.4376 (tpt) REVERT: B 80 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6494 (ttpt) REVERT: B 108 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6391 (mp10) REVERT: B 164 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7897 (mmmm) REVERT: B 165 ASP cc_start: 0.7681 (p0) cc_final: 0.6690 (t0) REVERT: B 200 ASN cc_start: 0.6673 (m-40) cc_final: 0.6449 (m-40) REVERT: C 1 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.4351 (ttt) REVERT: C 61 ARG cc_start: 0.7782 (tmt170) cc_final: 0.7426 (tmt170) REVERT: C 113 ASP cc_start: 0.6486 (p0) cc_final: 0.5836 (t70) REVERT: C 199 MET cc_start: 0.2854 (mtt) cc_final: 0.1383 (ttt) REVERT: C 214 PHE cc_start: 0.7078 (m-80) cc_final: 0.6866 (m-10) REVERT: C 229 MET cc_start: 0.4653 (OUTLIER) cc_final: 0.3782 (pmm) REVERT: D 40 MET cc_start: 0.4321 (tpt) cc_final: 0.3621 (tpt) REVERT: D 75 MET cc_start: 0.7082 (tpp) cc_final: 0.6688 (tpp) REVERT: D 139 MET cc_start: 0.7378 (pmm) cc_final: 0.6630 (pmm) outliers start: 45 outliers final: 34 residues processed: 268 average time/residue: 0.1372 time to fit residues: 53.0747 Evaluate side-chains 253 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 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 378 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 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1122 PHE 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 112 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 130 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN D 213 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 = 0.230961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.182785 restraints weight = 19413.140| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.93 r_work: 0.3856 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16776 Z= 0.127 Angle : 0.605 20.220 22891 Z= 0.298 Chirality : 0.042 0.149 2551 Planarity : 0.004 0.088 2772 Dihedral : 16.937 151.080 2648 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 13.41 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1911 helix: 0.59 (0.21), residues: 603 sheet: 0.18 (0.22), residues: 537 loop : -0.95 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 91 TYR 0.016 0.001 TYR C 250 PHE 0.023 0.001 PHE C 215 TRP 0.028 0.002 TRP D 28 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00294 (16772) covalent geometry : angle 0.56485 (22879) hydrogen bonds : bond 0.03408 ( 813) hydrogen bonds : angle 4.82870 ( 2213) metal coordination : bond 0.00916 ( 4) metal coordination : angle 9.48254 ( 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 270 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7934 (mtpp) REVERT: A 368 ASP cc_start: 0.7964 (t0) cc_final: 0.7550 (m-30) REVERT: A 446 ARG cc_start: 0.7515 (tmm160) cc_final: 0.7297 (tmm-80) REVERT: A 462 ASP cc_start: 0.7327 (t70) cc_final: 0.6805 (m-30) REVERT: A 487 MET cc_start: 0.8347 (mtp) cc_final: 0.8102 (mtp) REVERT: A 728 ARG cc_start: 0.7769 (ptp-110) cc_final: 0.7365 (ptp-170) REVERT: A 756 ASP cc_start: 0.6870 (p0) cc_final: 0.6563 (p0) REVERT: A 793 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7197 (ptt-90) REVERT: A 797 MET cc_start: 0.7871 (tpp) cc_final: 0.7475 (mmt) REVERT: A 831 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5573 (ttt) REVERT: A 1050 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7166 (mtpp) REVERT: A 1077 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7646 (ttm-80) REVERT: A 1122 PHE cc_start: 0.5202 (OUTLIER) cc_final: 0.4155 (t80) REVERT: A 1197 MET cc_start: 0.1858 (tpt) cc_final: 0.0041 (ttp) REVERT: B 1 MET cc_start: 0.5250 (tpp) cc_final: 0.4733 (tpp) REVERT: B 80 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6460 (ttpt) REVERT: B 108 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6372 (mp10) REVERT: B 115 GLU cc_start: 0.7079 (pm20) cc_final: 0.6766 (mt-10) REVERT: B 160 ILE cc_start: 0.7266 (mm) cc_final: 0.6908 (mm) REVERT: B 164 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7934 (mmmm) REVERT: B 165 ASP cc_start: 0.7684 (p0) cc_final: 0.6726 (t0) REVERT: B 200 ASN cc_start: 0.6668 (m-40) cc_final: 0.6452 (m-40) REVERT: C 1 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4231 (ttt) REVERT: C 61 ARG cc_start: 0.7787 (tmt170) cc_final: 0.7406 (tmt170) REVERT: C 113 ASP cc_start: 0.6445 (p0) cc_final: 0.5988 (t70) REVERT: C 199 MET cc_start: 0.2618 (mtt) cc_final: 0.1600 (ttm) REVERT: C 229 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.3728 (pmm) REVERT: C 244 MET cc_start: 0.5631 (tpt) cc_final: 0.4689 (tmm) REVERT: D 28 TRP cc_start: 0.6843 (m100) cc_final: 0.6004 (m100) REVERT: D 40 MET cc_start: 0.4388 (tpt) cc_final: 0.3697 (tpt) REVERT: D 75 MET cc_start: 0.7041 (tpp) cc_final: 0.6625 (tpp) REVERT: D 139 MET cc_start: 0.7535 (pmm) cc_final: 0.6758 (pmm) outliers start: 41 outliers final: 30 residues processed: 257 average time/residue: 0.1487 time to fit residues: 55.2618 Evaluate side-chains 253 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 378 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 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1122 PHE 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 1 MET 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 229 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 2 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 179 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 = 0.4701 r_free = 0.4701 target = 0.229201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180592 restraints weight = 19314.792| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.99 r_work: 0.3827 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16776 Z= 0.149 Angle : 0.625 20.837 22891 Z= 0.307 Chirality : 0.043 0.140 2551 Planarity : 0.004 0.040 2772 Dihedral : 16.939 151.619 2648 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.89 % Allowed : 13.41 % Favored : 83.70 % 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 aren not related in a simple way. whole: -0.34 (0.19), residues: 1911 helix: 0.51 (0.21), residues: 604 sheet: 0.08 (0.22), residues: 544 loop : -0.95 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 91 TYR 0.017 0.001 TYR C 250 PHE 0.027 0.002 PHE A 285 TRP 0.022 0.002 TRP D 28 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00351 (16772) covalent geometry : angle 0.58382 (22879) hydrogen bonds : bond 0.03614 ( 813) hydrogen bonds : angle 4.87677 ( 2213) metal coordination : bond 0.01489 ( 4) metal coordination : angle 9.76565 ( 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 281 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7885 (mtpp) REVERT: A 368 ASP cc_start: 0.8019 (t0) cc_final: 0.7573 (m-30) REVERT: A 462 ASP cc_start: 0.7406 (t70) cc_final: 0.6898 (m-30) REVERT: A 487 MET cc_start: 0.8411 (mtp) cc_final: 0.8150 (mtp) REVERT: A 728 ARG cc_start: 0.7699 (ptp-110) cc_final: 0.7265 (ptp-170) REVERT: A 756 ASP cc_start: 0.6892 (p0) cc_final: 0.6580 (p0) REVERT: A 793 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7232 (ptt-90) REVERT: A 831 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5636 (ttt) REVERT: A 848 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: A 941 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 1000 GLU cc_start: 0.7647 (pt0) cc_final: 0.7295 (pm20) REVERT: A 1077 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7666 (ttm-80) REVERT: A 1122 PHE cc_start: 0.5234 (OUTLIER) cc_final: 0.3987 (t80) REVERT: A 1197 MET cc_start: 0.1789 (tpt) cc_final: 0.0040 (ttp) REVERT: B 1 MET cc_start: 0.5321 (tpp) cc_final: 0.4869 (tpp) REVERT: B 80 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6451 (ttpt) REVERT: B 115 GLU cc_start: 0.7104 (pm20) cc_final: 0.6796 (mt-10) REVERT: B 165 ASP cc_start: 0.7729 (p0) cc_final: 0.6782 (t0) REVERT: B 200 ASN cc_start: 0.6699 (m-40) cc_final: 0.6417 (m-40) REVERT: C 1 MET cc_start: 0.4725 (OUTLIER) cc_final: 0.4157 (ttm) REVERT: C 61 ARG cc_start: 0.7740 (tmt170) cc_final: 0.7233 (tmt170) REVERT: C 113 ASP cc_start: 0.6457 (p0) cc_final: 0.5918 (t70) REVERT: C 199 MET cc_start: 0.2759 (mtt) cc_final: 0.1766 (ttm) REVERT: C 229 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.3800 (pmm) REVERT: C 244 MET cc_start: 0.5615 (tpt) cc_final: 0.4409 (tmm) REVERT: D 28 TRP cc_start: 0.6963 (m100) cc_final: 0.5934 (m100) REVERT: D 75 MET cc_start: 0.7047 (tpp) cc_final: 0.6593 (tpp) REVERT: D 104 GLU cc_start: 0.7062 (tp30) cc_final: 0.6740 (tp30) REVERT: D 139 MET cc_start: 0.7519 (pmm) cc_final: 0.6754 (pmm) outliers start: 49 outliers final: 36 residues processed: 267 average time/residue: 0.1428 time to fit residues: 55.1761 Evaluate