Starting phenix.real_space_refine on Fri Jun 28 10:43:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy7_26866/06_2024/7uy7_26866.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 52 5.16 5 C 9774 2.51 5 N 2483 2.21 5 O 2841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15161 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4634 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 13, 'TRANS': 538} Chain breaks: 3 Chain: "B" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2378 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 284} Chain breaks: 2 Chain: "C" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1315 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "E" Number of atoms: 6408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6408 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 6 Chain: "F" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2906 SG CYS A 398 64.316 80.845 59.373 1.00108.69 S ATOM 2928 SG CYS A 401 66.766 81.052 62.374 1.00107.51 S ATOM 3018 SG CYS A 412 63.667 83.058 62.401 1.00125.64 S ATOM 3040 SG CYS A 415 66.495 83.823 59.787 1.00129.44 S Time building chain proxies: 9.11, per 1000 atoms: 0.60 Number of scatterers: 15161 At special positions: 0 Unit cell: (138.6, 144.1, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 52 16.00 P 10 15.00 O 2841 8.00 N 2483 7.00 C 9774 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: 5.66 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 900 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 398 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 415 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 412 " Number of angles added : 6 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 21 sheets defined 44.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.279A pdb=" N LEU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.587A pdb=" N LEU A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.591A pdb=" N GLN A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.926A pdb=" N LEU A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.789A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.640A pdb=" N PHE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.788A pdb=" N ILE A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 4.048A pdb=" N ILE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 Processing helix chain 'A' and resid 599 through 622 Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.525A pdb=" N GLU B 12 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 13' Processing helix chain 'B' and resid 108 through 136 removed outlier: 4.381A pdb=" N GLU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.642A pdb=" N LEU B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.840A pdb=" N ILE B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 254 through 272 removed outlier: 5.233A pdb=" N ASP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 removed outlier: 3.774A pdb=" N PHE B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.848A pdb=" N ASN B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 352 Processing helix chain 'C' and resid 15 through 23 removed outlier: 4.527A pdb=" N ASP C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 48 through 61 removed outlier: 4.007A pdb=" N ASN C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 removed outlier: 3.501A pdb=" N ALA C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.750A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.508A pdb=" N ASN C 164 " --> pdb=" O ILE C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'D' and resid 186 through 197 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.771A pdb=" N ASP E 250 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 251 " --> pdb=" O ILE E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 251' Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.733A pdb=" N THR E 398 " --> pdb=" O THR E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 498 removed outlier: 3.966A pdb=" N ASN E 496 " --> pdb=" O ASP E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 removed outlier: 4.044A pdb=" N SER E 515 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 547 Processing helix chain 'E' and resid 559 through 567 removed outlier: 3.580A pdb=" N ILE E 563 " --> pdb=" O THR E 559 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 564 " --> pdb=" O VAL E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 574 No H-bonds generated for 'chain 'E' and resid 573 through 574' Processing helix chain 'E' and resid 575 through 580 removed outlier: 4.096A pdb=" N LEU E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 580 " --> pdb=" O TRP E 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 575 through 580' Processing helix chain 'E' and resid 595 through 604 removed outlier: 3.580A pdb=" N MET E 602 " --> pdb=" O PHE E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 620 removed outlier: 3.537A pdb=" N GLU E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E 619 " --> pdb=" O SER E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 635 Processing helix chain 'E' and resid 643 through 652 removed outlier: 4.353A pdb=" N GLN E 648 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 652 " --> pdb=" O GLN E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 679 removed outlier: 3.714A pdb=" N LEU E 657 " --> pdb=" O THR E 653 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET E 675 " --> pdb=" O ALA E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 692 Processing helix chain 'E' and resid 694 through 701 removed outlier: 4.155A pdb=" N SER E 698 " --> pdb=" O ILE E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 718 removed outlier: 3.534A pdb=" N ARG E 706 " --> pdb=" O GLN E 702 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 711 " --> pdb=" O ASN E 707 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 749 removed outlier: 3.522A pdb=" N GLN E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 790 through 800 removed outlier: 3.785A pdb=" N ILE E 796 " --> pdb=" O TYR E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 818 Processing helix chain 'E' and resid 819 through 822 removed outlier: 3.811A pdb=" N GLY E 822 " --> pdb=" O PRO E 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 819 through 822' Processing helix chain 'E' and resid 871 through 893 removed outlier: 3.519A pdb=" N SER E 875 " --> pdb=" O ALA E 871 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 887 " --> pdb=" O GLN E 883 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 888 " --> pdb=" O ARG E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 923 removed outlier: 3.732A pdb=" N THR E 902 " --> pdb=" O GLN E 898 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 910 " --> pdb=" O LYS E 906 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS E 911 " --> pdb=" O GLN E 907 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 918 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 919 " --> pdb=" O ASN E 915 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 921 " --> pdb=" O MET E 917 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 922 " --> pdb=" O TYR E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 930 through 955 removed outlier: 3.813A pdb=" N GLU E 953 " --> pdb=" O LYS E 949 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 955 " --> pdb=" O ILE E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 994 Processing helix chain 'E' and resid 1054 through 1067 Processing helix chain 'E' and resid 1072 through 1080 removed outlier: 3.817A pdb=" N ASP E1077 " --> pdb=" O ASN E1073 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E1078 " --> pdb=" O MET E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1082 through 1087 removed outlier: 3.589A pdb=" N ASP E1087 " --> pdb=" O GLN E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1192 removed outlier: 4.212A pdb=" N ILE E1188 " --> pdb=" O LEU E1184 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E1189 " --> pdb=" O PHE E1185 " (cutoff:3.500A) Processing helix chain 'E' and resid 1193 through 1195 No H-bonds generated for 'chain 'E' and resid 1193 through 1195' Processing helix chain 'E' and resid 1199 through 1207 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.763A pdb=" N ILE A 67 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 73 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.715A pdb=" N TYR A 82 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.852A pdb=" N PHE A 123 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 152 " --> pdb=" O PHE A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163 removed outlier: 4.024A pdb=" N GLU A 163 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 203 " --> pdb=" O GLU A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.640A pdb=" N SER A 297 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 266 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 311 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 268 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.640A pdb=" N SER A 297 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 266 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 311 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 268 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 380 through 397 removed outlier: 6.352A pdb=" N LYS A 387 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLN A 431 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 389 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU A 429 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU A 589 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 591 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR A 443 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N TYR A 593 " --> pdb=" O TYR A 443 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 505 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL A 594 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 503 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 569 through 575 removed outlier: 3.753A pdb=" N TYR A 575 " --> pdb=" O LYS A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 580 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 28 removed outlier: 3.819A pdb=" N LEU B 27 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N GLU B 58 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N CYS B 96 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 100 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 82 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B 103 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR B 80 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.689A pdb=" N LYS B 276 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 288 " --> pdb=" O LYS B 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 removed outlier: 5.102A pdb=" N LEU C 137 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 139 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN C 107 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR C 94 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE C 46 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR C 96 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 127 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 39 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 261 through 262 removed outlier: 4.123A pdb=" N LEU E 262 " --> pdb=" O SER E 405 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER E 405 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.742A pdb=" N ASP E 264 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 280 " --> pdb=" O CYS E 293 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 282 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE E 426 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 294 " --> pdb=" O PHE E 426 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL E 428 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN E 296 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 307 through 308 removed outlier: 6.701A pdb=" N TYR E 307 " --> pdb=" O SER E 382 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 356 through 362 removed outlier: 3.762A pdb=" N GLY E 356 " --> pdb=" O TYR E 347 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR E 347 " --> pdb=" O GLY E 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 358 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS E 345 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 341 " --> pdb=" O GLN E 362 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL E 721 " --> pdb=" O ASP E 344 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 346 " --> pdb=" O VAL E 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 526 through 528 removed outlier: 7.062A pdb=" N LYS E 456 " --> pdb=" O PHE E 475 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU E 477 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER E 454 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET E 479 " --> pdb=" O CYS E 452 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS E 452 " --> pdb=" O MET E 479 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR E 481 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 450 " --> pdb=" O TYR E 481 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 453 " --> pdb=" O VAL E 552 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 551 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 778 through 779 removed outlier: 3.714A pdb=" N ASN E1007 " --> pdb=" O LEU E1019 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 783 through 784 Processing sheet with id=AC2, first strand: chain 'E' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'E' and resid 962 through 963 642 hydrogen bonds defined for protein. 1809 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: 5.76 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4586 1.34 - 1.46: 2377 1.46 - 1.58: 8400 1.58 - 1.70: 20 1.70 - 1.82: 81 Bond restraints: 15464 Sorted by residual: bond pdb=" CA THR E 964 " pdb=" CB THR E 964 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.62e+00 bond pdb=" C3' DT F 9 " pdb=" O3' DT F 9 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.27e-02 6.20e+03 1.84e+00 bond pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" N LYS A 494 " pdb=" CA LYS A 494 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.19e-02 7.06e+03 1.32e+00 ... (remaining 15459 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 237 105.65 - 112.73: 8095 112.73 - 119.81: 5037 119.81 - 126.89: 7376 126.89 - 133.97: 117 Bond angle restraints: 20862 Sorted by residual: angle pdb=" N LYS A 494 " pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 111.07 120.47 -9.40 1.07e+00 8.73e-01 7.71e+01 angle pdb=" C ILE A 495 " pdb=" N PHE A 496 " pdb=" CA PHE A 496 " ideal model delta sigma weight residual 120.28 126.65 -6.37 1.34e+00 5.57e-01 2.26e+01 angle pdb=" CA ILE A 495 " pdb=" C ILE A 495 " pdb=" N PHE A 496 " ideal model delta sigma weight residual 117.15 112.76 4.39 1.14e+00 7.69e-01 1.48e+01 angle pdb=" N GLN B 349 " pdb=" CA GLN B 349 " pdb=" CB GLN B 349 " ideal model delta sigma weight residual 110.28 115.52 -5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 111.36 114.61 -3.25 1.09e+00 8.42e-01 8.91e+00 ... (remaining 20857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 9160 32.78 - 65.55: 231 65.55 - 98.32: 23 98.32 - 131.10: 0 131.10 - 163.87: 1 Dihedral angle restraints: 9415 sinusoidal: 4013 harmonic: 5402 Sorted by residual: dihedral pdb=" C THR E 964 " pdb=" N THR E 964 " pdb=" CA THR E 964 " pdb=" CB THR E 964 " ideal model delta harmonic sigma weight residual -122.00 -132.47 10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C4' DT F 9 " pdb=" C3' DT F 9 " pdb=" O3' DT F 9 " pdb=" P DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 56.13 163.87 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA PHE A 473 " pdb=" C PHE A 473 " pdb=" N ILE A 474 " pdb=" CA ILE A 474 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2058 0.069 - 0.137: 257 0.137 - 0.206: 9 0.206 - 0.275: 0 0.275 - 0.343: 2 Chirality restraints: 2326 Sorted by residual: chirality pdb=" CA THR E 964 " pdb=" N THR E 964 " pdb=" C THR E 964 " pdb=" CB THR E 964 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA LYS A 494 " pdb=" N LYS A 494 " pdb=" C LYS A 494 " pdb=" CB LYS A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 2323 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 970 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO E 971 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 971 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 971 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " 0.142 9.50e-02 1.11e+02 6.39e-02 2.85e+00 pdb=" NE ARG B 191 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 792 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO E 793 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 793 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 793 " -0.020 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1242 2.74 - 3.28: 16562 3.28 - 3.82: 25942 3.82 - 4.36: 30353 4.36 - 4.90: 49034 Nonbonded interactions: 123133 Sorted by model distance: nonbonded pdb=" O SER E 390 " pdb=" OG1 THR E 394 " model vdw 2.203 2.440 nonbonded pdb=" O SER C 116 " pdb=" OH TYR C 123 " model vdw 2.207 2.440 nonbonded pdb=" O SER B 342 " pdb=" ND1 HIS B 346 " model vdw 2.217 2.520 nonbonded pdb=" O TYR A 242 " pdb=" ND2 ASN A 324 " model vdw 2.236 2.520 nonbonded pdb=" O GLU A 534 " pdb=" NE2 GLN A 538 " model vdw 2.258 2.520 ... (remaining 123128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 13.940 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.056 15464 Z= 0.142 Angle : 0.557 9.396 20862 Z= 0.307 Chirality : 0.043 0.343 2326 Planarity : 0.003 0.064 2602 Dihedral : 15.121 163.875 5905 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1776 helix: 0.98 (0.21), residues: 670 sheet: -0.59 (0.35), residues: 250 loop : -1.36 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 576 HIS 0.011 0.001 HIS B 194 PHE 0.013 0.001 PHE A 473 TYR 0.015 0.001 TYR B 116 ARG 0.010 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6445 (mpp) cc_final: 0.6167 (mpp) REVERT: A 454 ASN cc_start: 0.8879 (t0) cc_final: 0.8614 (t0) REVERT: B 192 ILE cc_start: 0.9019 (tp) cc_final: 0.8528 (tp) REVERT: B 289 VAL cc_start: 0.8220 (p) cc_final: 0.7957 (m) REVERT: E 531 ASN cc_start: 0.7352 (p0) cc_final: 0.6696 (t0) REVERT: E 639 ILE cc_start: 0.8655 (mp) cc_final: 0.8423 (tt) REVERT: E 811 ILE cc_start: 0.7482 (mp) cc_final: 0.7113 (mt) REVERT: E 815 MET cc_start: 0.7817 (pmm) cc_final: 0.7601 (mpp) REVERT: E 877 LEU cc_start: 0.8509 (pp) cc_final: 0.8164 (mm) REVERT: E 1074 MET cc_start: 0.8468 (mpp) cc_final: 0.8222 (mpp) REVERT: E 1191 MET cc_start: 0.8419 (ptp) cc_final: 0.8061 (mpp) outliers start: 3 outliers final: 1 residues processed: 177 average time/residue: 0.2693 time to fit residues: 71.1484 Evaluate side-chains 101 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 567 ASN B 89 ASN B 94 GLN B 120 GLN B 346 HIS B 360 HIS C 80 ASN E 716 ASN ** E1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15464 Z= 0.186 Angle : 0.552 7.001 20862 Z= 0.295 Chirality : 0.044 0.173 2326 Planarity : 0.003 0.042 2602 Dihedral : 9.097 164.551 2033 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.18 % Allowed : 6.20 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1776 helix: 1.04 (0.20), residues: 686 sheet: -0.55 (0.36), residues: 237 loop : -1.42 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 695 HIS 0.008 0.001 HIS B 346 PHE 0.031 0.002 PHE C 73 TYR 0.021 0.002 TYR C 96 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6738 (mmm) cc_final: 0.6064 (mmp) REVERT: A 198 MET cc_start: 0.6545 (mpp) cc_final: 0.6168 (mmm) REVERT: A 375 MET cc_start: 0.3117 (mmt) cc_final: 0.2886 (mmt) REVERT: A 477 TYR cc_start: 0.6523 (p90) cc_final: 0.6169 (p90) REVERT: B 346 HIS cc_start: 0.8615 (m90) cc_final: 0.8352 (m90) REVERT: C 73 PHE cc_start: 0.8786 (m-80) cc_final: 0.8526 (m-80) REVERT: E 531 ASN cc_start: 0.7556 (p0) cc_final: 0.7097 (t0) REVERT: E 604 MET cc_start: 0.8955 (tmm) cc_final: 0.8234 (tmm) REVERT: E 811 ILE cc_start: 0.7489 (mp) cc_final: 0.7072 (mp) REVERT: E 815 MET cc_start: 0.7908 (pmm) cc_final: 0.7656 (mpp) REVERT: E 877 LEU cc_start: 0.8541 (pp) cc_final: 0.8210 (mm) REVERT: E 1191 MET cc_start: 0.8156 (ptp) cc_final: 0.7879 (mpp) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.2545 time to fit residues: 56.0904 Evaluate side-chains 87 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15464 Z= 0.217 Angle : 0.555 7.023 20862 Z= 0.297 Chirality : 0.043 0.180 2326 Planarity : 0.003 0.046 2602 Dihedral : 9.141 165.594 2033 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1776 helix: 0.95 (0.20), residues: 698 sheet: -0.67 (0.35), residues: 230 loop : -1.52 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 695 HIS 0.004 0.001 HIS A 466 PHE 0.019 0.002 PHE B 348 TYR 0.016 0.001 TYR E 676 ARG 0.006 0.001 ARG E 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6690 (mmm) cc_final: 0.5970 (mmp) REVERT: A 198 MET cc_start: 0.6334 (mpp) cc_final: 0.6087 (mpp) REVERT: A 477 TYR cc_start: 0.6675 (p90) cc_final: 0.6393 (p90) REVERT: A 499 ASP cc_start: 0.8509 (p0) cc_final: 0.8302 (p0) REVERT: C 73 PHE cc_start: 0.8831 (m-80) cc_final: 0.8556 (m-80) REVERT: D 193 TYR cc_start: 0.8412 (t80) cc_final: 0.8149 (t80) REVERT: E 639 ILE cc_start: 0.8702 (mp) cc_final: 0.8459 (tt) REVERT: E 811 ILE cc_start: 0.7421 (mp) cc_final: 0.7040 (mp) REVERT: E 815 MET cc_start: 0.8037 (pmm) cc_final: 0.7730 (mpp) REVERT: E 1191 MET cc_start: 0.8230 (ptp) cc_final: 0.7970 (mpp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2573 time to fit residues: 53.2438 Evaluate side-chains 92 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.892 > 50: distance: 30 - 176: 30.143 distance: 41 - 162: 9.168 distance: 44 - 159: 7.859 distance: 56 - 144: 3.062 distance: 59 - 141: 4.544 distance: 73 - 123: 4.704 distance: 76 - 120: 3.210 distance: 86 - 105: 3.887 distance: 89 - 102: 3.722 distance: 103 - 104: 3.782 distance: 103 - 106: 7.991 distance: 104 - 111: 7.632 distance: 107 - 108: 6.070 distance: 108 - 109: 4.444 distance: 109 - 110: 3.456 distance: 111 - 112: 6.040 distance: 112 - 113: 4.922 distance: 112 - 115: 3.899 distance: 113 - 114: 11.556 distance: 113 - 120: 4.578 distance: 115 - 116: 9.467 distance: 116 - 117: 7.760 distance: 118 - 119: 3.597 distance: 120 - 121: 3.541 distance: 121 - 122: 3.679 distance: 121 - 124: 4.359 distance: 122 - 123: 4.321 distance: 122 - 129: 9.291 distance: 124 - 125: 6.759 distance: 125 - 126: 12.295 distance: 126 - 127: 14.101 distance: 126 - 128: 7.679 distance: 129 - 130: 4.999 distance: 130 - 131: 3.415 distance: 131 - 132: 11.947 distance: 131 - 141: 8.281 distance: 133 - 134: 7.968 distance: 134 - 135: 5.271 distance: 134 - 136: 7.017 distance: 135 - 137: 6.570 distance: 136 - 138: 7.961 distance: 137 - 139: 6.055 distance: 138 - 139: 5.743 distance: 139 - 140: 4.203 distance: 141 - 142: 6.087 distance: 142 - 143: 4.066 distance: 142 - 145: 8.959 distance: 143 - 144: 9.403 distance: 143 - 150: 5.409 distance: 145 - 146: 7.349 distance: 146 - 147: 5.262 distance: 147 - 148: 4.884 distance: 148 - 149: 3.258 distance: 150 - 151: 4.358 distance: 151 - 152: 5.427 distance: 151 - 154: 3.860 distance: 152 - 153: 4.308 distance: 152 - 159: 7.368 distance: 154 - 155: 8.663 distance: 155 - 156: 4.944 distance: 156 - 157: 3.964 distance: 157 - 158: 6.017 distance: 160 - 161: 7.785 distance: 160 - 163: 5.559 distance: 161 - 168: 7.813 distance: 164 - 165: 3.575 distance: 165 - 167: 9.983 distance: 169 - 170: 18.181 distance: 169 - 172: 4.228 distance: 170 - 171: 11.655 distance: 170 - 176: 48.553 distance: 172 - 173: 8.551 distance: 172 - 174: 16.232 distance: 173 - 175: 10.189 distance: 176 - 177: 42.469 distance: 177 - 178: 20.033 distance: 177 - 180: 12.890 distance: 178 - 179: 5.694 distance: 178 - 187: 5.819 distance: 180 - 181: 7.611 distance: 181 - 182: 4.175 distance: 181 - 183: 14.889 distance: 182 - 184: 10.199 distance: 183 - 185: 6.105 distance: 184 - 186: 12.021 distance: 185 - 186: 8.902 distance: 187 - 188: 6.233 distance: 188 - 189: 8.595 distance: 188 - 191: 10.408 distance: 189 - 190: 26.773 distance: 189 - 195: 3.050 distance: 191 - 192: 7.020 distance: 192 - 193: 7.495 distance: 192 - 194: 4.434