Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bq1_7129/05_2023/6bq1_7129_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 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: 5 Type Number sf(0) Gaussians S 216 5.16 5 C 23649 2.51 5 N 6447 2.21 5 O 6849 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 981": "NH1" <-> "NH2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1183": "NH1" <-> "NH2" Residue "A ARG 1220": "NH1" <-> "NH2" Residue "A ARG 1326": "NH1" <-> "NH2" Residue "A ARG 1488": "NH1" <-> "NH2" Residue "A ARG 1489": "NH1" <-> "NH2" Residue "A ARG 1561": "NH1" <-> "NH2" Residue "A ARG 1574": "NH1" <-> "NH2" Residue "A ARG 1643": "NH1" <-> "NH2" Residue "A ARG 1662": "NH1" <-> "NH2" Residue "A TYR 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1733": "NH1" <-> "NH2" Residue "A ARG 1757": "NH1" <-> "NH2" Residue "A TYR 1803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1885": "NH1" <-> "NH2" Residue "A ARG 1922": "NH1" <-> "NH2" Residue "A ARG 1936": "NH1" <-> "NH2" Residue "A ARG 1941": "NH1" <-> "NH2" Residue "A PHE 1980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2022": "NH1" <-> "NH2" Residue "A ARG 2028": "NH1" <-> "NH2" Residue "A ARG 2068": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 981": "NH1" <-> "NH2" Residue "E ASP 1135": "OD1" <-> "OD2" Residue "E ARG 1158": "NH1" <-> "NH2" Residue "E ARG 1183": "NH1" <-> "NH2" Residue "E ARG 1220": "NH1" <-> "NH2" Residue "E ARG 1326": "NH1" <-> "NH2" Residue "E ARG 1488": "NH1" <-> "NH2" Residue "E ARG 1489": "NH1" <-> "NH2" Residue "E ARG 1561": "NH1" <-> "NH2" Residue "E ARG 1574": "NH1" <-> "NH2" Residue "E ARG 1643": "NH1" <-> "NH2" Residue "E ARG 1662": "NH1" <-> "NH2" Residue "E ARG 1733": "NH1" <-> "NH2" Residue "E ARG 1757": "NH1" <-> "NH2" Residue "E TYR 1803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1885": "NH1" <-> "NH2" Residue "E ARG 1922": "NH1" <-> "NH2" Residue "E ARG 1936": "NH1" <-> "NH2" Residue "E ARG 1941": "NH1" <-> "NH2" Residue "E ARG 2022": "NH1" <-> "NH2" Residue "E ARG 2028": "NH1" <-> "NH2" Residue "E ARG 2068": "NH1" <-> "NH2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 266": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37163 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1509, 10673 Classifications: {'peptide': 1509} Incomplete info: {'truncation_to_alanine': 476} Link IDs: {'PTRANS': 54, 'TRANS': 1454} Chain breaks: 33 Unresolved non-hydrogen bonds: 952 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 476 Planarities with less than four sites: {'UNK:plan-1': 476} Unresolved non-hydrogen planarities: 476 Chain: "B" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5774 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 698} Chain breaks: 6 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2091 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Chain: "E" Number of atoms: 10678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1510, 10678 Classifications: {'peptide': 1510} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 54, 'TRANS': 1455} Chain breaks: 33 Unresolved non-hydrogen bonds: 954 Unresolved non-hydrogen angles: 1431 Unresolved non-hydrogen dihedrals: 477 Planarities with less than four sites: {'UNK:plan-1': 477} Unresolved non-hydrogen planarities: 477 Chain: "F" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5774 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 698} Chain breaks: 6 Chain: "G" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2091 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'E4S': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'E4S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.91, per 1000 atoms: 0.56 Number of scatterers: 37163 At special positions: 0 Unit cell: (258.7, 200.2, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 F 2 9.00 O 6849 8.00 N 6447 7.00 C 23649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 17.12 Conformation dependent library (CDL) restraints added in 4.7 seconds 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9626 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 250 helices and 6 sheets defined 83.1% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 71 through 87 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.636A pdb=" N UNK A 208 " --> pdb=" O UNK A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.514A pdb=" N UNK A 330 " --> pdb=" O UNK A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.934A pdb=" N UNK A 415 " --> pdb=" O UNK A 411 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N UNK A 416 " --> pdb=" O UNK A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.530A pdb=" N UNK A 427 " --> pdb=" O UNK A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.873A pdb=" N UNK A 444 " --> pdb=" O UNK A 440 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N UNK A 447 " --> pdb=" O UNK A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 473 removed outlier: 3.534A pdb=" N UNK A 472 " --> pdb=" O UNK A 468 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK A 473 " --> pdb=" O UNK A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 952 removed outlier: 3.914A pdb=" N ASP A 941 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 976 removed outlier: 3.570A pdb=" N ASN A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 996 removed outlier: 4.135A pdb=" N VAL A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.860A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.820A pdb=" N ALA A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1085 removed outlier: 4.126A pdb=" N ASN A1085 " --> pdb=" O GLN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 4.135A pdb=" N VAL A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1087 through 1091' Processing helix chain 'A' and resid 1098 through 1109 Processing helix chain 'A' and resid 1136 through 1157 Processing helix chain 'A' and resid 1170 through 1183 Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1208 through 1215 Processing helix chain 'A' and resid 1224 through 1240 Processing helix chain 'A' and resid 1245 through 1262 Processing helix chain 'A' and resid 1265 through 1267 No H-bonds generated for 'chain 'A' and resid 1265 through 1267' Processing helix chain 'A' and resid 1293 through 1312 removed outlier: 5.104A pdb=" N TYR A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1327 Processing helix chain 'A' and resid 1343 through 1361 removed outlier: 3.698A pdb=" N ILE A1346 " --> pdb=" O VAL A1343 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A1347 " --> pdb=" O ALA A1344 " (cutoff:3.500A) Proline residue: A1348 - end of helix removed outlier: 3.608A pdb=" N LEU A1353 " --> pdb=" O PHE A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1387 removed outlier: 3.653A pdb=" N ALA A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A1383 " --> pdb=" O TYR A1379 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1416 removed outlier: 4.421A pdb=" N GLU A1402 " --> pdb=" O LYS A1398 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1507 removed outlier: 3.718A pdb=" N ARG A1488 " --> pdb=" O TYR A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1533 Processing helix chain 'A' and resid 1541 through 1550 Processing helix chain 'A' and resid 1552 through 1559 Proline residue: A1559 - end of helix Processing helix chain 'A' and resid 1567 through 1578 Processing helix chain 'A' and resid 1580 through 1582 No H-bonds generated for 'chain 'A' and resid 1580 through 1582' Processing helix chain 'A' and resid 1589 through 1593 removed outlier: 3.601A pdb=" N LEU A1593 " --> pdb=" O ALA A1589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1589 through 1593' Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1617 through 1620 No H-bonds generated for 'chain 'A' and resid 1617 through 1620' Processing helix chain 'A' and resid 1622 through 1624 No H-bonds generated for 'chain 'A' and resid 1622 through 1624' Processing helix chain 'A' and resid 1632 through 1644 Processing helix chain 'A' and resid 1647 through 1656 removed outlier: 3.866A pdb=" N TYR A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) Proline residue: A1655 - end of helix Processing helix chain 'A' and resid 1658 through 1662 Processing helix chain 'A' and resid 1668 through 1679 Processing helix chain 'A' and resid 1681 through 1695 Processing helix chain 'A' and resid 1709 through 1722 Processing helix chain 'A' and resid 1726 through 1746 Processing helix chain 'A' and resid 1752 through 1768 removed outlier: 4.272A pdb=" N GLU A1756 " --> pdb=" O LYS A1753 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1875 removed