side-chains 250 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 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 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 75 MET 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 112 SER 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 172 SER 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: 0.9980 chunk 162 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** 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 = 0.4683 r_free = 0.4683 target = 0.227073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.179020 restraints weight = 19388.282| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.90 r_work: 0.3823 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16776 Z= 0.182 Angle : 0.668 21.466 22891 Z= 0.325 Chirality : 0.044 0.154 2551 Planarity : 0.004 0.040 2772 Dihedral : 16.959 151.035 2648 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.60 % Allowed : 14.65 % Favored : 82.75 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 1911 helix: 0.40 (0.21), residues: 600 sheet: 0.09 (0.22), residues: 541 loop : -1.01 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 91 TYR 0.016 0.002 TYR C 250 PHE 0.026 0.002 PHE A 285 TRP 0.016 0.002 TRP D 28 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00433 (16772) covalent geometry : angle 0.62125 (22879) hydrogen bonds : bond 0.03884 ( 813) hydrogen bonds : angle 4.98387 ( 2213) metal coordination : bond 0.02049 ( 4) metal coordination : angle 10.79276 ( 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 264 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.455 Fit side-chains REVERT: A 462 ASP cc_start: 0.7363 (t70) cc_final: 0.6930 (m-30) REVERT: A 487 MET cc_start: 0.8425 (mtp) cc_final: 0.8164 (mtp) REVERT: A 728 ARG cc_start: 0.7755 (ptp-110) cc_final: 0.7356 (ptp-170) REVERT: A 756 ASP cc_start: 0.6931 (p0) cc_final: 0.6608 (p0) REVERT: A 831 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5825 (ttt) REVERT: A 941 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7618 (mt) REVERT: A 1077 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7766 (ttm-80) REVERT: A 1122 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.4129 (t80) REVERT: A 1197 MET cc_start: 0.1876 (tpt) cc_final: 0.0139 (ttp) REVERT: B 1 MET cc_start: 0.5422 (tpp) cc_final: 0.5008 (tpp) REVERT: B 80 LYS cc_start: 0.7376 (mmtt) cc_final: 0.6448 (ttpt) REVERT: B 160 ILE cc_start: 0.7513 (mm) cc_final: 0.7214 (mm) REVERT: B 164 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7716 (mmmm) REVERT: B 165 ASP cc_start: 0.7705 (p0) cc_final: 0.6639 (t0) REVERT: C 1 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4331 (ttm) REVERT: C 39 SER cc_start: 0.7754 (t) cc_final: 0.7422 (p) REVERT: C 61 ARG cc_start: 0.7708 (tmt170) cc_final: 0.7225 (tmt170) REVERT: C 113 ASP cc_start: 0.6409 (p0) cc_final: 0.5864 (t70) REVERT: C 199 MET cc_start: 0.2692 (mtt) cc_final: 0.1831 (ttm) REVERT: C 210 ARG cc_start: 0.6457 (ppt170) cc_final: 0.5894 (ptm-80) REVERT: C 229 MET cc_start: 0.4783 (OUTLIER) cc_final: 0.3830 (pmm) REVERT: D 28 TRP cc_start: 0.7132 (m100) cc_final: 0.6019 (m100) REVERT: D 40 MET cc_start: 0.4444 (tpt) cc_final: 0.3888 (tpt) REVERT: D 75 MET cc_start: 0.7167 (tpp) cc_final: 0.6653 (tpp) REVERT: D 104 GLU cc_start: 0.7043 (tp30) cc_final: 0.6769 (tp30) REVERT: D 139 MET cc_start: 0.7615 (pmm) cc_final: 0.6814 (pmm) outliers start: 44 outliers final: 34 residues processed: 249 average time/residue: 0.1334 time to fit residues: 48.2429 Evaluate side-chains 247 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 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 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1122 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 75 MET 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 112 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 179 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 = 0.4706 r_free = 0.4706 target = 0.229605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.181595 restraints weight = 19442.061| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.93 r_work: 0.3867 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16776 Z= 0.134 Angle : 0.653 23.311 22891 Z= 0.310 Chirality : 0.043 0.195 2551 Planarity : 0.004 0.041 2772 Dihedral : 16.901 150.232 2648 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.30 % Allowed : 15.36 % Favored : 82.34 % 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 aren not related in a simple way. whole: -0.30 (0.19), residues: 1911 helix: 0.52 (0.21), residues: 603 sheet: 0.11 (0.22), residues: 538 loop : -0.89 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 91 TYR 0.016 0.001 TYR C 250 PHE 0.024 0.001 PHE A 285 TRP 0.019 0.002 TRP D 28 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00313 (16772) covalent geometry : angle 0.59203 (22879) hydrogen bonds : bond 0.03504 ( 813) hydrogen bonds : angle 4.89463 ( 2213) metal coordination : bond 0.01853 ( 4) metal coordination : angle 12.01007 ( 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: 39 poor density : 225 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7910 (mtpp) REVERT: A 368 ASP cc_start: 0.8150 (t0) cc_final: 0.7556 (m-30) REVERT: A 462 ASP cc_start: 0.7381 (t70) cc_final: 0.6912 (m-30) REVERT: A 487 MET cc_start: 0.8358 (mtp) cc_final: 0.8080 (mtp) REVERT: A 722 ARG cc_start: 0.6887 (ttm170) cc_final: 0.6480 (ttm170) REVERT: A 728 ARG cc_start: 0.7749 (ptp-110) cc_final: 0.7361 (ptp-170) REVERT: A 756 ASP cc_start: 0.6861 (p0) cc_final: 0.6569 (p0) REVERT: A 797 MET cc_start: 0.7900 (tpp) cc_final: 0.7482 (mmt) REVERT: A 831 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5681 (ttt) REVERT: A 941 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7521 (mp) REVERT: A 1077 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7652 (ttm-80) REVERT: A 1122 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.4061 (t80) REVERT: A 1197 MET cc_start: 0.1878 (tpt) cc_final: 0.0152 (ttp) REVERT: B 1 MET cc_start: 0.5371 (tpp) cc_final: 0.5005 (tpp) REVERT: B 80 LYS cc_start: 0.7329 (mmtt) cc_final: 0.6429 (ttpt) REVERT: B 160 ILE cc_start: 0.7287 (mm) cc_final: 0.6922 (mm) REVERT: B 164 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7559 (mmmm) REVERT: B 165 ASP cc_start: 0.7678 (p0) cc_final: 0.6660 (t0) REVERT: C 1 MET cc_start: 0.4739 (OUTLIER) cc_final: 0.4273 (ttm) REVERT: C 39 SER cc_start: 0.7716 (t) cc_final: 0.7418 (p) REVERT: C 61 ARG cc_start: 0.7712 (tmt170) cc_final: 0.7300 (tmt170) REVERT: C 113 ASP cc_start: 0.6373 (p0) cc_final: 0.5863 (t70) REVERT: C 199 MET cc_start: 0.2515 (mtt) cc_final: 0.1766 (ttm) REVERT: C 210 ARG cc_start: 0.6516 (ppt170) cc_final: 0.6061 (ptm-80) REVERT: C 229 MET cc_start: 0.4803 (OUTLIER) cc_final: 0.3843 (pmm) REVERT: C 244 MET cc_start: 0.6290 (tpt) cc_final: 0.5468 (tmm) REVERT: D 40 MET cc_start: 0.4387 (tpt) cc_final: 0.3785 (tpt) REVERT: D 75 MET cc_start: 0.7123 (tpp) cc_final: 0.6610 (tpp) REVERT: D 104 GLU cc_start: 0.7082 (tp30) cc_final: 0.6806 (tp30) REVERT: D 139 MET cc_start: 0.7615 (pmm) cc_final: 0.6950 (pmm) outliers start: 39 outliers final: 34 residues processed: 253 average time/residue: 0.1300 time to fit residues: 48.0100 Evaluate side-chains 252 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 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 613 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1122 PHE 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 1 MET 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 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: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 39 optimal weight: 0.1980 chunk 147 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** 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 = 0.4684 r_free = 0.4684 target = 0.227062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178431 restraints weight = 19362.721| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.96 r_work: 0.3814 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16776 Z= 0.172 Angle : 0.680 24.342 22891 Z= 0.326 Chirality : 0.044 0.187 2551 Planarity : 0.004 0.040 2772 Dihedral : 16.908 151.009 2648 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 15.48 % Favored : 82.16 % 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 aren not related in a simple way. whole: -0.38 (0.19), residues: 1911 helix: 0.43 (0.21), residues: 600 sheet: 0.10 (0.22), residues: 539 loop : -0.96 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.015 0.001 TYR C 250 PHE 0.027 0.002 PHE A 285 TRP 0.018 0.002 TRP A1166 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00410 (16772) covalent geometry : angle 0.62301 (22879) hydrogen bonds : bond 0.03824 ( 813) hydrogen bonds : angle 4.97442 ( 2213) metal coordination : bond 0.02721 ( 4) metal coordination : angle 11.95121 ( 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 251 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.513 Fit side-chains REVERT: A 237 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7968 (mtpp) REVERT: A 462 ASP cc_start: 0.7340 (t70) cc_final: 0.6882 (m-30) REVERT: A 487 MET cc_start: 0.8424 (mtp) cc_final: 0.8121 (mtp) REVERT: A 722 ARG cc_start: 0.6853 (ttm170) cc_final: 0.6409 (ttm170) REVERT: A 728 ARG cc_start: 0.7686 (ptp-110) cc_final: 0.7291 (ptp-170) REVERT: A 756 ASP cc_start: 0.6957 (p0) cc_final: 0.6633 (p0) REVERT: A 831 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5837 (ttt) REVERT: A 941 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 1122 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.4213 (t80) REVERT: A 1197 MET cc_start: 0.1855 (tpt) cc_final: 0.0129 (ttp) REVERT: B 1 MET cc_start: 0.5485 (tpp) cc_final: 0.4651 (tpp) REVERT: B 80 LYS cc_start: 0.7339 (mmtt) cc_final: 0.6378 (ttpt) REVERT: B 160 ILE cc_start: 0.7446 (mm) cc_final: 0.7128 (mm) REVERT: B 164 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7476 (mmmm) REVERT: B 165 ASP cc_start: 0.7609 (p0) cc_final: 0.6664 (t0) REVERT: C 1 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4340 (ttm) REVERT: C 39 SER cc_start: 0.7684 (t) cc_final: 0.7307 (p) REVERT: C 61 ARG cc_start: 0.7763 (tmt170) cc_final: 0.7322 (tmt170) REVERT: C 113 ASP cc_start: 0.6404 (p0) cc_final: 0.5863 (t70) REVERT: C 199 MET cc_start: 0.2820 (mtt) cc_final: 0.2043 (ttm) REVERT: C 210 ARG cc_start: 0.6572 (ppt170) cc_final: 0.6092 (ptm-80) REVERT: C 229 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.3789 (pmm) REVERT: C 244 MET cc_start: 0.6210 (tpt) cc_final: 0.5428 (tmm) REVERT: D 25 GLU cc_start: 0.6890 (tm-30) cc_final: 0.5451 (pm20) REVERT: D 28 TRP cc_start: 0.7234 (m100) cc_final: 0.6170 (m100) REVERT: D 40 MET cc_start: 0.4476 (tpt) cc_final: 0.3606 (tpt) REVERT: D 75 MET cc_start: 0.7229 (tpp) cc_final: 0.6649 (tpp) REVERT: D 104 GLU cc_start: 0.7095 (tp30) cc_final: 0.6806 (tp30) REVERT: D 139 MET cc_start: 0.7602 (pmm) cc_final: 0.6844 (pmm) outliers start: 40 outliers final: 35 residues processed: 237 average time/residue: 0.1358 time to fit residues: 46.9130 Evaluate side-chains 247 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 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 613 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1122 PHE 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 1 MET 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 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: 4.9990 chunk 172 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 147 optimal weight: 0.0270 chunk 184 optimal weight: 4.9990 chunk 176 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** 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 = 0.4715 r_free = 0.4715 target = 0.230571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.182852 restraints weight = 19322.378| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.79 r_work: 0.3897 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16776 Z= 0.122 Angle : 0.637 24.532 22891 Z= 0.304 Chirality : 0.042 0.139 2551 Planarity : 0.004 0.042 2772 Dihedral : 16.780 149.889 2648 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.89 % Allowed : 16.01 % Favored : 82.10 % 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 aren not related in a simple way. whole: -0.20 (0.19), residues: 1911 helix: 0.61 (0.21), residues: 602 sheet: 0.20 (0.22), residues: 538 loop : -0.89 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 955 TYR 0.016 0.001 TYR C 250 PHE 0.032 0.001 PHE A 285 TRP 0.018 0.002 TRP D 28 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00280 (16772) covalent geometry : angle 0.57928 (22879) hydrogen bonds : bond 0.03353 ( 813) hydrogen bonds : angle 4.82558 ( 2213) metal coordination : bond 0.01236 ( 4) metal coordination : angle 11.58767 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.83 seconds wall clock time: 72 minutes 1.63 seconds (4321.63 seconds total)