Starting phenix.real_space_refine on Mon Mar 25 01:08:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/03_2024/7tyr_26192.pdb" } resolution = 3.33 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13911 atoms to isotropic. 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 202 5.16 5 C 20214 2.51 5 N 5348 2.21 5 O 5846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A ASP 1132": "OD1" <-> "OD2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A GLU 1557": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1728": "OE1" <-> "OE2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1751": "OE1" <-> "OE2" Residue "A GLU 1769": "OE1" <-> "OE2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A GLU 1838": "OE1" <-> "OE2" Residue "A GLU 2087": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A PHE 2309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2339": "OE1" <-> "OE2" Residue "A GLU 2430": "OE1" <-> "OE2" Residue "A GLU 2528": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2895": "OE1" <-> "OE2" Residue "A GLU 2974": "OE1" <-> "OE2" Residue "A ASP 2980": "OD1" <-> "OD2" Residue "A TYR 3114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3140": "OE1" <-> "OE2" Residue "A ASP 3180": "OD1" <-> "OD2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A PHE 3382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3427": "OE1" <-> "OE2" Residue "A GLU 3478": "OE1" <-> "OE2" Residue "A ASP 3507": "OD1" <-> "OD2" Residue "A PHE 3585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ASP 3778": "OD1" <-> "OD2" Residue "A GLU 3823": "OE1" <-> "OE2" Residue "A ASP 3851": "OD1" <-> "OD2" Residue "A GLU 3875": "OE1" <-> "OE2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C GLU 409": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 31173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3905, 31162 Classifications: {'peptide': 3905} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 179, 'TRANS': 3725} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 3905, 31162 Classifications: {'peptide': 3905} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 179, 'TRANS': 3725} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 31806 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 8, 'TRANS': 43} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A4011 " occ=0.40 ... (20 atoms not shown) pdb=" CZ BPHE A4011 " occ=0.60 Time building chain proxies: 31.77, per 1000 atoms: 1.01 Number of scatterers: 31610 At special positions: 0 Unit cell: (128.52, 149.04, 185.76, 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 202 16.00 O 5846 8.00 N 5348 7.00 C 20214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1942 " - pdb=" SG CYS A2093 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 12.23 Conformation dependent library (CDL) restraints added in 11.3 seconds 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7566 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 6 sheets defined 71.1% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 removed outlier: 4.056A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.152A pdb=" N GLN A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.138A pdb=" N SER A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.534A pdb=" N GLN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.549A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 181 removed outlier: 4.051A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.934A pdb=" N ASN A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.805A pdb=" N VAL A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 4.155A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 306 through 330 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.830A pdb=" N PHE A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.800A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 446 through 449 removed outlier: 3.703A pdb=" N TYR A 449 " --> pdb=" O PHE A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 450 through 470 Processing helix chain 'A' and resid 472 through 492 Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.655A pdb=" N PHE A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.590A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 579 removed outlier: 3.927A pdb=" N LEU A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 removed outlier: 3.902A pdb=" N TRP A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.646A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.930A pdb=" N GLU A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.296A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.568A pdb=" N LYS A 692 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 718 removed outlier: 3.701A pdb=" N TYR A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.501A pdb=" N LEU A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.612A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 Processing helix chain 'A' and resid 762 through 780 Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 802 Proline residue: A 794 - end of helix removed outlier: 3.753A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 847 through 863 removed outlier: 3.803A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.176A pdb=" N LYS A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 958 through 973 Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 978 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1023 through 1044 removed outlier: 3.656A pdb=" N LYS A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1092 removed outlier: 3.669A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1100 through 1114 Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.533A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1226 removed outlier: 6.735A pdb=" N VAL A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N SER A1218 " --> pdb=" O GLU A1214 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A1219 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.668A pdb=" N ALA A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1273 removed outlier: 3.892A pdb=" N LEU A1254 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A1273 " --> pdb=" O THR A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1283 Processing helix chain 'A' and resid 1289 through 1301 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1323 through 1352 removed outlier: 3.747A pdb=" N GLU A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1360 removed outlier: 4.282A pdb=" N LEU A1358 " --> pdb=" O GLU A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1363 No H-bonds generated for 'chain 'A' and resid 1361 through 1363' Processing helix chain 'A' and resid 1364 through 1378 Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 4.439A pdb=" N ILE A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A1383 " --> pdb=" O PRO A1379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1378 through 1383' Processing helix chain 'A' and resid 1388 through 1408 removed outlier: 3.894A pdb=" N MET A1392 " --> pdb=" O ASP A1388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A1394 " --> pdb=" O GLN A1390 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Proline residue: A1396 - end of helix removed outlier: 3.625A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 4.125A pdb=" N GLU A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1432 removed outlier: 3.655A pdb=" N GLU A1429 " --> pdb=" O ALA A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.847A pdb=" N ARG A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1477 through 1491 removed outlier: 3.822A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1522 removed outlier: 4.082A pdb=" N GLY A1522 " --> pdb=" O ALA A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.521A pdb=" N ILE A1567 " --> pdb=" O PHE A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 Processing helix chain 'A' and resid 1589 through 1606 Processing helix chain 'A' and resid 1613 through 1624 Processing helix chain 'A' and resid 1625 through 1628 Processing helix chain 'A' and resid 1629 through 1634 removed outlier: 3.980A pdb=" N TRP A1633 " --> pdb=" O CYS A1629 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A1634 " --> pdb=" O ASP A1630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1629 through 1634' Processing helix chain 'A' and resid 1638 through 1657 Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.777A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1695 Processing helix chain 'A' and resid 1696 through 1700 Processing helix chain 'A' and resid 1704 through 1707 Processing helix chain 'A' and resid 1708 through 1722 Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1788 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1812 through 1822 removed outlier: 3.816A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1830 Processing helix chain 'A' and resid 1832 through 1852 removed outlier: 5.385A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 3.519A pdb=" N ASP A1864 " --> pdb=" O GLU A1860 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 4.092A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1924 Processing helix chain 'A' and resid 1934 through 1954 removed outlier: 4.216A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1976 removed outlier: 3.692A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2048 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2123 through 2135 Processing helix chain 'A' and resid 2139 through 2152 removed outlier: 3.596A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 4.376A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2164 through 2173 removed outlier: 3.627A pdb=" N LEU A2168 " --> pdb=" O TRP A2164 " (cutoff:3.500A) Processing helix chain 'A' and resid 2183 through 2195 Processing helix chain 'A' and resid 2205 through 2220 removed outlier: 3.539A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A2210 " --> pdb=" O PRO A2206 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A2211 " --> pdb=" O LYS A2207 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A2220 " --> pdb=" O LEU A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2252 through 2261 removed outlier: 3.632A pdb=" N ILE A2256 " --> pdb=" O PRO A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2269 through 2282 removed outlier: 4.410A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2299 Processing helix chain 'A' and resid 2300 through 2306 removed outlier: 3.777A pdb=" N VAL A2304 " --> pdb=" O PHE A2300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2333 Processing helix chain 'A' and resid 2338 through 2354 removed outlier: 4.116A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A2353 " --> pdb=" O LEU A2349 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2369 removed outlier: 3.511A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.629A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2403 removed outlier: 4.000A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2418 removed outlier: 3.532A pdb=" N GLN A2414 " --> pdb=" O GLU A2410 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2418 " --> pdb=" O GLN A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2426 Processing helix chain 'A' and resid 2430 through 2443 Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 3.533A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2485 removed outlier: 3.668A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2509 removed outlier: 3.506A pdb=" N GLN A2496 " --> pdb=" O ASP A2492 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2527 Processing helix chain 'A' and resid 2536 through 2545 removed outlier: 3.952A pdb=" N LEU A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2551 removed outlier: 3.511A pdb=" N GLU A2551 " --> pdb=" O PRO A2548 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2787 through 2799 removed outlier: 4.024A pdb=" N ILE A2791 " --> pdb=" O HIS A2787 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2823 removed outlier: 3.903A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.599A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2866 through 2871 removed outlier: 4.084A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2900 Processing helix chain 'A' and resid 2917 through 2934 Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 4.078A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2978 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3018 removed outlier: 4.471A pdb=" N SER A3018 " --> pdb=" O CYS A3014 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3032 Processing helix chain 'A' and resid 3033 through 3040 Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3071 removed outlier: 3.944A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3072 through 3082 removed outlier: 3.870A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3093 Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.565A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A3100 " --> pdb=" O VAL A3096 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A3102 " --> pdb=" O ARG A3098 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3146 removed outlier: 3.955A pdb=" N ARG A3125 " --> pdb=" O LEU A3121 " (cutoff:3.500A) Processing helix chain 'A' and resid 3147 through 3151 removed outlier: 3.694A pdb=" N ASN A3150 " --> pdb=" O LYS A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.662A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3205 through 3211 Processing helix chain 'A' and resid 3212 through 3221 removed outlier: 3.677A pdb=" N ASP A3216 " --> pdb=" O GLY A3212 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A3219 " --> pdb=" O SER A3215 " (cutoff:3.500A) Processing helix chain 'A' and resid 3226 through 3249 removed outlier: 3.583A pdb=" N LEU A3230 " --> pdb=" O ASP A3226 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3267 removed outlier: 3.562A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 3.850A pdb=" N ARG A3289 " --> pdb=" O HIS A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3305 removed outlier: 3.953A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) Processing helix chain 'A' and resid 3309 through 3317 removed outlier: 4.220A pdb=" N TYR A3315 " --> pdb=" O ASN A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3343 removed outlier: 3.627A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.576A pdb=" N ILE A3351 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3364 removed outlier: 3.556A pdb=" N GLY A3364 " --> pdb=" O LEU A3360 " (cutoff:3.500A) Processing helix chain 'A' and resid 3371 through 3394 Processing helix chain 'A' and resid 3405 through 3430 removed outlier: 4.413A pdb=" N VAL A3409 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A3430 " --> pdb=" O LYS A3426 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3440 Processing helix chain 'A' and resid 3441 through 3456 Processing helix chain 'A' and resid 3458 through 3464 Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 4.068A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3487 removed outlier: 3.864A pdb=" N THR A3479 " --> pdb=" O TYR A3475 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER A3481 " --> pdb=" O GLU A3477 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU A3482 " --> pdb=" O GLU A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3488 through 3490 No H-bonds generated for 'chain 'A' and resid 3488 through 3490' Processing helix chain 'A' and resid 3491 through 3495 Processing helix chain 'A' and resid 3498 through 3504 Processing helix chain 'A' and resid 3508 through 3510 No H-bonds generated for 'chain 'A' and resid 3508 through 3510' Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 3.580A pdb=" N GLN A3515 " --> pdb=" O ALA A3511 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS A3516 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.899A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3563 Processing helix chain 'A' and resid 3566 through 3577 Processing helix chain 'A' and resid 3582 through 3596 removed outlier: 3.517A pdb=" N TRP A3588 " --> pdb=" O LEU A3584 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A3593 " --> pdb=" O SER A3589 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A3594 " --> pdb=" O ASN A3590 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A3595 " --> pdb=" O ASP A3591 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3615 removed outlier: 3.757A pdb=" N TYR A3610 " --> pdb=" O ILE A3606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3644 removed outlier: 5.754A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU A3639 " --> pdb=" O THR A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3654 removed outlier: 3.996A pdb=" N LEU A3652 " --> pdb=" O GLY A3648 " (cutoff:3.500A) Processing helix chain 'A' and resid 3656 through 3659 removed outlier: 4.045A pdb=" N PHE A3659 " --> pdb=" O LEU A3656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3656 through 3659' Processing helix chain 'A' and resid 3660 through 3673 removed outlier: 4.220A pdb=" N ASN A3664 " --> pdb=" O ASN A3660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A3668 " --> pdb=" O ASN A3664 " (cutoff:3.500A) Processing helix chain 'A' and resid 3679 through 3684 removed outlier: 3.612A pdb=" N CYS A3683 " --> pdb=" O ASN A3679 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3758 through 3777 Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 4.181A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.997A pdb=" N MET A3856 " --> pdb=" O VAL A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.981A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3993 Processing helix chain 'A' and resid 3995 through 4007 Processing helix chain 'A' and resid 4012 through 4023 Processing helix chain 'A' and resid 4039 through 4052 removed outlier: 3.650A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 1540 through 1541 Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3722 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 6.657A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1798 hydrogen bonds defined for protein. 5286 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: 19.40 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5662 1.32 - 1.45: 7868 1.45 - 1.57: 18437 1.57 - 1.70: 0 1.70 - 1.82: 317 Bond restraints: 32284 Sorted by residual: bond pdb=" N VAL A3878 " pdb=" CA VAL A3878 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.52e+01 bond pdb=" N ARG A2915 " pdb=" CA ARG A2915 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.23e-02 6.61e+03 1.17e+01 bond pdb=" N ASP C 389 " pdb=" CA ASP C 389 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.91e+00 bond pdb=" N ARG A2158 " pdb=" CA ARG A2158 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.91e+00 bond pdb=" N THR A 965 " pdb=" CA THR A 965 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.23e-02 6.61e+03 9.39e+00 ... (remaining 32279 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.55: 732 105.55 - 112.74: 16898 112.74 - 119.92: 11765 119.92 - 127.11: 13916 127.11 - 134.29: 348 Bond angle restraints: 43659 Sorted by residual: angle pdb=" N TYR A3715 " pdb=" CA TYR A3715 " pdb=" C TYR A3715 " ideal model delta sigma weight residual 111.28 103.96 7.32 1.09e+00 8.42e-01 4.51e+01 angle pdb=" C ASP A 723 " pdb=" CA ASP A 723 " pdb=" CB ASP A 723 " ideal model delta sigma weight residual 116.63 109.46 7.17 1.16e+00 7.43e-01 3.83e+01 angle pdb=" C GLU A3714 " pdb=" CA GLU A3714 " pdb=" CB GLU A3714 " ideal model delta sigma weight residual 110.04 118.54 -8.50 1.51e+00 4.39e-01 3.17e+01 angle pdb=" N LYS A3302 " pdb=" CA LYS A3302 " pdb=" C LYS A3302 " ideal model delta sigma weight residual 111.36 105.38 5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" N ARG A1938 " pdb=" CA ARG A1938 " pdb=" C ARG A1938 " ideal model delta sigma weight residual 111.07 105.63 5.44 1.07e+00 8.73e-01 2.58e+01 ... (remaining 43654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16290 17.98 - 35.95: 2457 35.95 - 53.93: 743 53.93 - 71.90: 177 71.90 - 89.88: 82 Dihedral angle restraints: 19749 sinusoidal: 8111 harmonic: 11638 Sorted by residual: dihedral pdb=" CA MET A2605 " pdb=" C MET A2605 " pdb=" N PHE A2606 " pdb=" CA PHE A2606 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 791 " pdb=" CB ASP A 791 " pdb=" CG ASP A 791 " pdb=" OD1 ASP A 791 " ideal model delta sinusoidal sigma weight residual -30.00 -89.90 59.90 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ILE A1085 " pdb=" C ILE A1085 " pdb=" N TYR A1086 " pdb=" CA TYR A1086 " ideal model delta harmonic sigma weight residual 180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 19746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4118 0.061 - 0.122: 655 0.122 - 0.183: 114 0.183 - 0.244: 14 0.244 - 0.305: 2 Chirality restraints: 4903 Sorted by residual: chirality pdb=" CA LEU A4021 " pdb=" N LEU A4021 " pdb=" C LEU A4021 " pdb=" CB LEU A4021 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 640 " pdb=" N GLU A 640 " pdb=" C GLU A 640 " pdb=" CB GLU A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4900 not shown) Planarity restraints: 5587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A2161 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.64e+01 pdb=" C ALA A2161 " -0.070 2.00e-02 2.50e+03 pdb=" O ALA A2161 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A2162 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 793 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 794 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 794 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 794 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A3716 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C HIS A3716 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS A3716 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A3717 " 0.018 2.00e-02 2.50e+03 ... (remaining 5584 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1050 2.72 - 3.26: 32164 3.26 - 3.81: 51118 3.81 - 4.35: 62784 4.35 - 4.90: 104135 Nonbonded interactions: 251251 Sorted by model distance: nonbonded pdb=" CG1 VAL C 381 " pdb=" ND1 HIS C 382 " model vdw 2.171 3.540 nonbonded pdb=" O THR A 206 " pdb=" OG1 THR A 209 " model vdw 2.224 2.440 nonbonded pdb=" O ASP A3411 " pdb=" OG1 THR A3415 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A1675 " pdb=" O ALA A1692 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASP A2044 " pdb=" OG SER A2051 " model vdw 2.247 2.440 ... (remaining 251246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.030 Extract box with map and model: 29.080 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 114.270 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32284 Z= 0.267 Angle : 0.758 10.580 43659 Z= 0.476 Chirality : 0.048 0.305 4903 Planarity : 0.005 0.077 5587 Dihedral : 19.611 89.881 12180 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 2.70 % Allowed : 29.48 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 3948 helix: 1.24 (0.10), residues: 2507 sheet: 1.37 (0.76), residues: 43 loop : -2.04 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 300 HIS 0.009 0.001 HIS A1115 PHE 0.033 0.001 PHE A3382 TYR 0.015 0.001 TYR A3828 ARG 0.010 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 599 time to evaluate : 3.753 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: A 8 VAL cc_start: 0.7662 (p) cc_final: 0.7372 (p) REVERT: A 134 LEU cc_start: 0.7964 (tt) cc_final: 0.7742 (tp) REVERT: A 541 MET cc_start: 0.8029 (tpp) cc_final: 0.7692 (mmm) REVERT: A 2224 PHE cc_start: 0.8197 (t80) cc_final: 0.7985 (t80) REVERT: A 2500 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7682 (mmtm) REVERT: A 3576 ASP cc_start: 0.8764 (t0) cc_final: 0.8309 (t0) outliers start: 95 outliers final: 20 residues processed: 660 average time/residue: 0.4822 time to fit residues: 491.4216 Evaluate side-chains 323 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 302 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 LYS Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2500 LYS Chi-restraints excluded: chain A residue 2915 ARG Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 309 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 358 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 613 HIS A 676 ASN A 857 GLN A1084 ASN A1466 ASN A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS ** A2177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN A2352 HIS A2977 ASN ** A3059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3440 GLN ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3760 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32284 Z= 0.184 Angle : 0.626 14.504 43659 Z= 0.313 Chirality : 0.039 0.193 4903 Planarity : 0.005 0.093 5587 Dihedral : 5.317 70.565 4317 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.21 % Allowed : 28.60 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3948 helix: 1.69 (0.11), residues: 2547 sheet: 0.99 (0.73), residues: 43 loop : -1.94 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2164 HIS 0.010 0.001 HIS A2352 PHE 0.029 0.001 PHE A2157 TYR 0.019 0.001 TYR C 391 ARG 0.010 0.000 ARG A2776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7127 (tpp) cc_final: 0.6479 (ttt) REVERT: A 208 MET cc_start: 0.6683 (ppp) cc_final: 0.5992 (mtt) REVERT: A 916 GLU cc_start: 0.7903 (tt0) cc_final: 0.7618 (tt0) REVERT: A 3218 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.1296 (mmp) REVERT: A 3411 ASP cc_start: 0.8667 (t70) cc_final: 0.8332 (t0) REVERT: A 3576 ASP cc_start: 0.8829 (t0) cc_final: 0.8516 (t0) REVERT: A 4087 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7531 (m-70) outliers start: 78 outliers final: 30 residues processed: 395 average time/residue: 0.4471 time to fit residues: 288.4574 Evaluate side-chains 312 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1476 HIS Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 1607 GLU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1845 VAL Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2041 SER Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2352 HIS Chi-restraints excluded: chain A residue 2915 ARG Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3591 ASP Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 320 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3150 ASN A3590 ASN ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32284 Z= 0.195 Angle : 0.606 14.644 43659 Z= 0.301 Chirality : 0.039 0.199 4903 Planarity : 0.004 0.085 5587 Dihedral : 4.781 61.796 4297 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.44 % Allowed : 28.12 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3948 helix: 1.84 (0.11), residues: 2553 sheet: 0.72 (0.70), residues: 43 loop : -1.87 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2164 HIS 0.020 0.001 HIS A2352 PHE 0.021 0.001 PHE A 153 TYR 0.017 0.001 TYR A 748 ARG 0.008 0.000 ARG A2776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 302 time to evaluate : 4.071 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: A 144 MET cc_start: 0.7362 (tpp) cc_final: 0.6900 (ttt) REVERT: A 208 MET cc_start: 0.6785 (ppp) cc_final: 0.6054 (mtt) REVERT: A 541 MET cc_start: 0.7881 (mmm) cc_final: 0.7524 (mmm) REVERT: A 686 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6879 (t) REVERT: A 718 MET cc_start: 0.8347 (ptt) cc_final: 0.8073 (ptt) REVERT: A 916 GLU cc_start: 0.7942 (tt0) cc_final: 0.7648 (tt0) REVERT: A 2094 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7318 (tpt) REVERT: A 3139 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 3218 MET cc_start: 0.2611 (OUTLIER) cc_final: 0.1250 (mmp) REVERT: A 3411 ASP cc_start: 0.8672 (t70) cc_final: 0.8336 (t0) REVERT: A 3576 ASP cc_start: 0.8854 (t0) cc_final: 0.8560 (t0) REVERT: A 3590 ASN cc_start: 0.7427 (m-40) cc_final: 0.7200 (m-40) REVERT: A 3612 ARG cc_start: 0.7229 (tmm160) cc_final: 0.7024 (ttt-90) REVERT: A 4087 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7665 (m-70) outliers start: 86 outliers final: 41 residues processed: 368 average time/residue: 0.4190 time to fit residues: 255.3806 Evaluate side-chains 327 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1871 MET Chi-restraints excluded: chain A residue 1912 THR Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1939 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2344 LEU Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2915 ARG Chi-restraints excluded: chain A residue 3115 SER Chi-restraints excluded: chain A residue 3142 ILE Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3337 ILE Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3401 TRP Chi-restraints excluded: chain A residue 3643 HIS Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 188 optimal weight: 0.2980 chunk 341 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3037 GLN A3059 GLN ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32284 Z= 0.174 Angle : 0.595 17.686 43659 Z= 0.292 Chirality : 0.039 0.173 4903 Planarity : 0.004 0.073 5587 Dihedral : 4.524 57.504 4289 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.84 % Allowed : 28.58 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3948 helix: 1.97 (0.11), residues: 2556 sheet: 0.53 (0.70), residues: 43 loop : -1.81 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2164 HIS 0.004 0.001 HIS A1115 PHE 0.029 0.001 PHE A 88 TYR 0.015 0.001 TYR A2160 ARG 0.008 0.000 ARG A2776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7369 (ttp) cc_final: 0.6685 (ppp) REVERT: A 144 MET cc_start: 0.7349 (tpp) cc_final: 0.6443 (ttt) REVERT: A 208 MET cc_start: 0.6877 (ppp) cc_final: 0.6192 (mtt) REVERT: A 541 MET cc_start: 0.7914 (mmm) cc_final: 0.7652 (mmm) REVERT: A 686 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6844 (t) REVERT: A 718 MET cc_start: 0.8343 (ptt) cc_final: 0.8075 (ptt) REVERT: A 913 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7772 (tpt170) REVERT: A 916 GLU cc_start: 0.7932 (tt0) cc_final: 0.7730 (tt0) REVERT: A 1524 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 2094 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7348 (tpt) REVERT: A 3139 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 3218 MET cc_start: 0.2685 (OUTLIER) cc_final: 0.1165 (mmm) REVERT: A 3411 ASP cc_start: 0.8660 (t70) cc_final: 0.8337 (t0) REVERT: A 3576 ASP cc_start: 0.8856 (t0) cc_final: 0.8470 (t0) REVERT: A 4087 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: C 372 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.3627 (mp) outliers start: 65 outliers final: 35 residues processed: 348 average time/residue: 0.4454 time to fit residues: 252.2887 Evaluate side-chains 318 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1476 HIS Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1871 MET Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2344 LEU Chi-restraints excluded: chain A residue 3115 SER Chi-restraints excluded: chain A residue 3142 ILE Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3337 ILE Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3401 TRP Chi-restraints excluded: chain A residue 3643 HIS Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1738 ASN ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2266 ASN ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32284 Z= 0.239 Angle : 0.612 15.412 43659 Z= 0.301 Chirality : 0.040 0.234 4903 Planarity : 0.004 0.070 5587 Dihedral : 4.380 59.878 4285 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.21 % Allowed : 28.06 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3948 helix: 1.96 (0.11), residues: 2557 sheet: 0.36 (0.68), residues: 45 loop : -1.78 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A3588 HIS 0.033 0.001 HIS A1476 PHE 0.042 0.001 PHE A 156 TYR 0.012 0.001 TYR A3540 ARG 0.009 0.000 ARG A3763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 285 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7258 (ttp) cc_final: 0.6579 (ppp) REVERT: A 144 MET cc_start: 0.7382 (tpp) cc_final: 0.6561 (ttt) REVERT: A 541 MET cc_start: 0.7913 (mmm) cc_final: 0.7657 (mmm) REVERT: A 577 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 620 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: A 686 VAL cc_start: 0.7256 (OUTLIER) cc_final: 0.6981 (t) REVERT: A 718 MET cc_start: 0.8381 (ptt) cc_final: 0.8101 (ptt) REVERT: A 1524 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7563 (pp) REVERT: A 2094 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7439 (tpt) REVERT: A 2312 TYR cc_start: 0.7444 (m-10) cc_final: 0.7189 (m-10) REVERT: A 3139 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 3218 MET cc_start: 0.2766 (OUTLIER) cc_final: 0.1195 (mmm) REVERT: A 3576 ASP cc_start: 0.8913 (t0) cc_final: 0.8602 (t0) REVERT: A 4087 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7916 (m-70) REVERT: C 372 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.3831 (mp) outliers start: 78 outliers final: 54 residues processed: 339 average time/residue: 0.4198 time to fit residues: 239.2121 Evaluate side-chains 326 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1476 HIS Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1631 SER Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1871 MET Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1939 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2160 TYR Chi-restraints excluded: chain A residue 2208 ASP Chi-restraints excluded: chain A residue 2344 LEU Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2405 VAL Chi-restraints excluded: chain A residue 2517 LEU Chi-restraints excluded: chain A residue 2547 SER Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2826 LEU Chi-restraints excluded: chain A residue 3115 SER Chi-restraints excluded: chain A residue 3142 ILE Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3401 TRP Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3643 HIS Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 0.7980 chunk 343 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 382 optimal weight: 0.7980 chunk 317 optimal weight: 0.2980 chunk 176 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 126 optimal weight: 0.0270 chunk 200 optimal weight: 9.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN ** A2105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32284 Z= 0.162 Angle : 0.584 15.319 43659 Z= 0.286 Chirality : 0.038 0.166 4903 Planarity : 0.004 0.066 5587 Dihedral : 4.281 59.562 4284 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.04 % Allowed : 27.95 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.14), residues: 3948 helix: 2.05 (0.11), residues: 2550 sheet: 0.34 (0.68), residues: 45 loop : -1.76 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3588 HIS 0.019 0.001 HIS A1476 PHE 0.021 0.001 PHE A2260 TYR 0.015 0.001 TYR A2589 ARG 0.007 0.000 ARG A3763 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 283 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7320 (tpp) cc_final: 0.6707 (ttt) REVERT: A 541 MET cc_start: 0.7917 (mmm) cc_final: 0.7657 (mmm) REVERT: A 620 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: A 686 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6949 (t) REVERT: A 718 MET cc_start: 0.8332 (ptt) cc_final: 0.8042 (ptt) REVERT: A 1524 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7430 (pp) REVERT: A 3139 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 3218 MET cc_start: 0.2748 (OUTLIER) cc_final: 0.1239 (mmm) REVERT: A 3411 ASP cc_start: 0.8725 (t70) cc_final: 0.8409 (t0) REVERT: A 3576 ASP cc_start: 0.8883 (t0) cc_final: 0.8496 (t0) REVERT: A 4087 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7889 (m-70) REVERT: C 372 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.3797 (mp) outliers start: 72 outliers final: 50 residues processed: 337 average time/residue: 0.4155 time to fit residues: 234.7188 Evaluate side-chains 319 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 263 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1476 HIS Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1871 MET Chi-restraints excluded: chain A residue 1912 THR Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2041 SER Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2344 LEU Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 3115 SER Chi-restraints excluded: chain A residue 3142 ILE Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3401 TRP Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3643 HIS Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9896 > 50: distance: 37 - 53: 16.807 distance: 45 - 73: 37.067 distance: 48 - 53: 15.729 distance: 49 - 81: 35.061 distance: 53 - 54: 12.279 distance: 54 - 55: 28.709 distance: 54 - 57: 17.739 distance: 55 - 56: 16.675 distance: 55 - 64: 16.903 distance: 58 - 59: 6.582 distance: 59 - 60: 17.459 distance: 60 - 61: 10.203 distance: 61 - 62: 24.248 distance: 61 - 63: 19.985 distance: 65 - 66: 4.832 distance: 65 - 68: 16.574 distance: 66 - 67: 16.994 distance: 68 - 69: 30.144 distance: 69 - 70: 6.199 distance: 70 - 71: 17.839 distance: 70 - 72: 6.984 distance: 73 - 74: 11.871 distance: 74 - 75: 59.040 distance: 74 - 77: 29.570 distance: 75 - 76: 4.575 distance: 75 - 81: 40.409 distance: 77 - 78: 3.960 distance: 78 - 79: 40.456 distance: 78 - 80: 20.811 distance: 81 - 82: 25.819 distance: 82 - 83: 37.747 distance: 82 - 85: 25.423 distance: 83 - 84: 9.114 distance: 83 - 89: 28.051 distance: 85 - 86: 18.634 distance: 86 - 87: 60.365 distance: 86 - 88: 12.347 distance: 89 - 90: 12.612 distance: 90 - 91: 15.094 distance: 90 - 93: 12.978 distance: 91 - 92: 15.924 distance: 91 - 97: 15.362 distance: 92 - 118: 22.081 distance: 93 - 94: 26.074 distance: 94 - 95: 4.528 distance: 94 - 96: 20.813 distance: 97 - 98: 24.292 distance: 97 - 103: 24.662 distance: 98 - 99: 27.282 distance: 98 - 101: 26.672 distance: 99 - 100: 14.646 distance: 99 - 104: 30.250 distance: 101 - 102: 8.807 distance: 102 - 103: 21.012 distance: 104 - 105: 18.727 distance: 105 - 108: 12.264 distance: 106 - 107: 4.929 distance: 106 - 111: 13.078 distance: 108 - 109: 17.060 distance: 108 - 110: 35.761 distance: 111 - 112: 14.697 distance: 112 - 113: 33.040 distance: 112 - 115: 7.246 distance: 113 - 114: 27.873 distance: 113 - 118: 14.964 distance: 115 - 116: 18.638 distance: 115 - 117: 46.140 distance: 118 - 119: 14.069 distance: 119 - 120: 29.514 distance: 119 - 122: 13.744 distance: 120 - 121: 16.086 distance: 120 - 127: 30.130 distance: 122 - 123: 21.557 distance: 123 - 124: 7.347 distance: 124 - 126: 24.509 distance: 127 - 128: 10.391 distance: 128 - 129: 17.317 distance: 128 - 131: 18.410 distance: 129 - 130: 9.856 distance: 129 - 138: 8.883 distance: 131 - 132: 6.084 distance: 132 - 133: 8.737 distance: 132 - 134: 14.570 distance: 133 - 135: 7.710 distance: 134 - 136: 10.064 distance: 135 - 137: 12.157 distance: 136 - 137: 10.808