outlier: 3.839A pdb=" N ALA A1861 " --> pdb=" O GLN A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1924 Processing helix chain 'A' and resid 1930 through 1953 removed outlier: 3.651A pdb=" N GLN A1934 " --> pdb=" O LEU A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1969 No H-bonds generated for 'chain 'A' and resid 1967 through 1969' Processing helix chain 'A' and resid 1976 through 1978 No H-bonds generated for 'chain 'A' and resid 1976 through 1978' Processing helix chain 'A' and resid 1998 through 2002 Processing helix chain 'A' and resid 2011 through 2028 Processing helix chain 'A' and resid 2031 through 2040 Processing helix chain 'A' and resid 2053 through 2061 Processing helix chain 'A' and resid 2067 through 2083 removed outlier: 3.825A pdb=" N ALA A2071 " --> pdb=" O GLU A2067 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN A2072 " --> pdb=" O ARG A2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 135 through 153 Processing helix chain 'B' and resid 168 through 194 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.946A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 255 through 271 Processing helix chain 'B' and resid 324 through 341 Processing helix chain 'B' and resid 356 through 375 removed outlier: 3.623A pdb=" N ALA B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 391 removed outlier: 4.926A pdb=" N LYS B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 431 through 441 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 466 through 485 removed outlier: 3.955A pdb=" N LYS B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 510 Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 565 through 578 Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'B' and resid 599 through 616 Processing helix chain 'B' and resid 689 through 709 removed outlier: 3.611A pdb=" N MET B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 725 removed outlier: 3.764A pdb=" N LEU B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 742 Processing helix chain 'B' and resid 746 through 759 removed outlier: 3.527A pdb=" N ALA B 758 " --> pdb=" O GLU B 754 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 759 " --> pdb=" O GLU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 776 Processing helix chain 'B' and resid 780 through 793 Processing helix chain 'B' and resid 798 through 809 Processing helix chain 'B' and resid 814 through 830 Processing helix chain 'B' and resid 836 through 838 No H-bonds generated for 'chain 'B' and resid 836 through 838' Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.866A pdb=" N GLU C 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Proline residue: C 55 - end of helix Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.914A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 250 removed outlier: 4.255A pdb=" N GLY C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN C 250 " --> pdb=" O PHE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 270 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.501A pdb=" N SER C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 54 through 67 Processing helix chain 'E' and resid 71 through 87 Processing helix chain 'E' and resid 91 through 102 Processing helix chain 'E' and resid 105 through 118 Processing helix chain 'E' and resid 123 through 137 Processing helix chain 'E' and resid 142 through 154 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.680A pdb=" N UNK E 205 " --> pdb=" O UNK E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 224 Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 240 through 253 Processing helix chain 'E' and resid 257 through 270 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 292 through 307 Processing helix chain 'E' and resid 311 through 324 Processing helix chain 'E' and resid 328 through 341 Processing helix chain 'E' and resid 346 through 360 Processing helix chain 'E' and resid 365 through 378 Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 398 through 406 Processing helix chain 'E' and resid 410 through 421 removed outlier: 3.929A pdb=" N UNK E 416 " --> pdb=" O UNK E 412 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK E 417 " --> pdb=" O UNK E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 437 removed outlier: 3.530A pdb=" N UNK E 428 " --> pdb=" O UNK E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 457 Processing helix chain 'E' and resid 466 through 474 removed outlier: 3.534A pdb=" N UNK E 473 " --> pdb=" O UNK E 469 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK E 474 " --> pdb=" O UNK E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 933 through 952 removed outlier: 3.913A pdb=" N ASP E 941 " --> pdb=" O ILE E 937 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS E 942 " --> pdb=" O ALA E 938 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 958 through 975 Processing helix chain 'E' and resid 980 through 996 removed outlier: 3.820A pdb=" N VAL E 985 " --> pdb=" O ARG E 981 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1000 No H-bonds generated for 'chain 'E' and resid 998 through 1000' Processing helix chain 'E' and resid 1004 through 1020 removed outlier: 3.860A pdb=" N LYS E1008 " --> pdb=" O GLY E1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 1047 through 1070 removed outlier: 3.819A pdb=" N ALA E1059 " --> pdb=" O LYS E1055 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E1060 " --> pdb=" O ASP E1056 " (cutoff:3.500A) Processing helix chain 'E' and resid 1073 through 1085 removed outlier: 4.127A pdb=" N ASN E1085 " --> pdb=" O GLN E1081 " (cutoff:3.500A) Processing helix chain 'E' and resid 1087 through 1091 removed outlier: 4.135A pdb=" N VAL E1091 " --> pdb=" O HIS E1087 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1087 through 1091' Processing helix chain 'E' and resid 1098 through 1109 Processing helix chain 'E' and resid 1136 through 1157 Processing helix chain 'E' and resid 1170 through 1183 Processing helix chain 'E' and resid 1186 through 1201 Processing helix chain 'E' and resid 1208 through 1215 Processing helix chain 'E' and resid 1224 through 1240 Processing helix chain 'E' and resid 1245 through 1262 Processing helix chain 'E' and resid 1265 through 1267 No H-bonds generated for 'chain 'E' and resid 1265 through 1267' Processing helix chain 'E' and resid 1293 through 1312 removed outlier: 5.104A pdb=" N TYR E1311 " --> pdb=" O GLU E1307 " (cutoff:3.500A) Processing helix chain 'E' and resid 1315 through 1327 Processing helix chain 'E' and resid 1343 through 1361 removed outlier: 3.698A pdb=" N ILE E1346 " --> pdb=" O VAL E1343 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY E1347 " --> pdb=" O ALA E1344 " (cutoff:3.500A) Proline residue: E1348 - end of helix removed outlier: 3.609A pdb=" N LEU E1353 " --> pdb=" O PHE E1350 " (cutoff:3.500A) Processing helix chain 'E' and resid 1368 through 1387 removed outlier: 3.653A pdb=" N ALA E1382 " --> pdb=" O ILE E1378 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E1383 " --> pdb=" O TYR E1379 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER E1387 " --> pdb=" O PHE E1383 " (cutoff:3.500A) Processing helix chain 'E' and resid 1397 through 1416 removed outlier: 4.421A pdb=" N GLU E1402 " --> pdb=" O LYS E1398 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP E1403 " --> pdb=" O ARG E1399 " (cutoff:3.500A) Processing helix chain 'E' and resid 1478 through 1507 removed outlier: 3.717A pdb=" N ARG E1488 " --> pdb=" O TYR E1484 " (cutoff:3.500A) Processing helix chain 'E' and resid 1522 through 1533 Processing helix chain 'E' and resid 1541 through 1550 Processing helix chain 'E' and resid 1552 through 1559 Proline residue: E1559 - end of helix Processing helix chain 'E' and resid 1567 through 1578 Processing helix chain 'E' and resid 1580 through 1582 No H-bonds generated for 'chain 'E' and resid 1580 through 1582' Processing helix chain 'E' and resid 1589 through 1594 removed outlier: 3.584A pdb=" N LEU E1593 " --> pdb=" O ALA E1589 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1611 No H-bonds generated for 'chain 'E' and resid 1609 through 1611' Processing helix chain 'E' and resid 1617 through 1620 No H-bonds generated for 'chain 'E' and resid 1617 through 1620' Processing helix chain 'E' and resid 1622 through 1624 No H-bonds generated for 'chain 'E' and resid 1622 through 1624' Processing helix chain 'E' and resid 1632 through 1644 Processing helix chain 'E' and resid 1647 through 1656 removed outlier: 3.866A pdb=" N TYR E1653 " --> pdb=" O ALA E1649 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E1654 " --> pdb=" O ILE E1650 " (cutoff:3.500A) Proline residue: E1655 - end of helix Processing helix chain 'E' and resid 1658 through 1662 Processing helix chain 'E' and resid 1668 through 1679 Processing helix chain 'E' and resid 1681 through 1695 Processing helix chain 'E' and resid 1709 through 1722 Processing helix chain 'E' and resid 1726 through 1746 Processing helix chain 'E' and resid 1752 through 1768 removed outlier: 4.271A pdb=" N GLU E1756 " --> pdb=" O LYS E1753 " (cutoff:3.500A) Processing helix chain 'E' and resid 1855 through 1875 removed outlier: 3.839A pdb=" N ALA E1861 " --> pdb=" O GLN E1857 " (cutoff:3.500A) Processing helix chain 'E' and resid 1916 through 1924 Processing helix chain 'E' and resid 1930 through 1953 Processing helix chain 'E' and resid 1967 through 1969 No H-bonds generated for 'chain 'E' and resid 1967 through 1969' Processing helix chain 'E' and resid 1976 through 1978 No H-bonds generated for 'chain 'E' and resid 1976 through 1978' Processing helix chain 'E' and resid 1998 through 2002 Processing helix chain 'E' and resid 2011 through 2028 Processing helix chain 'E' and resid 2031 through 2040 Processing helix chain 'E' and resid 2053 through 2061 Processing helix chain 'E' and resid 2067 through 2083 removed outlier: 3.826A pdb=" N ALA E2071 " --> pdb=" O GLU E2067 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E2072 " --> pdb=" O ARG E2068 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 26 through 32 Processing helix chain 'F' and resid 43 through 59 Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 93 through 110 Processing helix chain 'F' and resid 114 through 120 Processing helix chain 'F' and resid 135 through 153 Processing helix chain 'F' and resid 168 through 194 Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.946A pdb=" N ALA F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 247 Processing helix chain 'F' and resid 255 through 271 Processing helix chain 'F' and resid 324 through 341 Processing helix chain 'F' and resid 356 through 375 removed outlier: 3.624A pdb=" N ALA F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 391 removed outlier: 4.926A pdb=" N LYS F 391 " --> pdb=" O GLU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 409 Processing helix chain 'F' and resid 414 through 426 Processing helix chain 'F' and resid 431 through 441 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 466 through 485 removed outlier: 3.954A pdb=" N LYS F 471 " --> pdb=" O GLU F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 510 Processing helix chain 'F' and resid 515 through 527 Processing helix chain 'F' and resid 531 through 544 Processing helix chain 'F' and resid 549 through 561 Processing helix chain 'F' and resid 565 through 578 Processing helix chain 'F' and resid 583 through 596 Processing helix chain 'F' and resid 599 through 616 Processing helix chain 'F' and resid 689 through 709 removed outlier: 3.610A pdb=" N MET F 693 " --> pdb=" O LEU F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 725 removed outlier: 3.765A pdb=" N LEU F 725 " --> pdb=" O GLU F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 742 Processing helix chain 'F' and resid 746 through 759 removed outlier: 3.528A pdb=" N ALA F 758 " --> pdb=" O GLU F 754 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 759 " --> pdb=" O GLU F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 765 through 776 Processing helix chain 'F' and resid 780 through 793 Processing helix chain 'F' and resid 798 through 809 Processing helix chain 'F' and resid 814 through 830 Processing helix chain 'F' and resid 836 through 838 No H-bonds generated for 'chain 'F' and resid 836 through 838' Processing helix chain 'G' and resid 8 through 16 Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 36 through 44 Processing helix chain 'G' and resid 51 through 65 removed outlier: 3.867A pdb=" N GLU G 54 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Proline residue: G 55 - end of helix Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 197 through 209 Processing helix chain 'G' and resid 216 through 221 removed outlier: 3.913A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 250 removed outlier: 4.256A pdb=" N GLY G 243 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN G 250 " --> pdb=" O PHE G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 270 Processing helix chain 'G' and resid 273 through 285 removed outlier: 3.501A pdb=" N SER G 285 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1031 through 1033 Processing sheet with id= B, first strand: chain 'A' and resid 1804 through 1806 removed outlier: 3.845A pdb=" N ALA A1847 " --> pdb=" O ALA A1805 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1963 through 1965 Processing sheet with id= D, first strand: chain 'E' and resid 1031 through 1033 Processing sheet with id= E, first strand: chain 'E' and resid 1804 through 1806 removed outlier: 3.845A pdb=" N ALA E1847 " --> pdb=" O ALA E1805 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 1963 through 1965 2290 hydrogen bonds defined for protein. 6684 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: 16.83 Time building geometry restraints manager: 18.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10104 1.33 - 1.46: 10091 1.46 - 1.58: 17294 1.58 - 1.71: 1 1.71 - 1.84: 347 Bond restraints: 37837 Sorted by residual: bond pdb=" C06 E4S E2201 " pdb=" N01 E4S E2201 " ideal model delta sigma weight residual 1.328 1.510 -0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C06 E4S A2201 " pdb=" N01 E4S A2201 " ideal model delta sigma weight residual 1.328 1.474 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C14 E4S E2201 " pdb=" C19 E4S E2201 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C27 E4S A2201 " pdb=" C28 E4S A2201 " ideal model delta sigma weight residual 1.388 1.528 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C27 E4S E2201 " pdb=" C28 E4S E2201 " ideal model delta sigma weight residual 1.388 1.527 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 37832 not shown) Histogram of bond angle deviations from ideal: 95.45 - 103.68: 550 103.68 - 111.91: 18967 111.91 - 120.14: 16695 120.14 - 128.36: 14861 128.36 - 136.59: 288 Bond angle restraints: 51361 Sorted by residual: angle pdb=" N ILE E1994 " pdb=" CA ILE E1994 " pdb=" C ILE E1994 " ideal model delta sigma weight residual 110.21 123.31 -13.10 1.13e+00 7.83e-01 1.34e+02 angle pdb=" N MET E1979 " pdb=" CA MET E1979 " pdb=" C MET E1979 " ideal model delta sigma weight residual 111.07 121.19 -10.12 1.07e+00 8.73e-01 8.95e+01 angle pdb=" N HIS E1702 " pdb=" CA HIS E1702 " pdb=" C HIS E1702 " ideal model delta sigma weight residual 111.28 101.34 9.94 1.09e+00 8.42e-01 8.32e+01 angle pdb=" C VAL E1586 " pdb=" CA VAL E1586 " pdb=" CB VAL E1586 " ideal model delta sigma weight residual 114.35 105.69 8.66 1.06e+00 8.90e-01 6.67e+01 angle pdb=" C VAL A1586 " pdb=" CA VAL A1586 " pdb=" CB VAL A1586 " ideal model delta sigma weight residual 114.35 105.86 8.49 1.06e+00 8.90e-01 6.41e+01 ... (remaining 51356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 22407 22.99 - 45.97: 389 45.97 - 68.96: 13 68.96 - 91.94: 12 91.94 - 114.93: 4 Dihedral angle restraints: 22825 sinusoidal: 8124 harmonic: 14701 Sorted by residual: dihedral pdb=" N LYS E1956 " pdb=" C LYS E1956 " pdb=" CA LYS E1956 " pdb=" CB LYS E1956 " ideal model delta harmonic sigma weight residual 122.80 140.39 -17.59 0 2.50e+00 1.60e-01 4.95e+01 dihedral pdb=" C LYS E1956 " pdb=" N LYS E1956 " pdb=" CA LYS E1956 " pdb=" CB LYS E1956 " ideal model delta harmonic sigma weight residual -122.60 -139.70 17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" N TYR A1507 " pdb=" C TYR A1507 " pdb=" CA TYR A1507 " pdb=" CB TYR A1507 " ideal model delta harmonic sigma weight residual 122.80 138.09 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 22822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 5858 0.148 - 0.296: 70 0.296 - 0.444: 11 0.444 - 0.592: 4 0.592 - 0.739: 2 Chirality restraints: 5945 Sorted by residual: chirality pdb=" CA LYS E1956 " pdb=" N LYS E1956 " pdb=" C LYS E1956 " pdb=" CB LYS E1956 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA TYR A1507 " pdb=" N TYR A1507 " pdb=" C TYR A1507 " pdb=" CB TYR A1507 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" CA TYR E1507 " pdb=" N TYR E1507 " pdb=" C TYR E1507 " pdb=" CB TYR E1507 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 5942 not shown) Planarity restraints: 6593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1132 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C VAL A1132 " 0.083 2.00e-02 2.50e+03 pdb=" O VAL A1132 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS A1133 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1929 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C THR A1929 " -0.063 2.00e-02 2.50e+03 pdb=" O THR A1929 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A1930 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 E4S E2201 " 0.007 2.00e-02 2.50e+03 2.33e-02 1.22e+01 pdb=" C03 E4S E2201 " 0.005 2.00e-02 2.50e+03 pdb=" C04 E4S E2201 " -0.007 2.00e-02 2.50e+03 pdb=" C05 E4S E2201 " 0.048 2.00e-02 2.50e+03 pdb=" C06 E4S E2201 " -0.046 2.00e-02 2.50e+03 pdb=" C07 E4S E2201 " -0.005 2.00e-02 2.50e+03 pdb=" N01 E4S E2201 " 0.007 2.00e-02 2.50e+03 pdb=" O01 E4S E2201 " 0.005 2.00e-02 2.50e+03 pdb=" S01 E4S E2201 " -0.014 2.00e-02 2.50e+03 ... (remaining 6590 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 256 2.50 - 3.10: 29559 3.10 - 3.70: 59422 3.70 - 4.30: 83289 4.30 - 4.90: 131330 Nonbonded interactions: 303856 Sorted by model distance: nonbonded pdb=" O GLY E1112 " pdb=" OD2 ASP E1135 " model vdw 1.899 3.040 nonbonded pdb=" O CYS E1902 " pdb=" OG1 THR E1903 " model vdw 2.146 2.440 nonbonded pdb=" O CYS A1902 " pdb=" OG1 THR A1903 " model vdw 2.146 2.440 nonbonded pdb=" CZ PHE A1932 " pdb=" CD ARG A1936 " model vdw 2.195 3.740 nonbonded pdb=" O GLU C 112 " pdb=" NZ LYS C 116 " model vdw 2.195 2.520 ... (remaining 303851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 2 through 2085 or resid 2201)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.060 Extract box with map and model: 10.730 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 102.040 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.260 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:3.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 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 : 0.007 0.182 37837 Z= 0.477 Angle : 0.945 17.848 51361 Z= 0.535 Chirality : 0.053 0.739 5945 Planarity : 0.006 0.068 6593 Dihedral : 9.094 114.927 13199 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.06 % 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: -3.86 (0.11), residues: 3974 helix: -2.31 (0.08), residues: 2622 sheet: -1.24 (0.84), residues: 32 loop : -2.78 (0.15), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1039 time to evaluate : 4.103 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 outliers start: 4 outliers final: 2 residues processed: 1043 average time/residue: 0.4741 time to fit residues: 781.9251 Evaluate side-chains 558 residues out of total 3506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 556 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2591 time to fit residues: 5.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1081 GLN A1116 GLN ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN ** A1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 ASN A1557 GLN A1631 HIS A1702 HIS A1771 GLN A1779 ASN A1796 GLN A1857 GLN A1973 HIS A2072 ASN B 107 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN ** B 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 960 ASN E 967 HIS E1015 GLN ** E1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1116 GLN ** E1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1257 HIS E1527 ASN E1557 GLN E1779 ASN E1857 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2072 ASN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN F 351 HIS F 724 ASN F 730 HIS ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5056 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 37837 Z= 0.219 Angle : 0.695 10.452 51361 Z= 0.344 Chirality : 0.040 0.255 5945 Planarity : 0.005 0.080 6593 Dihedral : 6.223 112.385 5299 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 3974 helix: -0.57 (0.09), residues: 2644 sheet: -1.05 (0.75), residues: 32 loop : -2.57 (0.16), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 684 time to evaluate : 4.476 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 outliers start: 89 outliers final: 54 residues processed: 723 average time/residue: 0.4846 time to fit residues: 565.5663 Evaluate side-chains 577 residues out of total 3506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 523 time to evaluate : 3.206 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2865 time to fit residues: 33.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: