Starting phenix.real_space_refine on Sun Jun 22 20:48:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.map" model { file = "/net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fix_29212/06_2025/8fix_29212.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16099 2.51 5 N 4589 2.21 5 O 5097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25943 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "T" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10397 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "R" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna3p': 10} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15192 SG CYS D 72 102.008 116.349 90.749 1.00152.51 S ATOM 15300 SG CYS D 85 105.244 114.694 91.817 1.00144.54 S ATOM 15324 SG CYS D 88 102.262 113.409 92.321 1.00142.40 S ATOM 21012 SG CYS D 814 98.399 46.905 89.581 1.00 89.14 S ATOM 21577 SG CYS D 888 96.216 50.059 89.744 1.00 79.14 S ATOM 21628 SG CYS D 895 97.576 48.839 86.450 1.00 64.64 S ATOM 21649 SG CYS D 898 94.844 46.847 88.193 1.00 65.60 S Time building chain proxies: 13.80, per 1000 atoms: 0.53 Number of scatterers: 25943 At special positions: 0 Unit cell: (136.018, 147.594, 167.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 49 15.00 Mg 1 11.99 O 5097 8.00 N 4589 7.00 C 16099 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: 6.14 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 45 sheets defined 38.8% alpha, 12.2% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 9.58 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.826A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.590A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.540A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.610A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.583A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.135A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.404A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.883A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.792A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 819 through 826 removed outlier: 4.189A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.199A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.067A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.751A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 4.354A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.756A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 418 removed outlier: 4.031A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.702A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.672A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.604A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.258A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.576A pdb=" N CYS D 898 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.595A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.639A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.817A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.730A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.550A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.615A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 7.621A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 200 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 188 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.849A pdb=" N ILE A 144 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.424A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.619A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 188 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 206 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 56 removed outlier: 3.728A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.520A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.691A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.567A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.572A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.726A pdb=" N ARG C 101 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.790A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 removed outlier: 5.891A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.581A pdb=" N ASP C 189 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.568A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.082A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 4.167A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.713A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.847A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.439A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 775 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.677A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 841 removed outlier: 7.075A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 932 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C1053 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.023A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'C' and resid 1336 through 1339 removed outlier: 3.983A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111 removed outlier: 9.840A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.106A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 368 through 369 removed outlier: 5.879A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.106A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.716A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.882A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 822 " --> pdb=" O VAL D 880 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 849 through 850 removed outlier: 4.372A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 994 removed outlier: 6.265A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.572A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1026 through 1027 Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE8, first strand: chain 'D' and resid 1188 through 1191 removed outlier: 3.528A pdb=" N ILE D1190 " --> pdb=" O ARG D1173 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 7.012A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.11 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8775 1.35 - 1.47: 5707 1.47 - 1.60: 11716 1.60 - 1.73: 47 1.73 - 1.86: 184 Bond restraints: 26429 Sorted by residual: bond pdb=" N PHE C 812 " pdb=" CA PHE C 812 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.61e+00 bond pdb=" N PHE D1325 " pdb=" CA PHE D1325 " ideal model delta sigma weight residual 1.454 1.484 -0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N GLN D1326 " pdb=" CA GLN D1326 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.94e+00 bond pdb=" N MET C 741 " pdb=" CA MET C 741 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.17e-02 7.31e+03 5.94e+00 bond pdb=" N CYS D 70 " pdb=" CA CYS D 70 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.82e+00 ... (remaining 26424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 35471 2.68 - 5.36: 379 5.36 - 8.04: 48 8.04 - 10.72: 7 10.72 - 13.40: 1 Bond angle restraints: 35906 Sorted by residual: angle pdb=" N ASN D 458 " pdb=" CA ASN D 458 " pdb=" C ASN D 458 " ideal model delta sigma weight residual 111.39 103.84 7.55 1.38e+00 5.25e-01 2.99e+01 angle pdb=" CB MET C 239 " pdb=" CG MET C 239 " pdb=" SD MET C 239 " ideal model delta sigma weight residual 112.70 126.10 -13.40 3.00e+00 1.11e-01 2.00e+01 angle pdb=" CA ARG E 67 " pdb=" CB ARG E 67 " pdb=" CG ARG E 67 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C GLN D1326 " pdb=" N GLU D1327 " pdb=" CA GLU D1327 " ideal model delta sigma weight residual 120.94 127.53 -6.59 1.57e+00 4.06e-01 1.76e+01 angle pdb=" C PHE B 35 " pdb=" CA PHE B 35 " pdb=" CB PHE B 35 " ideal model delta sigma weight residual 110.84 104.42 6.42 1.66e+00 3.63e-01 1.50e+01 ... (remaining 35901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 15819 35.42 - 70.83: 323 70.83 - 106.25: 35 106.25 - 141.67: 1 141.67 - 177.09: 1 Dihedral angle restraints: 16179 sinusoidal: 7037 harmonic: 9142 Sorted by residual: dihedral pdb=" CA PRO C1185 " pdb=" C PRO C1185 " pdb=" N VAL C1186 " pdb=" CA VAL C1186 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" O4' U R 11 " pdb=" C1' U R 11 " pdb=" N1 U R 11 " pdb=" C2 U R 11 " ideal model delta sinusoidal sigma weight residual -160.00 -89.13 -70.87 1 1.50e+01 4.44e-03 2.87e+01 dihedral pdb=" CA ALA C 746 " pdb=" C ALA C 746 " pdb=" N GLY C 747 " pdb=" CA GLY C 747 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3367 0.056 - 0.112: 621 0.112 - 0.167: 99 0.167 - 0.223: 14 0.223 - 0.279: 4 Chirality restraints: 4105 Sorted by residual: chirality pdb=" CA PHE B 35 " pdb=" N PHE B 35 " pdb=" C PHE B 35 " pdb=" CB PHE B 35 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA GLU C1274 " pdb=" N GLU C1274 " pdb=" C GLU C1274 " pdb=" CB GLU C1274 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG E 67 " pdb=" N ARG E 67 " pdb=" C ARG E 67 " pdb=" CB ARG E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 4102 not shown) Planarity restraints: 4535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 775 " 0.058 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO C 776 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 776 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 776 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 127 " -0.055 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 128 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 94 " 0.049 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO C 95 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.041 5.00e-02 4.00e+02 ... (remaining 4532 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 175 2.53 - 3.12: 18993 3.12 - 3.71: 40404 3.71 - 4.31: 52890 4.31 - 4.90: 87957 Nonbonded interactions: 200419 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb=" OD2 ASP D 464 " model vdw 1.933 3.040 nonbonded pdb=" CE2 PHE C 812 " pdb=" CB PRO D 451 " model vdw 2.042 3.740 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.103 2.170 nonbonded pdb=" O PHE B 35 " pdb=" OG1 THR B 38 " model vdw 2.111 3.040 nonbonded pdb=" OG SER C 759 " pdb=" OG1 THR C 763 " model vdw 2.127 3.040 ... (remaining 200414 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 'A' and resid 7 through 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 68.620 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 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 : 0.003 0.069 26436 Z= 0.133 Angle : 0.695 13.404 35912 Z= 0.367 Chirality : 0.045 0.279 4105 Planarity : 0.005 0.089 4535 Dihedral : 14.470 177.085 10299 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.78 % Favored : 87.06 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3169 helix: -0.22 (0.14), residues: 1173 sheet: -1.94 (0.27), residues: 326 loop : -3.22 (0.12), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 409 HIS 0.016 0.001 HIS D 80 PHE 0.024 0.001 PHE C 230 TYR 0.020 0.001 TYR A 152 ARG 0.010 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.16131 ( 1012) hydrogen bonds : angle 6.21212 ( 2870) metal coordination : bond 0.03275 ( 7) metal coordination : angle 1.07531 ( 6) covalent geometry : bond 0.00273 (26429) covalent geometry : angle 0.69467 (35906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8120 (ttmt) REVERT: C 239 MET cc_start: 0.7824 (mmp) cc_final: 0.7239 (mmp) REVERT: C 285 ILE cc_start: 0.8526 (pt) cc_final: 0.8030 (mm) REVERT: C 311 CYS cc_start: 0.6307 (p) cc_final: 0.5526 (p) REVERT: C 547 VAL cc_start: 0.9024 (m) cc_final: 0.8811 (t) REVERT: C 805 MET cc_start: 0.6822 (ptm) cc_final: 0.6555 (ptt) REVERT: C 850 ILE cc_start: 0.5128 (mm) cc_final: 0.4857 (mp) REVERT: C 1216 ARG cc_start: 0.6790 (tpt90) cc_final: 0.6586 (mtt-85) REVERT: C 1276 TRP cc_start: 0.6255 (m-10) cc_final: 0.5863 (m-10) REVERT: C 1304 MET cc_start: 0.6594 (tmm) cc_final: 0.6362 (ttt) REVERT: D 180 MET cc_start: 0.3431 (tpt) cc_final: 0.2952 (tpt) REVERT: D 330 MET cc_start: 0.7849 (ppp) cc_final: 0.7467 (ptm) REVERT: D 973 LEU cc_start: 0.8271 (mt) cc_final: 0.7545 (mp) REVERT: D 1040 MET cc_start: 0.1275 (mmm) cc_final: 0.0643 (mmt) REVERT: D 1275 LEU cc_start: 0.8399 (tt) cc_final: 0.8112 (mp) REVERT: E 30 MET cc_start: 0.4118 (mmp) cc_final: 0.3828 (mmp) outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.3889 time to fit residues: 228.9468 Evaluate side-chains 255 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.0060 chunk 250 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 37 HIS C 65 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1236 ASN D 232 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.122616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091930 restraints weight = 74348.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095096 restraints weight = 39436.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097258 restraints weight = 25968.729| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26436 Z= 0.122 Angle : 0.607 11.846 35912 Z= 0.306 Chirality : 0.043 0.295 4105 Planarity : 0.005 0.060 4535 Dihedral : 11.342 173.170 4065 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 1.03 % Allowed : 9.28 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3169 helix: 0.56 (0.15), residues: 1186 sheet: -1.47 (0.28), residues: 331 loop : -2.83 (0.13), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1020 HIS 0.008 0.001 HIS A 66 PHE 0.031 0.001 PHE C 812 TYR 0.022 0.001 TYR C1213 ARG 0.008 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1012) hydrogen bonds : angle 4.75343 ( 2870) metal coordination : bond 0.00218 ( 7) metal coordination : angle 1.68596 ( 6) covalent geometry : bond 0.00275 (26429) covalent geometry : angle 0.60673 (35906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4355 (OUTLIER) cc_final: 0.3925 (mm) REVERT: A 231 PHE cc_start: 0.7087 (t80) cc_final: 0.6882 (t80) REVERT: C 124 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.5813 (ppp) REVERT: C 285 ILE cc_start: 0.8632 (pt) cc_final: 0.8400 (mm) REVERT: C 492 MET cc_start: 0.9052 (ppp) cc_final: 0.8785 (ppp) REVERT: C 515 MET cc_start: 0.6086 (ttp) cc_final: 0.5873 (ttp) REVERT: C 850 ILE cc_start: 0.5615 (mm) cc_final: 0.5071 (mm) REVERT: C 1304 MET cc_start: 0.6779 (tmm) cc_final: 0.6213 (ttt) REVERT: D 29 MET cc_start: 0.8661 (ppp) cc_final: 0.8196 (ppp) REVERT: D 118 LYS cc_start: 0.6365 (tptm) cc_final: 0.6134 (tptt) REVERT: D 180 MET cc_start: 0.3562 (tpt) cc_final: 0.3084 (tpt) REVERT: D 196 GLN cc_start: 0.9138 (mp10) cc_final: 0.8915 (mp10) REVERT: D 298 MET cc_start: 0.7974 (ttm) cc_final: 0.7598 (ttp) REVERT: D 321 LYS cc_start: 0.7205 (tptt) cc_final: 0.6094 (tptp) REVERT: D 973 LEU cc_start: 0.8698 (mt) cc_final: 0.8174 (mp) REVERT: D 1025 MET cc_start: 0.6869 (pmm) cc_final: 0.6179 (ppp) REVERT: D 1099 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.4886 (m-80) outliers start: 28 outliers final: 12 residues processed: 288 average time/residue: 0.3666 time to fit residues: 170.9933 Evaluate side-chains 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 253 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1099 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 283 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 316 optimal weight: 0.0770 chunk 132 optimal weight: 0.0040 overall best weight: 0.6752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1236 ASN C1288 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.121339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090856 restraints weight = 74174.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.093861 restraints weight = 40453.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.095905 restraints weight = 27139.146| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 26436 Z= 0.106 Angle : 0.548 10.493 35912 Z= 0.275 Chirality : 0.041 0.227 4105 Planarity : 0.004 0.053 4535 Dihedral : 11.256 169.485 4065 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 1.47 % Allowed : 11.68 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3169 helix: 0.87 (0.15), residues: 1186 sheet: -1.15 (0.29), residues: 330 loop : -2.62 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1020 HIS 0.012 0.001 HIS C1023 PHE 0.019 0.001 PHE C 253 TYR 0.016 0.001 TYR D1099 ARG 0.006 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 1012) hydrogen bonds : angle 4.41206 ( 2870) metal coordination : bond 0.00241 ( 7) metal coordination : angle 1.55373 ( 6) covalent geometry : bond 0.00242 (26429) covalent geometry : angle 0.54761 (35906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4266 (mm) REVERT: C 57 PHE cc_start: 0.6471 (t80) cc_final: 0.5911 (t80) REVERT: C 68 LEU cc_start: 0.3753 (OUTLIER) cc_final: 0.3539 (mt) REVERT: C 285 ILE cc_start: 0.8998 (pt) cc_final: 0.8550 (mm) REVERT: C 741 MET cc_start: 0.7333 (mmm) cc_final: 0.6992 (mmt) REVERT: C 805 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6550 (ppp) REVERT: C 850 ILE cc_start: 0.5688 (mm) cc_final: 0.5134 (mm) REVERT: C 953 LEU cc_start: 0.8943 (tt) cc_final: 0.8546 (pp) REVERT: C 1304 MET cc_start: 0.7017 (tmm) cc_final: 0.6341 (ttt) REVERT: D 29 MET cc_start: 0.8645 (ppp) cc_final: 0.8285 (ppp) REVERT: D 80 HIS cc_start: 0.7015 (t-90) cc_final: 0.6156 (p-80) REVERT: D 180 MET cc_start: 0.3643 (tpt) cc_final: 0.3106 (tpt) REVERT: D 196 GLN cc_start: 0.9205 (mp10) cc_final: 0.8780 (mp10) REVERT: D 298 MET cc_start: 0.8073 (ttm) cc_final: 0.7609 (ttp) REVERT: D 321 LYS cc_start: 0.7369 (tptt) cc_final: 0.6210 (tptp) REVERT: D 385 LEU cc_start: 0.8375 (tp) cc_final: 0.8079 (tp) REVERT: D 822 MET cc_start: 0.6553 (tpp) cc_final: 0.6199 (tpp) REVERT: D 973 LEU cc_start: 0.8766 (mt) cc_final: 0.8249 (mp) REVERT: D 1025 MET cc_start: 0.6998 (pmm) cc_final: 0.6366 (ppp) REVERT: D 1099 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.4849 (m-80) REVERT: D 1260 MET cc_start: 0.8714 (ttm) cc_final: 0.7982 (ttp) REVERT: D 1275 LEU cc_start: 0.7892 (mp) cc_final: 0.7379 (tt) outliers start: 40 outliers final: 23 residues processed: 287 average time/residue: 0.3650 time to fit residues: 170.1066 Evaluate side-chains 270 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1342 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 301 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 55 optimal weight: 0.0010 chunk 48 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 276 GLN C 387 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.114714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084154 restraints weight = 76178.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.086999 restraints weight = 43752.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088162 restraints weight = 26656.721| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26436 Z= 0.167 Angle : 0.620 14.944 35912 Z= 0.316 Chirality : 0.043 0.284 4105 Planarity : 0.005 0.056 4535 Dihedral : 11.367 166.414 4065 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 2.80 % Allowed : 14.44 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3169 helix: 0.92 (0.15), residues: 1182 sheet: -1.14 (0.28), residues: 339 loop : -2.36 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 115 HIS 0.010 0.001 HIS C 673 PHE 0.034 0.002 PHE A 231 TYR 0.016 0.002 TYR C1231 ARG 0.012 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 1012) hydrogen bonds : angle 4.47366 ( 2870) metal coordination : bond 0.00441 ( 7) metal coordination : angle 1.98299 ( 6) covalent geometry : bond 0.00372 (26429) covalent geometry : angle 0.61937 (35906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 254 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.4179 (mm) REVERT: C 124 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6424 (ppp) REVERT: C 688 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: C 741 MET cc_start: 0.7490 (mmm) cc_final: 0.7178 (mmm) REVERT: C 768 MET cc_start: 0.7722 (mtt) cc_final: 0.7458 (mtt) REVERT: C 805 MET cc_start: 0.7551 (ptt) cc_final: 0.7189 (ppp) REVERT: C 811 ASN cc_start: 0.9060 (p0) cc_final: 0.8648 (p0) REVERT: C 850 ILE cc_start: 0.6043 (mm) cc_final: 0.5482 (mm) REVERT: C 1023 HIS cc_start: 0.8404 (m170) cc_final: 0.7953 (m90) REVERT: C 1216 ARG cc_start: 0.7127 (tpt90) cc_final: 0.6919 (mtt-85) REVERT: C 1232 MET cc_start: 0.8036 (ppp) cc_final: 0.7576 (ppp) REVERT: C 1304 MET cc_start: 0.6587 (tmm) cc_final: 0.5737 (tmm) REVERT: D 29 MET cc_start: 0.8753 (ppp) cc_final: 0.8404 (ppp) REVERT: D 180 MET cc_start: 0.3675 (tpt) cc_final: 0.3035 (tpt) REVERT: D 298 MET cc_start: 0.7980 (ttm) cc_final: 0.7705 (ttp) REVERT: D 321 LYS cc_start: 0.7363 (tptt) cc_final: 0.6202 (tptp) REVERT: D 973 LEU cc_start: 0.8651 (mt) cc_final: 0.8074 (mp) REVERT: D 1025 MET cc_start: 0.7367 (pmm) cc_final: 0.6678 (ppp) REVERT: D 1040 MET cc_start: 0.2352 (mmm) cc_final: 0.1757 (mmt) REVERT: D 1099 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.5372 (t80) REVERT: D 1275 LEU cc_start: 0.7762 (mp) cc_final: 0.7235 (tt) outliers start: 76 outliers final: 42 residues processed: 301 average time/residue: 0.3618 time to fit residues: 176.8326 Evaluate side-chains 277 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 294 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 289 optimal weight: 0.0060 chunk 159 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 259 optimal weight: 0.0020 chunk 62 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.114818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084575 restraints weight = 75189.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087494 restraints weight = 43406.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088243 restraints weight = 27887.047| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26436 Z= 0.136 Angle : 0.576 12.640 35912 Z= 0.291 Chirality : 0.042 0.336 4105 Planarity : 0.004 0.054 4535 Dihedral : 11.297 164.778 4065 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 2.91 % Allowed : 15.69 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3169 helix: 1.05 (0.15), residues: 1181 sheet: -1.01 (0.30), residues: 315 loop : -2.25 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1020 HIS 0.010 0.001 HIS B 37 PHE 0.030 0.001 PHE D1034 TYR 0.013 0.001 TYR D 512 ARG 0.006 0.000 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1012) hydrogen bonds : angle 4.36552 ( 2870) metal coordination : bond 0.00358 ( 7) metal coordination : angle 1.59541 ( 6) covalent geometry : bond 0.00313 (26429) covalent geometry : angle 0.57563 (35906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4794 (OUTLIER) cc_final: 0.4238 (mm) REVERT: A 135 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (t0) REVERT: C 741 MET cc_start: 0.7243 (mmm) cc_final: 0.6993 (mmm) REVERT: C 768 MET cc_start: 0.7752 (mtt) cc_final: 0.7511 (mtt) REVERT: C 805 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7028 (ppp) REVERT: C 811 ASN cc_start: 0.9031 (p0) cc_final: 0.8658 (p0) REVERT: C 850 ILE cc_start: 0.6063 (mm) cc_final: 0.5498 (mm) REVERT: C 953 LEU cc_start: 0.9042 (tt) cc_final: 0.8575 (pp) REVERT: C 1085 MET cc_start: 0.7397 (mmt) cc_final: 0.7196 (mmt) REVERT: C 1232 MET cc_start: 0.8110 (ppp) cc_final: 0.7555 (ppp) REVERT: C 1304 MET cc_start: 0.6738 (tmm) cc_final: 0.5873 (tmm) REVERT: C 1315 MET cc_start: 0.6092 (tmm) cc_final: 0.5515 (ttp) REVERT: D 29 MET cc_start: 0.8703 (ppp) cc_final: 0.8401 (ppp) REVERT: D 237 MET cc_start: 0.6378 (tmm) cc_final: 0.6032 (tmm) REVERT: D 298 MET cc_start: 0.8092 (ttm) cc_final: 0.7729 (ttp) REVERT: D 321 LYS cc_start: 0.7469 (tptt) cc_final: 0.6329 (tptp) REVERT: D 385 LEU cc_start: 0.8375 (tp) cc_final: 0.8037 (tp) REVERT: D 435 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.5209 (mp10) REVERT: D 973 LEU cc_start: 0.8710 (mt) cc_final: 0.8204 (mp) REVERT: D 1025 MET cc_start: 0.7766 (pmm) cc_final: 0.6970 (ppp) REVERT: D 1040 MET cc_start: 0.2236 (mmm) cc_final: 0.2010 (mmt) REVERT: D 1260 MET cc_start: 0.8703 (ttm) cc_final: 0.8246 (ttp) outliers start: 79 outliers final: 52 residues processed: 299 average time/residue: 0.4311 time to fit residues: 209.7855 Evaluate side-chains 291 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1099 TYR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1342 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 206 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 134 optimal weight: 0.0270 chunk 231 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 276 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 80 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.108839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.079010 restraints weight = 72182.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.081229 restraints weight = 43577.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082381 restraints weight = 27938.338| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26436 Z= 0.206 Angle : 0.685 11.312 35912 Z= 0.348 Chirality : 0.044 0.265 4105 Planarity : 0.005 0.055 4535 Dihedral : 11.480 162.462 4065 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 3.24 % Allowed : 16.94 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 3169 helix: 0.72 (0.15), residues: 1176 sheet: -1.11 (0.29), residues: 327 loop : -2.23 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 115 HIS 0.010 0.001 HIS C 551 PHE 0.021 0.002 PHE D 437 TYR 0.026 0.002 TYR C 578 ARG 0.008 0.001 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 1012) hydrogen bonds : angle 4.71553 ( 2870) metal coordination : bond 0.00531 ( 7) metal coordination : angle 2.31653 ( 6) covalent geometry : bond 0.00475 (26429) covalent geometry : angle 0.68440 (35906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 234 time to evaluate : 5.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4221 (mm) REVERT: C 239 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7327 (mmp) REVERT: C 688 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: C 741 MET cc_start: 0.6846 (mmm) cc_final: 0.6578 (mmt) REVERT: C 796 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5635 (mp) REVERT: C 811 ASN cc_start: 0.8938 (p0) cc_final: 0.8714 (p0) REVERT: C 1085 MET cc_start: 0.7587 (mmt) cc_final: 0.7356 (mmt) REVERT: C 1232 MET cc_start: 0.8036 (ppp) cc_final: 0.7439 (ppp) REVERT: C 1304 MET cc_start: 0.6845 (tmm) cc_final: 0.5926 (tmm) REVERT: C 1315 MET cc_start: 0.6726 (tmm) cc_final: 0.6165 (ttp) REVERT: D 29 MET cc_start: 0.8800 (ppp) cc_final: 0.8382 (ppp) REVERT: D 134 ASP cc_start: 0.8488 (m-30) cc_final: 0.8082 (p0) REVERT: D 201 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9043 (tt) REVERT: D 235 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: D 237 MET cc_start: 0.6472 (tmm) cc_final: 0.6194 (tmt) REVERT: D 298 MET cc_start: 0.8077 (ttm) cc_final: 0.7538 (ttp) REVERT: D 321 LYS cc_start: 0.7470 (tptt) cc_final: 0.6496 (tptp) REVERT: D 385 LEU cc_start: 0.8594 (tp) cc_final: 0.8309 (tp) REVERT: D 435 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.5438 (mp10) REVERT: D 973 LEU cc_start: 0.8578 (mt) cc_final: 0.7932 (mp) REVERT: D 1025 MET cc_start: 0.7880 (pmm) cc_final: 0.6960 (ppp) REVERT: D 1040 MET cc_start: 0.2516 (mmm) cc_final: 0.2284 (mmt) REVERT: D 1143 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.5562 (t70) REVERT: D 1260 MET cc_start: 0.8771 (ttm) cc_final: 0.8077 (ttp) outliers start: 88 outliers final: 57 residues processed: 291 average time/residue: 0.5316 time to fit residues: 260.3485 Evaluate side-chains 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 271 optimal weight: 20.0000 chunk 288 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 166 optimal weight: 0.0670 chunk 14 optimal weight: 8.9990 chunk 188 optimal weight: 0.0670 overall best weight: 0.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.113575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.083146 restraints weight = 75670.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.085866 restraints weight = 43092.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.087033 restraints weight = 26843.790| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26436 Z= 0.114 Angle : 0.585 12.452 35912 Z= 0.291 Chirality : 0.042 0.359 4105 Planarity : 0.004 0.053 4535 Dihedral : 11.299 161.737 4065 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.21 % Allowed : 18.49 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3169 helix: 1.07 (0.15), residues: 1175 sheet: -0.96 (0.28), residues: 331 loop : -2.07 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1020 HIS 0.007 0.001 HIS D 777 PHE 0.020 0.001 PHE D1034 TYR 0.019 0.001 TYR D 512 ARG 0.004 0.000 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1012) hydrogen bonds : angle 4.37705 ( 2870) metal coordination : bond 0.00253 ( 7) metal coordination : angle 1.75124 ( 6) covalent geometry : bond 0.00261 (26429) covalent geometry : angle 0.58506 (35906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4286 (mm) REVERT: A 136 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 33 ARG cc_start: 0.6619 (ttt180) cc_final: 0.6161 (ttt90) REVERT: C 239 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7266 (mmp) REVERT: C 388 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7323 (mm) REVERT: C 704 MET cc_start: 0.8366 (mtt) cc_final: 0.7221 (mtt) REVERT: C 796 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5311 (mp) REVERT: C 811 ASN cc_start: 0.8806 (p0) cc_final: 0.8568 (p0) REVERT: C 850 ILE cc_start: 0.6147 (mm) cc_final: 0.5859 (mp) REVERT: C 1085 MET cc_start: 0.7223 (mmt) cc_final: 0.6920 (mmt) REVERT: C 1232 MET cc_start: 0.8139 (ppp) cc_final: 0.7562 (ppp) REVERT: C 1315 MET cc_start: 0.6666 (tmm) cc_final: 0.6106 (ttp) REVERT: D 29 MET cc_start: 0.8670 (ppp) cc_final: 0.8406 (ppp) REVERT: D 132 LEU cc_start: 0.9037 (pt) cc_final: 0.8613 (tp) REVERT: D 134 ASP cc_start: 0.8537 (m-30) cc_final: 0.8274 (p0) REVERT: D 298 MET cc_start: 0.8055 (ttm) cc_final: 0.7532 (ttp) REVERT: D 321 LYS cc_start: 0.7430 (tptt) cc_final: 0.6491 (tptp) REVERT: D 385 LEU cc_start: 0.8485 (tp) cc_final: 0.8130 (tp) REVERT: D 402 GLU cc_start: 0.7996 (pt0) cc_final: 0.7721 (pp20) REVERT: D 973 LEU cc_start: 0.8584 (mt) cc_final: 0.7901 (mp) REVERT: D 1025 MET cc_start: 0.7839 (pmm) cc_final: 0.7041 (ppp) REVERT: D 1143 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5626 (t70) REVERT: D 1260 MET cc_start: 0.8634 (ttm) cc_final: 0.8182 (ttp) outliers start: 60 outliers final: 45 residues processed: 285 average time/residue: 0.3716 time to fit residues: 175.3948 Evaluate side-chains 278 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 202 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 177 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS C 276 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1236 ASN D 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.111210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080788 restraints weight = 76027.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.083391 restraints weight = 44050.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084252 restraints weight = 28578.115| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26436 Z= 0.161 Angle : 0.627 13.876 35912 Z= 0.314 Chirality : 0.043 0.349 4105 Planarity : 0.004 0.054 4535 Dihedral : 11.328 160.627 4065 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer: Outliers : 2.54 % Allowed : 18.42 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3169 helix: 1.00 (0.15), residues: 1176 sheet: -1.01 (0.28), residues: 329 loop : -2.05 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1020 HIS 0.012 0.001 HIS C1023 PHE 0.026 0.002 PHE C 230 TYR 0.019 0.002 TYR C 578 ARG 0.006 0.000 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1012) hydrogen bonds : angle 4.48991 ( 2870) metal coordination : bond 0.00396 ( 7) metal coordination : angle 2.04745 ( 6) covalent geometry : bond 0.00372 (26429) covalent geometry : angle 0.62618 (35906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 233 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4378 (mm) REVERT: B 33 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6527 (ttt90) REVERT: B 51 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4946 (mmm) REVERT: C 239 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7020 (mmp) REVERT: C 431 LYS cc_start: 0.8553 (tptt) cc_final: 0.8062 (tptp) REVERT: C 688 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: C 796 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5374 (mp) REVERT: C 811 ASN cc_start: 0.8898 (p0) cc_final: 0.8676 (p0) REVERT: C 850 ILE cc_start: 0.6226 (mm) cc_final: 0.5625 (mm) REVERT: C 1023 HIS cc_start: 0.8391 (m90) cc_final: 0.8157 (m-70) REVERT: C 1085 MET cc_start: 0.7498 (mmt) cc_final: 0.7236 (mmt) REVERT: C 1232 MET cc_start: 0.7753 (ppp) cc_final: 0.7160 (ppp) REVERT: C 1315 MET cc_start: 0.6664 (tmm) cc_final: 0.6158 (ttp) REVERT: D 29 MET cc_start: 0.8777 (ppp) cc_final: 0.8452 (ppp) REVERT: D 235 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: D 298 MET cc_start: 0.8116 (ttm) cc_final: 0.7519 (ttp) REVERT: D 321 LYS cc_start: 0.7524 (tptt) cc_final: 0.6365 (tptp) REVERT: D 385 LEU cc_start: 0.8561 (tp) cc_final: 0.8273 (tp) REVERT: D 435 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5042 (mp10) REVERT: D 973 LEU cc_start: 0.8625 (mt) cc_final: 0.7924 (mp) REVERT: D 1040 MET cc_start: 0.0994 (mmt) cc_final: 0.0544 (mmm) REVERT: D 1143 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5384 (t70) outliers start: 69 outliers final: 54 residues processed: 279 average time/residue: 0.3578 time to fit residues: 163.4329 Evaluate side-chains 283 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 27 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 248 optimal weight: 0.4980 chunk 150 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082802 restraints weight = 75490.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085465 restraints weight = 42885.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.086351 restraints weight = 28049.118| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26436 Z= 0.120 Angle : 0.603 14.228 35912 Z= 0.298 Chirality : 0.043 0.334 4105 Planarity : 0.004 0.054 4535 Dihedral : 11.267 159.845 4065 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 2.54 % Allowed : 18.20 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3169 helix: 1.11 (0.15), residues: 1175 sheet: -0.92 (0.28), residues: 339 loop : -1.95 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1020 HIS 0.007 0.001 HIS D 777 PHE 0.025 0.001 PHE C 230 TYR 0.017 0.001 TYR D 512 ARG 0.005 0.000 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1012) hydrogen bonds : angle 4.36520 ( 2870) metal coordination : bond 0.00265 ( 7) metal coordination : angle 1.72604 ( 6) covalent geometry : bond 0.00276 (26429) covalent geometry : angle 0.60244 (35906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4478 (OUTLIER) cc_final: 0.3951 (mm) REVERT: B 33 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6427 (ttt90) REVERT: C 121 GLU cc_start: 0.6177 (tt0) cc_final: 0.5971 (mm-30) REVERT: C 239 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6832 (mmp) REVERT: C 388 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7530 (mm) REVERT: C 431 LYS cc_start: 0.8546 (tptt) cc_final: 0.8045 (tptp) REVERT: C 704 MET cc_start: 0.8317 (mtm) cc_final: 0.8109 (mtt) REVERT: C 796 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.5636 (mp) REVERT: C 850 ILE cc_start: 0.6181 (mm) cc_final: 0.5884 (mp) REVERT: C 1023 HIS cc_start: 0.8439 (m90) cc_final: 0.8183 (m-70) REVERT: C 1085 MET cc_start: 0.7448 (mmt) cc_final: 0.7166 (mmt) REVERT: C 1232 MET cc_start: 0.8191 (ppp) cc_final: 0.7620 (ppp) REVERT: D 29 MET cc_start: 0.8734 (ppp) cc_final: 0.8419 (ppp) REVERT: D 132 LEU cc_start: 0.9078 (pt) cc_final: 0.8717 (tp) REVERT: D 134 ASP cc_start: 0.8546 (m-30) cc_final: 0.8049 (p0) REVERT: D 201 LEU cc_start: 0.9371 (mm) cc_final: 0.8998 (tt) REVERT: D 235 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: D 237 MET cc_start: 0.6306 (tmt) cc_final: 0.6096 (tmt) REVERT: D 298 MET cc_start: 0.8088 (ttm) cc_final: 0.7518 (ttp) REVERT: D 316 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6851 (mp) REVERT: D 321 LYS cc_start: 0.7458 (tptt) cc_final: 0.6535 (tptp) REVERT: D 330 MET cc_start: 0.7644 (ppp) cc_final: 0.7081 (ppp) REVERT: D 385 LEU cc_start: 0.8509 (tp) cc_final: 0.8154 (tp) REVERT: D 435 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.4869 (mp10) REVERT: D 485 MET cc_start: 0.7049 (mmm) cc_final: 0.6770 (mmm) REVERT: D 929 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7203 (mp-120) REVERT: D 973 LEU cc_start: 0.8623 (mt) cc_final: 0.7930 (mp) REVERT: D 1025 MET cc_start: 0.6713 (ptp) cc_final: 0.5727 (ppp) REVERT: D 1040 MET cc_start: 0.0932 (mmt) cc_final: 0.0494 (mmm) REVERT: D 1143 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5282 (t70) REVERT: D 1260 MET cc_start: 0.8660 (ttm) cc_final: 0.8224 (ttp) outliers start: 69 outliers final: 48 residues processed: 283 average time/residue: 0.3475 time to fit residues: 161.8815 Evaluate side-chains 285 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 148 optimal weight: 6.9990 chunk 276 optimal weight: 30.0000 chunk 312 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.109889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079444 restraints weight = 76233.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081891 restraints weight = 44630.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.083125 restraints weight = 28435.148| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26436 Z= 0.183 Angle : 0.672 13.403 35912 Z= 0.336 Chirality : 0.044 0.346 4105 Planarity : 0.005 0.054 4535 Dihedral : 11.371 158.836 4065 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 2.32 % Allowed : 18.53 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3169 helix: 0.87 (0.15), residues: 1175 sheet: -1.10 (0.27), residues: 332 loop : -2.00 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1020 HIS 0.008 0.001 HIS C1116 PHE 0.021 0.002 PHE C 230 TYR 0.019 0.002 TYR C 578 ARG 0.006 0.001 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1012) hydrogen bonds : angle 4.61897 ( 2870) metal coordination : bond 0.00458 ( 7) metal coordination : angle 2.31695 ( 6) covalent geometry : bond 0.00425 (26429) covalent geometry : angle 0.67179 (35906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4356 (OUTLIER) cc_final: 0.3784 (mm) REVERT: B 199 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7143 (t0) REVERT: C 121 GLU cc_start: 0.6240 (tt0) cc_final: 0.6007 (mm-30) REVERT: C 239 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6695 (mmp) REVERT: C 369 MET cc_start: 0.5507 (ptm) cc_final: 0.4918 (ptm) REVERT: C 370 MET cc_start: 0.7969 (mmt) cc_final: 0.7611 (ppp) REVERT: C 388 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7185 (mm) REVERT: C 431 LYS cc_start: 0.8583 (tptt) cc_final: 0.8091 (tptp) REVERT: C 688 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: C 796 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.5715 (mp) REVERT: C 952 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: C 1023 HIS cc_start: 0.8474 (m90) cc_final: 0.8222 (m-70) REVERT: C 1232 MET cc_start: 0.8126 (ppp) cc_final: 0.7574 (ppp) REVERT: D 29 MET cc_start: 0.8794 (ppp) cc_final: 0.8502 (ppp) REVERT: D 134 ASP cc_start: 0.8641 (m-30) cc_final: 0.8170 (p0) REVERT: D 201 LEU cc_start: 0.9390 (mm) cc_final: 0.8975 (tt) REVERT: D 235 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: D 298 MET cc_start: 0.8238 (ttm) cc_final: 0.7665 (ttp) REVERT: D 316 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6794 (mp) REVERT: D 321 LYS cc_start: 0.7545 (tptt) cc_final: 0.6576 (tptp) REVERT: D 385 LEU cc_start: 0.8561 (tp) cc_final: 0.8260 (tp) REVERT: D 435 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.5221 (mp10) REVERT: D 929 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: D 973 LEU cc_start: 0.8649 (mt) cc_final: 0.7962 (mp) REVERT: D 1025 MET cc_start: 0.6785 (ptp) cc_final: 0.5792 (ppp) REVERT: D 1040 MET cc_start: 0.0927 (mmt) cc_final: 0.0469 (mmm) REVERT: D 1143 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5560 (t70) outliers start: 63 outliers final: 42 residues processed: 265 average time/residue: 0.3604 time to fit residues: 157.3944 Evaluate side-chains 271 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 0.0070 chunk 82 optimal weight: 4.9990 chunk 276 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 313 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.111324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081014 restraints weight = 75337.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.083399 restraints weight = 43363.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084628 restraints weight = 27857.099| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26436 Z= 0.139 Angle : 0.635 14.180 35912 Z= 0.313 Chirality : 0.043 0.354 4105 Planarity : 0.004 0.054 4535 Dihedral : 11.335 158.458 4065 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 2.28 % Allowed : 18.38 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3169 helix: 0.99 (0.15), residues: 1168 sheet: -0.93 (0.28), residues: 326 loop : -1.96 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1020 HIS 0.007 0.001 HIS C1116 PHE 0.021 0.001 PHE C 230 TYR 0.020 0.001 TYR D 512 ARG 0.005 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1012) hydrogen bonds : angle 4.48829 ( 2870) metal coordination : bond 0.00326 ( 7) metal coordination : angle 2.00634 ( 6) covalent geometry : bond 0.00324 (26429) covalent geometry : angle 0.63501 (35906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9467.19 seconds wall clock time: 168 minutes 13.65 seconds (10093.65 seconds total)