Starting phenix.real_space_refine on Sat Mar 16 10:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/03_2024/7mjp_23881_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/03_2024/7mjp_23881.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/7mjp_23881/03_2024/7mjp_23881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/03_2024/7mjp_23881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/03_2024/7mjp_23881_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/03_2024/7mjp_23881_neut_updated.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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 1 5.16 5 Cl 1 4.86 5 C 8398 2.51 5 N 2849 2.21 5 O 2899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 1812 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 12, 'TRANS': 353} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1460 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 18, 'GLU:plan': 24, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 582 Chain: "B" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1674 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 327} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1041 Unresolved non-hydrogen angles: 1341 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "E" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 7107 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1248} Link IDs: {'PTRANS': 47, 'TRANS': 1388} Chain breaks: 4 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 4520 Unresolved non-hydrogen angles: 5845 Unresolved non-hydrogen dihedrals: 3784 Unresolved non-hydrogen chiralities: 497 Planarities with less than four sites: {'GLN:plan1': 48, 'ARG:plan': 61, 'TYR:plan': 44, 'ASN:plan1': 65, 'TRP:plan': 28, 'ASP:plan': 56, 'PHE:plan': 75, 'GLU:plan': 65, 'HIS:plan': 33} Unresolved non-hydrogen planarities: 2295 Chain: "N" 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.15, per 1000 atoms: 0.65 Number of scatterers: 14163 At special positions: 0 Unit cell: (125.54, 170.734, 156.925, 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) Cl 1 17.00 S 1 16.00 P 15 15.00 O 2899 8.00 N 2849 7.00 C 8398 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=1, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG N 1 " - " ASN E 9 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 13 sheets defined 45.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 No H-bonds generated for 'chain 'A' and resid 17 through 20' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 97 removed outlier: 3.853A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 127 through 138 removed outlier: 4.577A pdb=" N ILE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 184 removed outlier: 3.931A pdb=" N ALA A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 removed outlier: 4.171A pdb=" N ASP A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 97 removed outlier: 4.144A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.920A pdb=" N GLY B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 153 through 184 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 69 through 96 removed outlier: 4.625A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 153 through 182 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 355 through 360 removed outlier: 4.007A pdb=" N ASP C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 69 through 97 removed outlier: 4.183A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.542A pdb=" N ALA D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 153 through 185 removed outlier: 5.588A pdb=" N HIS D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 279 removed outlier: 4.271A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 279' Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 355 through 361 removed outlier: 3.680A pdb=" N LYS D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 12 No H-bonds generated for 'chain 'E' and resid 10 through 12' Processing helix chain 'E' and resid 23 through 46 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 70 through 96 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 106 through 126 Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.925A pdb=" N GLN E 157 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 191 Processing helix chain 'E' and resid 216 through 219 Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 232 through 238 removed outlier: 3.534A pdb=" N ALA E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 257 through 277 removed outlier: 4.172A pdb=" N LYS E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 No H-bonds generated for 'chain 'E' and resid 286 through 289' Processing helix chain 'E' and resid 295 through 325 removed outlier: 3.939A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.993A pdb=" N LEU E 345 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 341 through 346' Processing helix chain 'E' and resid 348 through 393 removed outlier: 3.642A pdb=" N ALA E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 415 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'E' and resid 429 through 432 Processing helix chain 'E' and resid 434 through 497 removed outlier: 4.245A pdb=" N LEU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N SER E 451 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N SER E 452 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU E 454 " --> pdb=" O GLY E 450 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Proline residue: E 465 - end of helix Processing helix chain 'E' and resid 499 through 505 Processing helix chain 'E' and resid 512 through 558 removed outlier: 4.819A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 529 " --> pdb=" O SER E 525 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 4.174A pdb=" N HIS E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 605 removed outlier: 3.515A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 573 " --> pdb=" O PHE E 569 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS E 576 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) Proline residue: E 581 - end of helix removed outlier: 3.804A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 715 Processing helix chain 'E' and resid 762 through 767 Processing helix chain 'E' and resid 774 through 783 Processing helix chain 'E' and resid 786 through 792 Processing helix chain 'E' and resid 796 through 798 No H-bonds generated for 'chain 'E' and resid 796 through 798' Processing helix chain 'E' and resid 810 through 822 Processing helix chain 'E' and resid 841 through 854 Processing helix chain 'E' and resid 892 through 896 Processing helix chain 'E' and resid 901 through 909 Processing helix chain 'E' and resid 977 through 982 Processing helix chain 'E' and resid 988 through 1018 removed outlier: 3.955A pdb=" N LEU E 992 " --> pdb=" O PHE E 988 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E1008 " --> pdb=" O ILE E1004 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E1018 " --> pdb=" O TRP E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1072 removed outlier: 3.804A pdb=" N SER E1050 " --> pdb=" O CYS E1046 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1082 Processing helix chain 'E' and resid 1087 through 1101 removed outlier: 4.481A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1103 through 1127 Processing helix chain 'E' and resid 1129 through 1176 removed outlier: 3.933A pdb=" N ALA E1136 " --> pdb=" O ILE E1133 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 5.030A pdb=" N PHE E1149 " --> pdb=" O GLN E1146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER E1153 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS E1154 " --> pdb=" O VAL E1151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP E1161 " --> pdb=" O GLU E1158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN E1164 " --> pdb=" O ASP E1161 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU E1165 " --> pdb=" O SER E1162 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 4.180A pdb=" N HIS E1170 " --> pdb=" O LEU E1167 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1183 Processing helix chain 'E' and resid 1187 through 1235 removed outlier: 3.804A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1257 removed outlier: 3.598A pdb=" N GLY E1247 " --> pdb=" O LEU E1243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E1255 " --> pdb=" O ALA E1251 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1260 through 1283 removed outlier: 3.940A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR E1283 " --> pdb=" O ASN E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1295 through 1297 No H-bonds generated for 'chain 'E' and resid 1295 through 1297' Processing helix chain 'E' and resid 1350 through 1355 Processing helix chain 'E' and resid 1368 through 1370 No H-bonds generated for 'chain 'E' and resid 1368 through 1370' Processing helix chain 'E' and resid 1373 through 1375 No H-bonds generated for 'chain 'E' and resid 1373 through 1375' Processing helix chain 'E' and resid 1378 through 1383 Processing helix chain 'E' and resid 1415 through 1421 Processing helix chain 'E' and resid 1443 through 1460 removed outlier: 4.774A pdb=" N GLY E1448 " --> pdb=" O ASN E1444 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN E1451 " --> pdb=" O VAL E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1476 through 1488 Processing helix chain 'E' and resid 1506 through 1508 No H-bonds generated for 'chain 'E' and resid 1506 through 1508' Processing helix chain 'E' and resid 1529 through 1539 removed outlier: 3.994A pdb=" N GLU E1533 " --> pdb=" O LEU E1529 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP E1534 " --> pdb=" O LEU E1530 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY E1535 " --> pdb=" O ALA E1531 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL E1536 " --> pdb=" O GLN E1532 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE E1537 " --> pdb=" O GLU E1533 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 244 through 248 removed outlier: 4.526A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 294 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 300 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 322 through 324 Processing sheet with id= C, first strand: chain 'B' and resid 191 through 193 Processing sheet with id= D, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.686A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 224 through 230 Processing sheet with id= F, first strand: chain 'B' and resid 322 through 324 Processing sheet with id= G, first strand: chain 'C' and