Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:03:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/12_2022/6l53_0836.pdb" } resolution = 3.63 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A PHE 2142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2374": "NH1" <-> "NH2" Residue "A PHE 2417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13991 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1935, 13991 Classifications: {'peptide': 1935} Incomplete info: {'truncation_to_alanine': 304} Link IDs: {'CIS': 63, 'PCIS': 4, 'PTRANS': 63, 'TRANS': 1804} Chain breaks: 27 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1471 Unresolved non-hydrogen angles: 1868 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 10, 'TYR:plan': 20, 'ASN:plan1': 11, 'TRP:plan': 19, 'HIS:plan': 12, 'PHE:plan': 15, 'GLU:plan': 28, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 975 Time building chain proxies: 7.85, per 1000 atoms: 0.56 Number of scatterers: 13991 At special positions: 0 Unit cell: (130, 180.96, 132.08, 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 72 16.00 O 2701 8.00 N 2394 7.00 C 8824 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: 5.53 Conformation dependent library (CDL) restraints added in 2.3 seconds 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 2 sheets defined 58.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.737A pdb=" N ASP A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.031A pdb=" N GLU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.759A pdb=" N ALA A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.512A pdb=" N THR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.574A pdb=" N ASN A 181 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.103A pdb=" N SER A 204 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.885A pdb=" N GLU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.695A pdb=" N PHE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.987A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 293 removed outlier: 4.217A pdb=" N SER A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.829A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.560A pdb=" N CYS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.864A pdb=" N ILE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 342 through 356 Proline residue: A 348 - end of helix removed outlier: 3.592A pdb=" N ALA A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.658A pdb=" N GLU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.668A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 removed outlier: 3.560A pdb=" N LEU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 444 through 457 removed outlier: 4.177A pdb=" N PHE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.630A pdb=" N VAL A 462 " --> pdb=" O CYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.731A pdb=" N MET A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 removed outlier: 4.400A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 5.433A pdb=" N GLN A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 582 removed outlier: 4.380A pdb=" N LYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.650A pdb=" N ASP A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.511A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.835A pdb=" N SER A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.628A pdb=" N TYR A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 removed outlier: 3.862A pdb=" N LEU A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.721A pdb=" N LYS A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 4.018A pdb=" N VAL A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.615A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.964A pdb=" N GLN A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 937 through 948 removed outlier: 3.843A pdb=" N ILE A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 985 removed outlier: 3.702A pdb=" N ASN A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 981 " --> pdb=" O GLN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.649A pdb=" N TYR A 995 " --> pdb=" O LYS A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1016 removed outlier: 3.708A pdb=" N THR A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1073 through 1078 removed outlier: 3.614A pdb=" N VAL A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1085 removed outlier: 3.766A pdb=" N LEU A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1091 through 1106 removed outlier: 3.697A pdb=" N TRP A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1105 " --> pdb=" O GLY A1101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A1106 " --> pdb=" O LYS A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1120 removed outlier: 3.873A pdb=" N LYS A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1133 removed outlier: 4.057A pdb=" N LEU A1129 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1215 removed outlier: 3.561A pdb=" N ASP A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1297 removed outlier: 3.811A pdb=" N LYS A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER A1288 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1295 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1316 through 1331 removed outlier: 3.538A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 removed outlier: 3.739A pdb=" N LEU A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.609A pdb=" N VAL A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1368 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.705A pdb=" N ASN A1404 " --> pdb=" O THR A1400 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1406 " --> pdb=" O TYR A1402 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1420 Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 3.705A pdb=" N ALA A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 4.107A pdb=" N THR A1456 " --> pdb=" O GLN A1452 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A1459 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1460 " --> pdb=" O THR A1456 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 4.134A pdb=" N THR A1471 " --> pdb=" O LYS A1467 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A1472 " --> pdb=" O LYS A1468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1484 removed outlier: 3.876A pdb=" N LEU A1483 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A1484 " --> pdb=" O PRO A1481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1480 through 1484' Processing helix chain 'A' and resid 1488 through 1497 removed outlier: 4.148A pdb=" N THR A1493 " --> pdb=" O LYS A1489 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 3.578A pdb=" N THR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1533 " --> pdb=" O ALA A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1538 removed outlier: 4.117A pdb=" N LYS A1537 " --> pdb=" O ALA A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.704A pdb=" N GLN A1603 " --> pdb=" O PHE A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1632 removed outlier: 4.163A pdb=" N ALA A1621 " --> pdb=" O LYS A1617 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1628 " --> pdb=" O SER A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'A' and resid 1644 through 1655 removed outlier: 3.799A pdb=" N LYS A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A1651 " --> pdb=" O PRO A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1675 removed outlier: 3.860A pdb=" N GLU A1665 " --> pdb=" O ILE A1661 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1668 " --> pdb=" O GLU A1664 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1708 removed outlier: 3.548A pdb=" N ILE A1707 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1708 " --> pdb=" O VAL A1704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1703 through 1708' Processing helix chain 'A' and resid 1708 through 1713 removed outlier: 4.239A pdb=" N ILE A1712 " --> pdb=" O TRP A1708 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A1713 " --> pdb=" O ARG A1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1708 through 1713' Processing helix chain 'A' and resid 1729 through 1738 removed outlier: 3.842A pdb=" N LYS A1735 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A1736 " --> pdb=" O VAL A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1759 removed outlier: 3.575A pdb=" N SER A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1797 removed outlier: 3.594A pdb=" N VAL A1797 " --> pdb=" O LEU A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1812 removed outlier: 4.197A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A1812 " --> pdb=" O GLU A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1830 Processing helix chain 'A' and resid 1837 through 1851 removed outlier: 3.985A pdb=" N ILE A1841 " --> pdb=" O VAL A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1866 Processing helix chain 'A' and resid 1927 through 1940 removed outlier: 4.042A pdb=" N SER A1931 " --> pdb=" O GLN A1927 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A1936 " --> pdb=" O LYS A1932 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 removed outlier: 3.526A pdb=" N VAL A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1948 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1971 removed outlier: 3.715A pdb=" N VAL A1969 " --> pdb=" O LEU A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.801A pdb=" N ARG A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A1980 " --> pdb=" O TYR A1976 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1981 " --> pdb=" O VAL A1977 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A1986 " --> pdb=" O GLN A1982 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A1989 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1991 " --> pdb=" O GLU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2027 removed outlier: 3.542A pdb=" N PHE A2019 " --> pdb=" O LYS A2015 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A2020 " --> pdb=" O PRO A2016 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A2025 " --> pdb=" O LEU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2072 through 2080 removed outlier: 3.653A pdb=" N LEU A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A2079 " --> pdb=" O MET A2075 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A2080 " --> pdb=" O LEU A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2101 removed outlier: 3.935A pdb=" N LEU A2099 " --> pdb=" O SER A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 removed outlier: 3.559A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2180 removed outlier: 3.941A pdb=" N THR A2179 " --> pdb=" O MET A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2231 Processing helix chain 'A' and resid 2252 through 2258 removed outlier: 3.842A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A2258 " --> pdb=" O TYR A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2289 removed outlier: 3.991A pdb=" N GLU A2285 " --> pdb=" O LYS A2281 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2286 " --> pdb=" O ALA A2282 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2287 " --> pdb=" O VAL A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2301 Processing helix chain 'A' and resid 2308 through 2331 removed outlier: 3.541A pdb=" N ARG A2319 " --> pdb=" O GLN A2315 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A2330 " --> pdb=" O MET A2326 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A2331 " --> pdb=" O VAL A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2360 through 2364 removed outlier: 3.744A pdb=" N LYS A2363 " --> pdb=" O GLU A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.955A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2396 removed outlier: 3.537A pdb=" N SER A2395 " --> pdb=" O VAL A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2396 through 2406 removed outlier: 3.892A pdb=" N LEU A2400 " --> pdb=" O CYS A2396 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A2401 " --> pdb=" O GLU A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2419 removed outlier: 3.780A pdb=" N LEU A2411 " --> pdb=" O ARG A2407 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A2417 " --> pdb=" O LEU A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 removed outlier: 3.554A pdb=" N VAL A3612 " --> pdb=" O TYR A3608 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A3613 " --> pdb=" O ALA A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3645 Processing helix chain 'A' and resid 3654 through 3658 removed outlier: 3.734A pdb=" N THR A3658 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2138 through 2140 removed outlier: 3.786A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A2154 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2212 through 2213 505 hydrogen bonds defined for protein. 1449 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: 4.94 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4661 1.34 - 1.46: 2767 1.46 - 1.58: 6647 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14180 Sorted by residual: bond pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C CYS A 489 " pdb=" N GLN A 490 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.41e+00 bond pdb=" C HIS A 675 " pdb=" N ASP A 676 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" N ARG A2366 " pdb=" CA ARG A2366 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.07e+00 bond pdb=" N HIS A2278 " pdb=" CA HIS A2278 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.00e+00 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.75: 437 107.75 - 114.85: 8809 114.85 - 121.94: 7100 121.94 - 129.04: 2868 129.04 - 136.13: 112 Bond angle restraints: 19326 Sorted by residual: angle pdb=" N PRO A3627 " pdb=" CA PRO A3627 " pdb=" CB PRO A3627 " ideal model delta sigma weight residual 102.60 110.03 -7.43 1.17e+00 7.31e-01 4.03e+01 angle pdb=" N VAL A1046 " pdb=" CA VAL A1046 " pdb=" C VAL A1046 " ideal model delta sigma weight residual 113.20 108.49 4.71 9.60e-01 1.09e+00 2.41e+01 angle pdb=" C CYS A 489 " pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 123.00 136.13 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" N ARG A 903 " pdb=" CA ARG A 903 " pdb=" C ARG A 903 " ideal model delta sigma weight residual 113.18 107.62 5.56 1.33e+00 5.65e-01 1.75e+01 angle pdb=" CA LEU A2277 " pdb=" C LEU A2277 " pdb=" N HIS A2278 " ideal model delta sigma weight residual 116.20 124.53 -8.33 2.00e+00 2.50e-01 1.73e+01 ... (remaining 19321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8194 17.07 - 34.15: 310 34.15 - 51.22: 50 51.22 - 68.30: 12 68.30 - 85.37: 5 Dihedral angle restraints: 8571 sinusoidal: 2929 harmonic: 5642 Sorted by residual: dihedral pdb=" CA ILE A 901 " pdb=" C ILE A 901 " pdb=" N PRO A 902 " pdb=" CA PRO A 902 " ideal model delta harmonic sigma weight residual 180.00 128.38 51.62 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA LEU A1657 " pdb=" C LEU A1657 " pdb=" N PRO A1658 " pdb=" CA PRO A1658 " ideal model delta harmonic sigma weight residual -180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA ILE A1089 " pdb=" C ILE A1089 " pdb=" N GLN A1090 " pdb=" CA GLN A1090 " ideal model delta harmonic sigma weight residual -180.00 -147.02 -32.98 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2023 0.051 - 0.103: 351 0.103 - 0.154: 35 0.154 - 0.205: 7 0.205 - 0.257: 1 Chirality restraints: 2417 Sorted by residual: chirality pdb=" CA PRO A3627 " pdb=" N PRO A3627 " pdb=" C PRO A3627 " pdb=" CB PRO A3627 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLN A 490 " pdb=" N GLN A 490 " pdb=" C GLN A 490 " pdb=" CB GLN A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PRO A2276 " pdb=" N PRO A2276 " pdb=" C PRO A2276 " pdb=" CB PRO A2276 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 2414 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 901 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 902 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A2275 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A2276 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2276 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2276 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1346 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A1347 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1347 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1347 " 0.024 5.00e-02 4.00e+02 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 801 2.73 - 3.28: 14768 3.28 - 3.82: 20909 3.82 - 4.36: 25364 4.36 - 4.90: 41180 Nonbonded interactions: 103022 Sorted by model distance: nonbonded pdb=" O VAL A1094 " pdb=" OG SER A1097 " model vdw 2.193 2.440 nonbonded pdb=" O CYS A 492 " pdb=" OH TYR A 565 " model vdw 2.199 2.440 nonbonded pdb=" O ALA A 259 " pdb=" OG1 THR A 262 " model vdw 2.200 2.440 nonbonded pdb=" O SER A1608 " pdb=" OG SER A1618 " model vdw 2.233 2.440 nonbonded pdb=" O ASN A 111 " pdb=" OG SER A 115 " model vdw 2.250 2.440 ... (remaining 103017 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8824 2.51 5 N 2394 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.510 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.130 Process input model: 39.390 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 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 : 0.002 0.047 14180 Z= 0.151 Angle : 0.666 13.131 19326 Z= 0.358 Chirality : 0.040 0.257 2417 Planarity : 0.004 0.078 2459 Dihedral : 9.711 85.375 4875 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.85 % Favored : 89.89 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.16), residues: 1879 helix: -2.77 (0.13), residues: 917 sheet: -3.39 (0.85), residues: 29 loop : -3.83 (0.17), residues: 933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 402 time to evaluate : 1.735 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 outliers start: 49 outliers final: 16 residues processed: 444 average time/residue: 0.2657 time to fit residues: 170.9164 Evaluate side-chains 278 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1314 time to fit residues: 6.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 72.8664 > 50: distance: 73 - 78: 28.286 distance: 74 - 101: 34.095 distance: 78 - 79: 26.135 distance: 79 - 82: 42.179 distance: 80 - 81: 56.792 distance: 80 - 83: 69.496 distance: 81 - 109: 38.715 distance: 83 - 84: 41.082 distance: 84 - 85: 56.440 distance: 84 - 87: 40.188 distance: 85 - 86: 69.747 distance: 85 - 92: 42.781 distance: 87 - 88: 69.504 distance: 88 - 89: 40.838 distance: 89 - 90: 28.858 distance: 90 - 91: 52.438 distance: 92 - 93: 46.192 distance: 93 - 94: 32.821 distance: 93 - 96: 56.222 distance: 94 - 95: 53.890 distance: 94 - 101: 40.691 distance: 96 - 97: 40.088 distance: 97 - 98: 43.315 distance: 98 - 99: 46.461 distance: 98 - 100: 40.165 distance: 102 - 103: 39.808 distance: 102 - 105: 56.146 distance: 103 - 104: 45.848 distance: 103 - 109: 41.244 distance: 105 - 106: 16.314 distance: 106 - 107: 41.235 distance: 106 - 108: 40.177 distance: 109 - 110: 40.579 distance: 110 - 111: 41.229 distance: 110 - 113: 40.030 distance: 111 - 112: 54.617 distance: 111 - 123: 56.494 distance: 113 - 114: 37.330 distance: 114 - 115: 55.483 distance: 114 - 116: 57.229 distance: 115 - 117: 30.515 distance: 116 - 118: 63.223 distance: 116 - 119: 42.877 distance: 117 - 118: 53.082 distance: 118 - 120: 40.274 distance: 119 - 121: 19.919 distance: 120 - 122: 45.550 distance: 121 - 122: 24.535 distance: 123 - 124: 20.458 distance: 124 - 125: 44.377 distance: 124 - 127: 41.119 distance: 125 - 126: 56.997 distance: 125 - 129: 6.822 distance: 127 - 128: 42.217 distance: 129 - 130: 32.924 distance: 130 - 131: 14.820 distance: 130 - 133: 44.831 distance: 131 - 132: 47.796 distance: 131 - 135: 50.010 distance: 133 - 134: 57.763 distance: 135 - 136: 20.236 distance: 136 - 137: 56.728 distance: 136 - 139: 62.710 distance: 137 - 138: 67.740 distance: 137 - 141: 65.361 distance: 139 - 140: 20.155 distance: 141 - 142: 64.726 distance: 142 - 143: 65.620 distance: 142 - 145: 47.145 distance: 143 - 144: 37.431 distance: 143 - 148: 31.540 distance: 145 - 146: 40.295 distance: 145 - 147: 47.378 distance: 148 - 149: 52.533 distance: 149 - 150: 56.186 distance: 149 - 152: 68.142 distance: 150 - 151: 40.165 distance: 150 - 155: 34.208 distance: 152 - 153: 69.877 distance: 152 - 154: 39.966