Starting phenix.real_space_refine on Tue Nov 19 06:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/11_2024/8e57_27905.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 109 5.16 5 C 11967 2.51 5 N 2983 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18449 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8919 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1068} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {' CA': 1, 'BBI': 1, 'WFR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.22, per 1000 atoms: 0.77 Number of scatterers: 18449 At special positions: 0 Unit cell: (147.048, 137.022, 160.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 109 16.00 P 1 15.00 O 3385 8.00 N 2983 7.00 C 11967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 1 " - " ASN F 350 " " NAG C 1 " - " ASN F 615 " " NAG D 1 " - " ASN F 898 " " NAG F1203 " - " ASN F 891 " " NAG F1204 " - " ASN F 92 " " NAG F1205 " - " ASN F 606 " " NAG F1206 " - " ASN F 784 " " NAG F1207 " - " ASN F1001 " " NAG F1208 " - " ASN F 988 " " NAG H 1 " - " ASN F 827 " " NAG I 1 " - " ASN F 186 " " NAG J 1 " - " ASN F 470 " Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 3.4 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 16 sheets defined 57.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 80 through 108 removed outlier: 3.963A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 143 removed outlier: 3.892A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.537A pdb=" N LEU A 164 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.897A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.008A pdb=" N TYR A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 3.973A pdb=" N SER A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 457 through 486 removed outlier: 3.909A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 removed outlier: 3.584A pdb=" N MET A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.937A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.896A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 4.313A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.611A pdb=" N SER A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.661A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 673 removed outlier: 3.807A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.589A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.762A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 removed outlier: 3.553A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 removed outlier: 3.672A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix No H-bonds generated for 'chain 'A' and resid 900 through 905' Processing helix chain 'A' and resid 906 through 911 removed outlier: 4.201A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 928 Processing helix chain 'A' and resid 929 through 950 Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.885A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1071 removed outlier: 3.518A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 3.957A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1136 removed outlier: 3.610A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1173 removed outlier: 3.553A pdb=" N LEU A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1206 Processing helix chain 'A' and resid 1233 through 1249 removed outlier: 3.685A pdb=" N ARG A1236 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1267 Processing helix chain 'A' and resid 1268 through 1290 removed outlier: 3.662A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1356 through 1388 removed outlier: 4.899A pdb=" N ASP A1385 " --> pdb=" O MET A1381 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR A1386 " --> pdb=" O ASP A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.669A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1429 removed outlier: 3.959A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 27 Processing helix chain 'E' and resid 105 through 130 removed outlier: 3.627A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 removed outlier: 5.839A pdb=" N ASP E 134 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 135' Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.533A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 204 removed outlier: 3.540A pdb=" N CYS E 184 " --> pdb=" O TRP E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.788A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 110 removed outlier: 4.019A pdb=" N VAL F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 4.341A pdb=" N ASN F 138 " --> pdb=" O PRO F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 Processing helix chain 'F' and resid 190 through 202 removed outlier: 4.301A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.671A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.619A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 347 Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 427 through 433 removed outlier: 4.208A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 removed outlier: 3.867A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 481 through 484 removed outlier: 3.933A pdb=" N GLN F 484 " --> pdb=" O LEU F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.652A pdb=" N LEU F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.813A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.535A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.792A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.998A pdb=" N LEU F 651 " --> pdb=" O TYR F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 removed outlier: 3.577A pdb=" N ILE F 705 " --> pdb=" O ASN F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 726 Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.862A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 Processing helix chain 'F' and resid 764 through 773 Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.646A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.045A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.762A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.762A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.807A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.675A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AB4, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.212A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.420A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 895 through 907 removed outlier: 3.565A pdb=" N ASN F 898 " --> pdb=" O GLN F 983 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 998 hydrogen bonds defined for protein. 2846 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: 7.40 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5830 1.37 - 1.52: 8820 1.52 - 1.68: 4047 1.68 - 1.83: 172 1.83 - 1.99: 2 Bond restraints: 18871 Sorted by residual: bond pdb=" O18 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.592 1.798 -0.206 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C02 WFR A1903 " pdb=" C03 WFR A1903 " ideal model delta sigma weight residual 1.520 1.686 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" O20 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.610 1.767 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" C11 WFR A1903 " pdb=" N06 WFR A1903 " ideal model delta sigma weight residual 1.388 1.527 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C31 WFR A1903 " pdb=" C36 WFR A1903 " ideal model delta sigma weight residual 1.388 1.525 -0.137 2.00e-02 2.50e+03 4.72e+01 ... (remaining 18866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 25347 2.51 - 5.02: 206 5.02 - 7.54: 36 7.54 - 10.05: 13 10.05 - 12.56: 3 Bond angle restraints: 25605 Sorted by residual: angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 131.07 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 124.19 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O20 WFR A1903 " pdb=" P19 WFR A1903 " pdb=" O21 WFR A1903 " ideal model delta sigma weight residual 115.95 105.67 10.28 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O18 WFR A1903 " pdb=" P19 WFR A1903 " pdb=" O20 WFR A1903 " ideal model delta sigma weight residual 100.57 110.47 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CAW BBI A1902 " pdb=" CAV BBI A1902 " pdb=" OAU BBI A1902 " ideal model delta sigma weight residual 108.05 117.87 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 25600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 10498 22.10 - 44.20: 867 44.20 - 66.29: 126 66.29 - 88.39: 39 88.39 - 110.49: 13 Dihedral angle restraints: 11543 sinusoidal: 4956 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.94 60.94 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 39.08 53.92 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual 93.00 46.68 46.32 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 11540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 2937 0.216 - 0.432: 9 0.432 - 0.648: 5 0.648 - 0.864: 0 0.864 - 1.080: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" P19 WFR A1903 " pdb=" O18 WFR A1903 " pdb=" O20 WFR A1903 " pdb=" O21 WFR A1903 " both_signs ideal model delta sigma weight residual True 2.75 -3.83 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN F 827 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C23 WFR A1903 " pdb=" C24 WFR A1903 " pdb=" C25 WFR A1903 " pdb=" N22 WFR A1903 " both_signs ideal model delta sigma weight residual False 2.23 2.76 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 2949 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 52 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1112 " -0.011 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP A1112 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1112 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1112 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1112 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1112 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1112 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1112 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " -0.009 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE A 131 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.76: 3108 2.76 - 3.31: 18371 3.31 - 3.86: 31467 3.86 - 4.41: 38152 4.41 - 4.96: 64468 Nonbonded interactions: 155566 Sorted by model distance: nonbonded pdb=" OH TYR F 513 " pdb=" OE2 GLU F 567 " model vdw 2.214 3.040 nonbonded pdb=" O MET F 281 " pdb=" OG1 THR F 284 " model vdw 2.226 3.040 nonbonded pdb=" O TYR F 647 " pdb=" OG1 THR F 650 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR F 694 " pdb=" OD1 ASN F 696 " model vdw 2.238 3.040 nonbonded pdb=" O ILE A 289 " pdb=" OG SER A 322 " model vdw 2.246 3.040 ... (remaining 155561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.900 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.005 0.206 18871 Z= 0.338 Angle : 0.617 12.562 25605 Z= 0.293 Chirality : 0.052 1.080 2952 Planarity : 0.004 0.054 3192 Dihedral : 16.351 110.488 7250 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.66 % Allowed : 13.61 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.54 (0.18), residues: 2212 helix: 1.57 (0.15), residues: 1122 sheet: 0.18 (0.36), residues: 204 loop : -1.20 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1112 HIS 0.003 0.001 HIS A1397 PHE 0.032 0.001 PHE A 131 TYR 0.010 0.001 TYR A1360 ARG 0.004 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.6778 (ttp) cc_final: 0.6457 (ttm) REVERT: A 668 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6109 (tm-30) REVERT: F 673 LEU cc_start: 0.8161 (pp) cc_final: 0.7953 (pt) REVERT: F 826 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: F 868 ASP cc_start: 0.6818 (t70) cc_final: 0.6564 (m-30) outliers start: 13 outliers final: 9 residues processed: 257 average time/residue: 1.1038 time to fit residues: 327.5715 Evaluate side-chains 247 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 575 GLU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN A1105 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 685 ASN F 721 ASN F1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0881 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: