Starting phenix.real_space_refine on Sun Oct 13 10:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yes_33776/10_2024/7yes_33776.cif" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 77 5.16 5 C 9369 2.51 5 N 2480 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1369, 10906 Classifications: {'peptide': 1369} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 69, 'TRANS': 1297} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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 9165 SG CYS A1150 49.054 41.877 96.212 1.00 68.18 S ATOM 9187 SG CYS A1153 52.215 39.556 95.959 1.00 71.87 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 9.40, per 1000 atoms: 0.64 Number of scatterers: 14679 At special positions: 0 Unit cell: (178.45, 134.46, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 77 16.00 O 2752 8.00 N 2480 7.00 C 9369 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 - 3.00 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 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " Number of angles added : 2 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 56.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.543A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.060A pdb=" N CYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.782A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.565A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 166 removed outlier: 3.756A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.748A pdb=" N MET A 210 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.963A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.641A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.633A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.864A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.535A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.509A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.595A pdb=" N MET A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.584A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.927A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.505A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.944A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 633 through 640 removed outlier: 3.868A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.630A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.544A pdb=" N TYR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.887A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.533A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.715A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.679A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.688A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 905 No H-bonds generated for 'chain 'A' and resid 904 through 905' Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 929 through 943 removed outlier: 3.581A pdb=" N ILE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.721A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.599A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 995 removed outlier: 3.531A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.558A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.710A pdb=" N ASN A1065 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A1066 " --> pdb=" O ASN A1063 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1062 through 1066' Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.633A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1138 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1213 through 1230 removed outlier: 3.943A pdb=" N ARG A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.907A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.550A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.828A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1339 removed outlier: 3.513A pdb=" N ILE A1339 " --> pdb=" O ALA A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 4.240A pdb=" N ARG A1373 " --> pdb=" O ASP A1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 118 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 127 through 149 removed outlier: 3.690A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 177 through 187 removed outlier: 4.037A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.750A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'C' and resid 82 through 118 removed outlier: 3.812A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.893A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.776A pdb=" N GLU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 113 through 146 removed outlier: 3.989A pdb=" N GLY D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Proline residue: D 120 - end of helix removed outlier: 3.907A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 144 removed outlier: 4.649A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.844A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.873A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'B' and resid 294 through 296 removed outlier: 6.342A pdb=" N ILE B 295 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS B 326 " --> pdb=" O LEU B 338 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2041 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: 5.26 Time building geometry restraints manager: 3.98 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: 4764 1.34 - 1.46: 2398 1.46 - 1.57: 7740 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 15014 Sorted by residual: bond pdb=" N ILE A1267 " pdb=" CA ILE A1267 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ASN A1266 " pdb=" CA ASN A1266 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.06e+00 bond pdb=" N GLY A1265 " pdb=" CA GLY A1265 " ideal model delta sigma weight residual 1.449 1.478 -0.029 1.14e-02 7.69e+03 6.32e+00 bond pdb=" N GLN A 608 " pdb=" CA GLN A 608 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 6.22e+00 bond pdb=" N GLN A 814 " pdb=" CA GLN A 814 " ideal model delta sigma weight residual 1.465 1.488 -0.023 1.31e-02 5.83e+03 2.95e+00 ... (remaining 15009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 20043 1.67 - 3.33: 316 3.33 - 5.00: 45 5.00 - 6.67: 15 6.67 - 8.33: 5 Bond angle restraints: 20424 Sorted by residual: angle pdb=" C THR A 756 " pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C PHE A 526 " pdb=" N SER A 527 " pdb=" CA SER A 527 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA GLY A1265 " pdb=" C GLY A1265 " pdb=" O GLY A1265 " ideal model delta sigma weight residual 121.11 117.75 3.36 9.00e-01 1.23e+00 1.39e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 128.58 -7.04 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 ... (remaining 20419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8123 17.67 - 35.34: 760 35.34 - 53.01: 137 53.01 - 70.68: 21 70.68 - 88.35: 13 Dihedral angle restraints: 9054 sinusoidal: 3555 harmonic: 5499 Sorted by residual: dihedral pdb=" CA ILE A1191 " pdb=" C ILE A1191 " pdb=" N PRO A1192 " pdb=" CA PRO A1192 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1556 0.033 - 0.066: 564 0.066 - 0.098: 158 0.098 - 0.131: 57 0.131 - 0.164: 9 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CA PRO A1192 " pdb=" N PRO A1192 " pdb=" C PRO A1192 " pdb=" CB PRO A1192 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB ILE A1267 " pdb=" CA ILE A1267 " pdb=" CG1 ILE A1267 " pdb=" CG2 ILE A1267 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CG LEU A 114 " pdb=" CB LEU A 114 " pdb=" CD1 LEU A 114 " pdb=" CD2 LEU A 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2341 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1191 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO A1192 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A1192 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1192 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 303 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 304 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 467 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 468 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " 0.028 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1551 2.75 - 3.29: 14332 3.29 - 3.82: 23440 3.82 - 4.36: 26472 4.36 - 4.90: 48195 Nonbonded interactions: 113990 Sorted by model distance: nonbonded pdb=" O TYR A 32 " pdb=" OG1 THR A 70 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 10 " pdb=" OG SER A 14 " model vdw 2.248 3.040 nonbonded pdb=" NH1 ARG B 298 " pdb=" OG SER B 299 " model vdw 2.253 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.261 3.040 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.275 3.120 ... (remaining 113985 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 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.040 15014 Z= 0.162 Angle : 0.532 8.333 20424 Z= 0.281 Chirality : 0.039 0.164 2344 Planarity : 0.004 0.105 2618 Dihedral : 14.108 88.352 5488 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.75 % Favored : 92.60 % Rotamer: Outliers : 0.18 % Allowed : 0.31 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.91 (0.21), residues: 1863 helix: 2.15 (0.18), residues: 976 sheet: 1.30 (0.56), residues: 89 loop : -1.55 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1085 HIS 0.004 0.001 HIS C 166 PHE 0.013 0.001 PHE A1011 TYR 0.010 0.001 TYR A 800 ARG 0.006 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.639 Fit side-chains REVERT: A 594 MET cc_start: 0.6406 (tpp) cc_final: 0.6057 (tpt) REVERT: A 602 LYS cc_start: 0.8559 (tppp) cc_final: 0.8046 (ttpt) REVERT: A 1013 ASP cc_start: 0.7210 (m-30) cc_final: 0.6853 (m-30) REVERT: A 1054 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8765 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 209 average time/residue: 0.3793 time to fit residues: 112.2684 Evaluate side-chains 172 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 307 GLN A 446 ASN A 608 GLN E 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15014 Z= 0.205 Angle : 0.559 11.062 20424 Z= 0.289 Chirality : 0.041 0.162 2344 Planarity : 0.005 0.106 2618 Dihedral : 4.023 27.570 2014 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.97 % Favored : 92.44 % Rotamer: Outliers : 0.99 % Allowed : 6.72 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.96 (0.21), residues: 1863 helix: 2.04 (0.17), residues: 1002 sheet: 1.32 (0.56), residues: 89 loop : -1.42 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 PHE 0.015 0.001 PHE A 793 TYR 0.020 0.001 TYR A1088 ARG 0.006 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 1.799 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 181 average time/residue: 0.3748 time to fit residues: 95.0021 Evaluate side-chains 178 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 143 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 166 optimal weight: 0.3980 chunk 179 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15014 Z= 0.210 Angle : 0.546 10.849 20424 Z= 0.282 Chirality : 0.040 0.160 2344 Planarity : 0.004 0.106 2618 Dihedral : 4.070 27.765 2014 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.86 % Favored : 92.49 % Rotamer: Outliers : 1.60 % Allowed : 8.38 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.93 (0.21), residues: 1863 helix: 2.03 (0.17), residues: 1004 sheet: 1.22 (0.56), residues: 89 loop : -1.47 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 PHE 0.015 0.001 PHE A 411 TYR 0.013 0.001 TYR A 427 ARG 0.005 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.915 Fit side-chains REVERT: A 1015 MET cc_start: 0.7653 (mtp) cc_final: 0.7295 (mtp) REVERT: A 1380 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6783 (mm) outliers start: 25 outliers final: 19 residues processed: 179 average time/residue: 0.3750 time to fit residues: 95.0959 Evaluate side-chains 183 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 176 optimal weight: 0.8980 chunk 87 optimal weight: 0.0030 chunk 158 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15014 Z= 0.158 Angle : 0.530 11.484 20424 Z= 0.273 Chirality : 0.039 0.161 2344 Planarity : 0.004 0.106 2618 Dihedral : 3.993 28.099 2014 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.48 % Favored : 92.81 % Rotamer: Outliers : 1.05 % Allowed : 10.42 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1863 helix: 2.10 (0.17), residues: 1002 sheet: 1.32 (0.56), residues: 89 loop : -1.43 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 PHE 0.024 0.001 PHE A1011 TYR 0.010 0.001 TYR A 117 ARG 0.004 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.506 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 171 average time/residue: 0.2767 time to fit residues: 67.4247 Evaluate side-chains 174 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15014 Z= 0.314 Angle : 0.601 11.225 20424 Z= 0.309 Chirality : 0.043 0.172 2344 Planarity : 0.005 0.108 2618 Dihedral : 4.306 27.937 2014 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.51 % Favored : 91.73 % Rotamer: Outliers : 1.85 % Allowed : 10.73 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.80 (0.21), residues: 1863 helix: 1.97 (0.17), residues: 1001 sheet: 1.21 (0.57), residues: 89 loop : -1.60 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.008 0.001 HIS C 166 PHE 0.026 0.002 PHE A1011 TYR 0.018 0.001 TYR A 427 ARG 0.003 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 608 GLN cc_start: 0.7888 (pt0) cc_final: 0.7509 (mm110) REVERT: A 1380 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.6850 (mm) outliers start: 28 outliers final: 23 residues processed: 183 average time/residue: 0.3148 time to fit residues: 81.7503 Evaluate side-chains 180 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 5.9990 chunk 159 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 177 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: