Starting phenix.real_space_refine on Sun Jun 22 09:31:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.map" model { file = "/net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r9b_4769/06_2025/6r9b_4769.cif" } resolution = 3.8 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= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 16142 2.51 5 N 4503 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25880 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1790 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1648 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10260 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 7, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 9901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 9901 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 54, 'TRANS': 1268} Chain breaks: 6 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 266 Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 567 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Time building chain proxies: 14.26, per 1000 atoms: 0.55 Number of scatterers: 25880 At special positions: 0 Unit cell: (135.04, 168.8, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 5122 8.00 N 4503 7.00 C 16142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 814 " - pdb=" SG CYS D 895 " distance=2.87 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: 5.48 Conformation dependent library (CDL) restraints added in 3.2 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 29 sheets defined 37.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.621A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.588A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.664A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 35 through 48 removed outlier: 3.528A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.812A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.187A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.751A pdb=" N GLN C 86 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.875A pdb=" N ARG C 201 " --> pdb=" O ILE C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.644A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 4.175A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.466A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.735A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.973A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (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 482 removed outlier: 3.698A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.608A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 4.106A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 524 " --> pdb=" O PRO C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.583A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.663A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.673A pdb=" N GLY C 792 " --> pdb=" O THR C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 4.128A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 899 through 906 Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.671A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 Processing helix chain 'C' and resid 1005 through 1039 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.770A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1169 through 1176 Processing helix chain 'C' and resid 1192 through 1202 removed outlier: 4.514A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.652A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.734A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1322 through 1331 Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.192A pdb=" N ILE D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.605A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.647A pdb=" N GLY D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.299A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 229 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.534A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.530A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.500A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 539 removed outlier: 4.335A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.547A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.803A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 5.015A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.580A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 700 Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.610A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.658A pdb=" N ALA D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 787 Processing helix chain 'D' and resid 788 through 803 removed outlier: 3.751A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.521A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.618A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.527A pdb=" N ASP D 891 " --> pdb=" O CYS D 888 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 892 " --> pdb=" O ASP D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 892' Processing helix chain 'D' and resid 914 through 922 removed outlier: 3.683A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 936 removed outlier: 3.530A pdb=" N PHE D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 931 through 936' Processing helix chain 'D' and resid 1063 through 1068 Processing helix chain 'D' and resid 1134 through 1138 removed outlier: 3.770A pdb=" N LEU D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1134 through 1138' Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.902A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.611A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1286 removed outlier: 3.862A pdb=" N LYS D1286 " --> pdb=" O TYR D1282 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.566A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.083A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.720A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 29 through 43 removed outlier: 4.055A pdb=" N ASP F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 76 through 96 removed outlier: 3.767A pdb=" N ILE F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 4.073A pdb=" N ASN F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL F 108 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 26 removed outlier: 4.037A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.855A pdb=" N ILE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.763A pdb=" N PHE G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.927A pdb=" N LEU G 70 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 71' Processing helix chain 'G' and resid 76 through 108 removed outlier: 3.751A pdb=" N ILE G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 108 " --> pdb=" O TYR G 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.526A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.062A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.940A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.723A pdb=" N VAL B 26 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.602A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 70 Processing sheet with id=AA7, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.050A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.723A pdb=" N GLY C 154 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 187 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 195 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 204 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB1, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.551A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.844A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 604 through 605 removed outlier: 3.839A pdb=" N HIS C 604 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.795A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 724 through 728 removed outlier: 6.787A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AB8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.904A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 831 through 835 removed outlier: 7.750A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 838 through 839 Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AC3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.068A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 352 " --> pdb=" O HIS C1244 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.529A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 105 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 369 removed outlier: 6.518A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 548 through 552 removed outlier: 3.983A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 843 through 844 removed outlier: 4.381A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 950 through 951 removed outlier: 7.074A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.703A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 965 through 967 removed outlier: 4.238A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1264 through 1265 867 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.36 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7923 1.34 - 1.46: 3827 1.46 - 1.58: 14294 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26242 Sorted by residual: bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.335 1.377 -0.042 8.70e-03 1.32e+04 2.30e+01 bond pdb=" C LYS D 749 " pdb=" N PRO D 750 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.20e-02 6.94e+03 1.95e+01 bond pdb=" C ARG D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.37e+00 bond pdb=" CA CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sigma weight residual 1.530 1.497 0.033 1.69e-02 3.50e+03 3.88e+00 bond pdb=" CA CYS D 895 " pdb=" C CYS D 895 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.34e-02 5.57e+03 3.78e+00 ... (remaining 26237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 35132 3.16 - 6.32: 327 6.32 - 9.48: 67 9.48 - 12.64: 11 12.64 - 15.80: 4 Bond angle restraints: 35541 Sorted by residual: angle pdb=" C GLY C1318 " pdb=" N MET C1319 " pdb=" CA MET C1319 " ideal model delta sigma weight residual 120.67 136.47 -15.80 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N SER D 143 " pdb=" CA SER D 143 " pdb=" C SER D 143 " ideal model delta sigma weight residual 111.17 121.16 -9.99 1.41e+00 5.03e-01 5.02e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 106.72 117.23 -10.51 1.59e+00 3.96e-01 4.37e+01 angle pdb=" C GLY C1102 " pdb=" N VAL C1103 " pdb=" CA VAL C1103 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" N TYR D 144 " pdb=" CA TYR D 144 " pdb=" C TYR D 144 " ideal model delta sigma weight residual 110.80 124.35 -13.55 2.13e+00 2.20e-01 4.04e+01 ... (remaining 35536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 15360 15.17 - 30.34: 576 30.34 - 45.52: 150 45.52 - 60.69: 25 60.69 - 75.86: 21 Dihedral angle restraints: 16132 sinusoidal: 6347 harmonic: 9785 Sorted by residual: dihedral pdb=" C VAL D 886 " pdb=" N VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual -122.00 -142.71 20.71 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual 123.40 143.29 -19.89 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" CB CYS D 814 " pdb=" SG CYS D 814 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual 93.00 26.32 66.68 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4078 0.169 - 0.337: 27 0.337 - 0.506: 4 0.506 - 0.674: 1 0.674 - 0.843: 1 Chirality restraints: 4111 Sorted by residual: chirality pdb=" CA VAL D 886 " pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CB VAL D 886 " both_signs ideal model delta sigma weight residual False 2.44 1.60 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA TYR D 144 " pdb=" N TYR D 144 " pdb=" C TYR D 144 " pdb=" CB TYR D 144 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA VAL D 501 " pdb=" N VAL D 501 " pdb=" C VAL D 501 " pdb=" CB VAL D 501 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 4108 not shown) Planarity restraints: 4712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 925 " 0.057 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO D 926 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 926 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 926 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 923 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE D 923 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE D 923 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY D 924 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 427 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.036 5.00e-02 4.00e+02 ... (remaining 4709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7196 2.82 - 3.34: 22113 3.34 - 3.86: 39480 3.86 - 4.38: 43068 4.38 - 4.90: 75038 Nonbonded interactions: 186895 Sorted by model distance: nonbonded pdb=" OG SER C 815 " pdb=" O VAL C1075 " model vdw 2.296 3.040 nonbonded pdb=" O ARG D 425 " pdb=" OG1 THR D 428 " model vdw 2.303 3.040 nonbonded pdb=" OG SER D1032 " pdb=" O ILE D1115 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR F 7 " pdb=" OD2 ASP F 92 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP A 15 " pdb=" OG1 THR A 27 " model vdw 2.324 3.040 ... (remaining 186890 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 6 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 60 or (resid 61 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 70 or (resi \ d 71 and (name N or name CA or name C or name O or name CB )) or resid 72 throug \ h 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or re \ sid 79 through 116 or (resid 117 and (name N or name CA or name C or name O or n \ ame CB )) or resid 118 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or n \ ame C or name O or name CB )) or resid 126 through 131 or (resid 132 and (name N \ or name CA or name C or name O or name CB )) or resid 133 through 141 or (resid \ 142 through 143 and (name N or name CA or name C or name O or name CB )) or res \ id 144 through 159 or resid 172 through 176 or (resid 177 and (name N or name CA \ or name C or name O or name CB )) or resid 178 through 234 or (resid 235 and (n \ ame N or name CA or name C or name O or name CB )) or resid 236 through 237)) selection = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 5 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 108)) } 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=0.00 max=1.00 mean=0.92 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 54.410 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 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 : 0.006 0.835 26243 Z= 0.327 Angle : 0.880 15.800 35543 Z= 0.502 Chirality : 0.057 0.843 4111 Planarity : 0.006 0.085 4712 Dihedral : 9.765 75.860 9817 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 0.70 % Allowed : 2.57 % Favored : 96.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -4.57 (0.11), residues: 3373 helix: -2.95 (0.10), residues: 1172 sheet: -1.61 (0.31), residues: 233 loop : -3.42 (0.11), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1276 HIS 0.015 0.001 HIS C1023 PHE 0.022 0.002 PHE D 620 TYR 0.022 0.001 TYR C 215 ARG 0.006 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.15697 ( 867) hydrogen bonds : angle 6.80004 ( 2517) SS BOND : bond 0.83459 ( 1) SS BOND : angle 2.93733 ( 2) covalent geometry : bond 0.00337 (26242) covalent geometry : angle 0.87939 (35541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 742 time to evaluate : 2.934 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 330 HIS cc_start: 0.5248 (m-70) cc_final: 0.5042 (m-70) REVERT: C 611 GLU cc_start: 0.5726 (pt0) cc_final: 0.5400 (pp20) REVERT: C 704 MET cc_start: 0.5480 (mmp) cc_final: 0.4783 (ppp) REVERT: C 735 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8559 (tptm) REVERT: C 755 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7143 (mtpp) REVERT: C 767 GLN cc_start: 0.7252 (mm110) cc_final: 0.6915 (mm-40) REVERT: C 782 VAL cc_start: 0.7528 (p) cc_final: 0.7325 (m) REVERT: D 29 MET cc_start: 0.7671 (ttp) cc_final: 0.7410 (tpp) REVERT: D 475 GLU cc_start: 0.7058 (pm20) cc_final: 0.6810 (mp0) REVERT: F 38 HIS cc_start: 0.6427 (m-70) cc_final: 0.6082 (m90) REVERT: G 5 MET cc_start: 0.3567 (mmp) cc_final: 0.3000 (mmt) outliers start: 19 outliers final: 4 residues processed: 754 average time/residue: 0.4324 time to fit residues: 486.1549 Evaluate side-chains 387 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 383 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 885 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 40.0000 chunk 256 optimal weight: 10.0000 chunk 142 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 117 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 450 ASN C 518 ASN C 618 GLN C 832 HIS C 952 GLN C1080 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1244 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN D 702 GLN D 805 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1268 ASN D1350 ASN F 9 ASN F 13 HIS F 43 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.213421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.190467 restraints weight = 41477.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.189556 restraints weight = 70787.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.189616 restraints weight = 62819.232| |-----------------------------------------------------------------------------| r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 26243 Z= 0.190 Angle : 0.725 15.067 35543 Z= 0.376 Chirality : 0.047 0.308 4111 Planarity : 0.005 0.048 4712 Dihedral : 5.305 59.843 3669 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.05 % Allowed : 10.68 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -3.16 (0.13), residues: 3373 helix: -1.04 (0.14), residues: 1182 sheet: -1.76 (0.32), residues: 235 loop : -2.97 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 580 HIS 0.017 0.002 HIS D 364 PHE 0.027 0.002 PHE A 231 TYR 0.041 0.002 TYR F 15 ARG 0.006 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 867) hydrogen bonds : angle 4.82350 ( 2517) SS BOND : bond 0.01003 ( 1) SS BOND : angle 1.47846 ( 2) covalent geometry : bond 0.00433 (26242) covalent geometry : angle 0.72500 (35541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 418 time to evaluate : 2.588 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7412 (p) cc_final: 0.6643 (m) REVERT: B 215 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6410 (tm-30) REVERT: C 604 HIS cc_start: 0.6980 (p-80) cc_final: 0.6676 (p90) REVERT: C 704 MET cc_start: 0.5546 (mmp) cc_final: 0.5008 (ppp) REVERT: C 796 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6786 (pp) REVERT: C 805 MET cc_start: 0.7676 (mtp) cc_final: 0.7424 (ttm) REVERT: C 1085 MET cc_start: 0.7224 (mmp) cc_final: 0.5903 (mmt) REVERT: C 1285 TYR cc_start: 0.6189 (t80) cc_final: 0.5947 (t80) REVERT: D 448 GLN cc_start: 0.5727 (pm20) cc_final: 0.3695 (mt0) REVERT: D 638 SER cc_start: 0.7146 (t) cc_final: 0.6502 (p) REVERT: G 5 MET cc_start: 0.4214 (mmp) cc_final: 0.2398 (mmt) outliers start: 83 outliers final: 38 residues processed: 474 average time/residue: 0.4060 time to fit residues: 295.4316 Evaluate side-chains 348 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 18 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 318 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 149 optimal weight: 0.1980 chunk 225 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 84 ASN C 518 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C 932 GLN C1111 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 593 ASN ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 38 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.205294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.185030 restraints weight = 41883.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.184641 restraints weight = 87709.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.184694 restraints weight = 73333.354| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26243 Z= 0.231 Angle : 0.784 16.044 35543 Z= 0.401 Chirality : 0.049 0.285 4111 Planarity : 0.006 0.054 4712 Dihedral : 5.500 58.867 3669 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.98 % Favored : 90.96 % Rotamer: Outliers : 3.49 % Allowed : 13.14 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -2.77 (0.13), residues: 3373 helix: -0.56 (0.14), residues: 1215 sheet: -1.85 (0.30), residues: 251 loop : -2.85 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 236 HIS 0.017 0.002 HIS D 545 PHE 0.023 0.002 PHE A 231 TYR 0.035 0.003 TYR F 15 ARG 0.018 0.001 ARG D 883 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 867) hydrogen bonds : angle 4.80104 ( 2517) SS BOND : bond 0.00457 ( 1) SS BOND : angle 1.51389 ( 2) covalent geometry : bond 0.00529 (26242) covalent geometry : angle 0.78371 (35541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 376 time to evaluate : 2.681 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: 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: symmetry clash REVERT: A 131 CYS cc_start: 0.7497 (p) cc_final: 0.6815 (m) REVERT: B 215 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6391 (tm-30) REVERT: C 130 MET cc_start: 0.6990 (ttm) cc_final: 0.6584 (ttp) REVERT: C 185 ASP cc_start: 0.6674 (t0) cc_final: 0.6440 (m-30) REVERT: C 684 ASN cc_start: 0.8292 (p0) cc_final: 0.8016 (p0) REVERT: C 704 MET cc_start: 0.5654 (mmp) cc_final: 0.5073 (ppp) REVERT: C 805 MET cc_start: 0.7615 (mtp) cc_final: 0.7383 (ttm) REVERT: C 822 VAL cc_start: 0.7211 (t) cc_final: 0.6652 (p) REVERT: C 1177 ARG cc_start: 0.7204 (tmt90) cc_final: 0.6884 (mtp-110) REVERT: C 1232 MET cc_start: 0.8073 (mtp) cc_final: 0.7661 (mtp) REVERT: D 485 MET cc_start: 0.6245 (mtt) cc_final: 0.5963 (mtt) REVERT: D 490 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5248 (mt) REVERT: D 504 GLN cc_start: 0.5316 (mm110) cc_final: 0.5063 (mt0) REVERT: D 638 SER cc_start: 0.7912 (t) cc_final: 0.7237 (p) REVERT: D 835 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6998 (tt) REVERT: D 1254 GLU cc_start: 0.6837 (tt0) cc_final: 0.6328 (mt-10) REVERT: G 5 MET cc_start: 0.4214 (mmp) cc_final: 0.2907 (mmt) outliers start: 95 outliers final: 59 residues processed: 436 average time/residue: 0.3993 time to fit residues: 273.7946 Evaluate side-chains 390 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 190 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 195 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 117 HIS A 132 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 343 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 659 GLN C 725 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1116 HIS C1136 GLN C1220 GLN C1313 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 910 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.200197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.179405 restraints weight = 42156.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.179497 restraints weight = 84749.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.179167 restraints weight = 66268.078| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 26243 Z= 0.229 Angle : 0.759 15.182 35543 Z= 0.391 Chirality : 0.049 0.313 4111 Planarity : 0.005 0.058 4712 Dihedral : 5.376 31.027 3663 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 4.15 % Allowed : 14.10 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.47 (0.14), residues: 3373 helix: -0.26 (0.15), residues: 1200 sheet: -1.44 (0.32), residues: 258 loop : -2.73 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 580 HIS 0.017 0.002 HIS D 545 PHE 0.028 0.002 PHE C 514 TYR 0.032 0.002 TYR F 15 ARG 0.013 0.001 ARG D1231 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 867) hydrogen bonds : angle 4.86445 ( 2517) SS BOND : bond 0.00442 ( 1) SS BOND : angle 1.38666 ( 2) covalent geometry : bond 0.00530 (26242) covalent geometry : angle 0.75858 (35541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 339 time to evaluate : 2.578 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: A 131 CYS cc_start: 0.7590 (p) cc_final: 0.7041 (m) REVERT: A 133 LEU cc_start: 0.5296 (mt) cc_final: 0.4968 (mt) REVERT: B 215 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6849 (tp30) REVERT: C 130 MET cc_start: 0.7521 (ttm) cc_final: 0.7130 (ttp) REVERT: C 603 ILE cc_start: 0.8027 (mp) cc_final: 0.7725 (mt) REVERT: C 613 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6732 (t0) REVERT: C 704 MET cc_start: 0.6235 (mmp) cc_final: 0.4776 (tmm) REVERT: C 805 MET cc_start: 0.7676 (mtp) cc_final: 0.7250 (ttm) REVERT: D 504 GLN cc_start: 0.5745 (mm110) cc_final: 0.5536 (tt0) REVERT: D 1254 GLU cc_start: 0.6873 (tt0) cc_final: 0.6269 (mt-10) REVERT: G 5 MET cc_start: 0.4289 (mmp) cc_final: 0.2351 (mmt) outliers start: 113 outliers final: 60 residues processed: 416 average time/residue: 0.4049 time to fit residues: 264.0954 Evaluate side-chains 365 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1195 ILE Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 4 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 179 optimal weight: 0.0980 chunk 332 optimal weight: 30.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.202314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.180992 restraints weight = 42012.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.179976 restraints weight = 85427.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.180527 restraints weight = 79510.773| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26243 Z= 0.147 Angle : 0.677 12.767 35543 Z= 0.344 Chirality : 0.046 0.344 4111 Planarity : 0.004 0.060 4712 Dihedral : 5.003 29.201 3663 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 3.16 % Allowed : 16.26 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -2.25 (0.14), residues: 3373 helix: -0.00 (0.15), residues: 1214 sheet: -1.52 (0.32), residues: 267 loop : -2.63 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 236 HIS 0.014 0.001 HIS D 364 PHE 0.030 0.002 PHE C 224 TYR 0.032 0.002 TYR F 15 ARG 0.006 0.000 ARG G 23 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 867) hydrogen bonds : angle 4.57490 ( 2517) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.64533 ( 2) covalent geometry : bond 0.00337 (26242) covalent geometry : angle 0.67689 (35541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 2.924 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7545 (p) cc_final: 0.7086 (m) REVERT: B 215 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6752 (tp30) REVERT: C 130 MET cc_start: 0.7445 (ttm) cc_final: 0.7127 (ttp) REVERT: C 704 MET cc_start: 0.6299 (mmp) cc_final: 0.5397 (ttp) REVERT: C 1085 MET cc_start: 0.7318 (mmp) cc_final: 0.5609 (mmt) REVERT: C 1248 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.6075 (m) REVERT: C 1305 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5119 (m-10) REVERT: D 582 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7340 (mt) REVERT: D 1254 GLU cc_start: 0.6936 (tt0) cc_final: 0.6312 (mt-10) REVERT: F 5 MET cc_start: 0.4196 (ppp) cc_final: 0.3843 (ppp) REVERT: G 5 MET cc_start: 0.4346 (mmp) cc_final: 0.2706 (mmt) outliers start: 86 outliers final: 52 residues processed: 405 average time/residue: 0.4034 time to fit residues: 252.7564 Evaluate side-chains 368 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain G residue 47 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 135 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 276 optimal weight: 40.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1136 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.198434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.177818 restraints weight = 41934.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.177338 restraints weight = 91136.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.176300 restraints weight = 65282.450| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26243 Z= 0.204 Angle : 0.740 14.446 35543 Z= 0.376 Chirality : 0.048 0.283 4111 Planarity : 0.005 0.059 4712 Dihedral : 5.192 30.742 3663 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.69 % Rotamer: Outliers : 3.34 % Allowed : 16.85 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -2.24 (0.14), residues: 3373 helix: -0.04 (0.15), residues: 1213 sheet: -1.45 (0.31), residues: 277 loop : -2.62 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 236 HIS 0.013 0.001 HIS D 364 PHE 0.025 0.002 PHE C 224 TYR 0.029 0.002 TYR F 15 ARG 0.007 0.001 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 867) hydrogen bonds : angle 4.70660 ( 2517) SS BOND : bond 0.00287 ( 1) SS BOND : angle 1.00009 ( 2) covalent geometry : bond 0.00474 (26242) covalent geometry : angle 0.74044 (35541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 315 time to evaluate : 2.886 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: A 131 CYS cc_start: 0.7280 (p) cc_final: 0.7057 (m) REVERT: B 215 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6721 (tp30) REVERT: C 11 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8456 (mt) REVERT: C 130 MET cc_start: 0.7691 (ttm) cc_final: 0.7388 (ttp) REVERT: D 298 MET cc_start: 0.2083 (mmt) cc_final: 0.1735 (mpp) REVERT: D 837 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5849 (p0) REVERT: F 5 MET cc_start: 0.4369 (ppp) cc_final: 0.4169 (ppp) REVERT: G 5 MET cc_start: 0.4162 (mmp) cc_final: 0.3696 (tpp) outliers start: 91 outliers final: 64 residues processed: 384 average time/residue: 0.3938 time to fit residues: 237.6011 Evaluate side-chains 365 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 31 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 313 optimal weight: 20.0000 chunk 163 optimal weight: 0.5980 chunk 315 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.202502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.181916 restraints weight = 41966.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.181457 restraints weight = 81332.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.180535 restraints weight = 66983.295| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26243 Z= 0.121 Angle : 0.664 12.215 35543 Z= 0.335 Chirality : 0.046 0.249 4111 Planarity : 0.004 0.060 4712 Dihedral : 4.810 27.559 3663 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 2.20 % Allowed : 18.28 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -1.95 (0.14), residues: 3373 helix: 0.23 (0.15), residues: 1214 sheet: -1.28 (0.32), residues: 265 loop : -2.46 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 236 HIS 0.013 0.001 HIS D 364 PHE 0.022 0.001 PHE C 224 TYR 0.030 0.001 TYR F 15 ARG 0.010 0.000 ARG C 994 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 867) hydrogen bonds : angle 4.45022 ( 2517) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.53628 ( 2) covalent geometry : bond 0.00267 (26242) covalent geometry : angle 0.66403 (35541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 2.707 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: 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 76 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 131 CYS cc_start: 0.7475 (p) cc_final: 0.7243 (m) REVERT: B 185 TYR cc_start: 0.6512 (p90) cc_final: 0.6104 (p90) REVERT: B 204 GLU cc_start: 0.6584 (tp30) cc_final: 0.6382 (mm-30) REVERT: B 226 GLU cc_start: 0.7404 (tp30) cc_final: 0.6901 (tp30) REVERT: C 130 MET cc_start: 0.7474 (ttm) cc_final: 0.7158 (ttp) REVERT: C 704 MET cc_start: 0.6497 (mmp) cc_final: 0.5385 (ppp) REVERT: C 1085 MET cc_start: 0.7389 (mmp) cc_final: 0.5651 (mmt) REVERT: D 582 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7401 (mt) REVERT: D 638 SER cc_start: 0.8096 (t) cc_final: 0.7447 (p) REVERT: D 643 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6463 (t0) REVERT: D 837 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5486 (p0) REVERT: G 5 MET cc_start: 0.4178 (mmp) cc_final: 0.2944 (mmt) outliers start: 60 outliers final: 42 residues processed: 377 average time/residue: 0.3716 time to fit residues: 222.2922 Evaluate side-chains 346 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 47 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 240 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 327 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 188 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.197178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.176266 restraints weight = 42081.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.176500 restraints weight = 91548.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.176006 restraints weight = 68140.825| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.7610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26243 Z= 0.207 Angle : 0.758 14.867 35543 Z= 0.383 Chirality : 0.048 0.293 4111 Planarity : 0.005 0.057 4712 Dihedral : 5.157 31.808 3663 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 3.05 % Allowed : 18.02 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -2.03 (0.14), residues: 3373 helix: 0.11 (0.15), residues: 1212 sheet: -1.35 (0.32), residues: 268 loop : -2.46 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 236 HIS 0.011 0.002 HIS D 364 PHE 0.022 0.002 PHE C 514 TYR 0.030 0.002 TYR F 15 ARG 0.007 0.001 ARG G 23 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 867) hydrogen bonds : angle 4.69972 ( 2517) SS BOND : bond 0.00237 ( 1) SS BOND : angle 1.07297 ( 2) covalent geometry : bond 0.00481 (26242) covalent geometry : angle 0.75769 (35541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 2.647 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: 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 76 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: C 11 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 130 MET cc_start: 0.7808 (ttm) cc_final: 0.7529 (ttp) REVERT: C 704 MET cc_start: 0.6598 (mmp) cc_final: 0.5554 (ttp) REVERT: C 1078 LYS cc_start: 0.5806 (mmtm) cc_final: 0.5350 (tptp) REVERT: D 643 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 1254 GLU cc_start: 0.6781 (tt0) cc_final: 0.6113 (mt-10) REVERT: G 5 MET cc_start: 0.4191 (mmp) cc_final: 0.3128 (mmt) outliers start: 83 outliers final: 54 residues processed: 382 average time/residue: 0.3809 time to fit residues: 228.5246 Evaluate side-chains 347 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 150 optimal weight: 0.9980 chunk 189 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 233 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1244 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.202316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.183176 restraints weight = 42292.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.181884 restraints weight = 79778.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.182154 restraints weight = 72140.418| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.7562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26243 Z= 0.123 Angle : 0.694 12.045 35543 Z= 0.347 Chirality : 0.046 0.285 4111 Planarity : 0.004 0.060 4712 Dihedral : 4.799 26.721 3663 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 2.02 % Allowed : 20.08 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -1.78 (0.14), residues: 3373 helix: 0.30 (0.15), residues: 1216 sheet: -1.05 (0.34), residues: 247 loop : -2.31 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.012 0.001 HIS D 364 PHE 0.023 0.001 PHE C 224 TYR 0.032 0.001 TYR F 15 ARG 0.005 0.000 ARG G 23 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 867) hydrogen bonds : angle 4.45781 ( 2517) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.41304 ( 2) covalent geometry : bond 0.00274 (26242) covalent geometry : angle 0.69366 (35541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 2.928 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: B 185 TYR cc_start: 0.6501 (p90) cc_final: 0.6124 (p90) REVERT: B 226 GLU cc_start: 0.7405 (tp30) cc_final: 0.6992 (tp30) REVERT: C 704 MET cc_start: 0.6459 (mmp) cc_final: 0.5439 (ppp) REVERT: C 1085 MET cc_start: 0.7406 (mmp) cc_final: 0.5634 (mmt) REVERT: D 270 ARG cc_start: 0.4989 (tmt170) cc_final: 0.4784 (tmt170) REVERT: D 582 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7343 (mt) REVERT: D 638 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7805 (p) REVERT: D 643 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6886 (t70) REVERT: G 5 MET cc_start: 0.4142 (mmp) cc_final: 0.3156 (mmt) outliers start: 55 outliers final: 38 residues processed: 354 average time/residue: 0.3935 time to fit residues: 219.6468 Evaluate side-chains 339 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3631 > 50: distance: 16 - 20: 30.589 distance: 20 - 21: 9.284 distance: 21 - 22: 24.396 distance: 21 - 24: 33.088 distance: 22 - 23: 26.523 distance: 24 - 25: 18.779 distance: 27 - 28: 27.952 distance: 27 - 30: 5.038 distance: 28 - 29: 49.570 distance: 28 - 37: 10.877 distance: 30 - 31: 24.663 distance: 31 - 32: 40.118 distance: 31 - 33: 34.453 distance: 32 - 34: 26.858 distance: 33 - 35: 12.678 distance: 34 - 36: 39.328 distance: 35 - 36: 33.333 distance: 38 - 39: 19.010 distance: 39 - 40: 24.835 distance: 39 - 41: 31.836 distance: 41 - 42: 42.478 distance: 42 - 43: 10.230 distance: 42 - 45: 12.938 distance: 43 - 44: 9.799 distance: 43 - 50: 23.855 distance: 45 - 46: 8.633 distance: 46 - 47: 5.346 distance: 47 - 48: 18.727 distance: 50 - 51: 32.704 distance: 51 - 52: 14.206 distance: 51 - 54: 20.739 distance: 52 - 53: 22.830 distance: 52 - 57: 17.459 distance: 54 - 55: 23.922 distance: 54 - 56: 19.083 distance: 57 - 58: 6.031 distance: 58 - 59: 28.043 distance: 58 - 61: 23.144 distance: 59 - 60: 43.546 distance: 59 - 66: 20.881 distance: 61 - 62: 20.042 distance: 62 - 63: 12.573 distance: 63 - 64: 12.418 distance: 64 - 65: 10.600 distance: 66 - 67: 18.439 distance: 67 - 68: 15.722 distance: 67 - 70: 27.567 distance: 68 - 69: 38.251 distance: 68 - 71: 18.278 distance: 71 - 77: 28.669 distance: 72 - 73: 22.942 distance: 72 - 75: 13.652 distance: 73 - 74: 33.342 distance: 73 - 78: 19.759 distance: 75 - 76: 19.926 distance: 76 - 77: 5.463 distance: 78 - 79: 22.422 distance: 79 - 80: 15.875 distance: 79 - 82: 29.406 distance: 80 - 81: 11.421 distance: 80 - 87: 32.875 distance: 82 - 83: 19.579 distance: 83 - 84: 14.304 distance: 84 - 85: 23.164 distance: 84 - 86: 41.441 distance: 87 - 88: 11.285 distance: 88 - 89: 10.187 distance: 88 - 91: 11.233 distance: 89 - 90: 12.383 distance: 89 - 94: 15.226 distance: 91 - 92: 19.699 distance: 91 - 93: 9.742