resid 198 through 202 Processing sheet with id= H, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.512A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 291 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= J, first strand: chain 'D' and resid 198 through 202 Processing sheet with id= K, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.440A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 296 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 309 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 298 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 322 through 324 Processing sheet with id= M, first strand: chain 'D' and resid 329 through 331 963 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2829 1.30 - 1.43: 2898 1.43 - 1.56: 8407 1.56 - 1.69: 32 1.69 - 1.81: 3 Bond restraints: 14169 Sorted by residual: bond pdb=" O5 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.448 1.643 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" O4 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.453 1.645 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E1601 " pdb=" C5 ATP E1601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 ... (remaining 14164 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.80: 131 104.80 - 112.65: 7681 112.65 - 120.50: 5985 120.50 - 128.35: 5947 128.35 - 136.20: 16 Bond angle restraints: 19760 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 122.73 17.14 1.00e+00 1.00e+00 2.94e+02 ... (remaining 19755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8282 23.45 - 46.90: 65 46.90 - 70.35: 27 70.35 - 93.80: 5 93.80 - 117.24: 3 Dihedral angle restraints: 8382 sinusoidal: 241 harmonic: 8141 Sorted by residual: dihedral pdb=" CA LEU E1325 " pdb=" C LEU E1325 " pdb=" N LYS E1326 " pdb=" CA LYS E1326 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL E1298 " pdb=" C VAL E1298 " pdb=" N PRO E1299 " pdb=" CA PRO E1299 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL E1496 " pdb=" C VAL E1496 " pdb=" N VAL E1497 " pdb=" CA VAL E1497 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 2695 0.381 - 0.762: 1 0.762 - 1.143: 0 1.143 - 1.524: 0 1.524 - 1.905: 1 Chirality restraints: 2697 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.07e+01 chirality pdb=" CA CYS E 263 " pdb=" N CYS E 263 " pdb=" C CYS E 263 " pdb=" CB CYS E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA VAL A 241 " pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CB VAL A 241 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2694 not shown) Planarity restraints: 2825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 9 " 0.052 2.00e-02 2.50e+03 7.86e-02 7.72e+01 pdb=" CG ASN E 9 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 9 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 9 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 104 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C TYR C 104 " -0.099 2.00e-02 2.50e+03 pdb=" O TYR C 104 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 105 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 581 " -0.027 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C PRO E 581 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO E 581 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU E 582 " -0.031 2.00e-02 2.50e+03 ... (remaining 2822 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 4 2.16 - 2.85: 5637 2.85 - 3.53: 19629 3.53 - 4.22: 23515 4.22 - 4.90: 39962 Nonbonded interactions: 88747 Sorted by model distance: nonbonded pdb=" CD PRO E1392 " pdb=" CB ARG E1450 " model vdw 1.477 3.840 nonbonded pdb=" O GLY E1397 " pdb=" O THR E1437 " model vdw 1.985 3.040 nonbonded pdb=" ND2 ASN E 9 " pdb=" N2 NAG N 1 " model vdw 2.004 2.560 nonbonded pdb=" CG PRO E1392 " pdb=" CB ARG E1450 " model vdw 2.150 3.840 nonbonded pdb=" N ARG B 195 " pdb=" O2A ATP B 501 " model vdw 2.228 2.520 ... (remaining 88742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 366) selection = (chain 'B' and ((resid 30 through 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 through 366)) selection = (chain 'C' and resid 30 through 366) selection = (chain 'D' and resid 30 through 366) } 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: 0.070 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: 1.540 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 44.790 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 : 0.008 0.195 14169 Z= 0.567 Angle : 1.114 20.778 19760 Z= 0.812 Chirality : 0.073 1.905 2697 Planarity : 0.005 0.057 2824 Dihedral : 10.540 117.245 3050 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.16), residues: 2800 helix: 0.86 (0.15), residues: 1291 sheet: -0.22 (0.35), residues: 210 loop : -2.70 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.577 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1269 time to fit residues: 20.4761 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 252 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14169 Z= 0.196 Angle : 0.549 10.694 19760 Z= 0.332 Chirality : 0.047 0.175 2697 Planarity : 0.003 0.034 2824 Dihedral : 9.429 79.677 3039 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.68 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.16), residues: 2800 helix: 1.12 (0.15), residues: 1281 sheet: -0.32 (0.34), residues: 231 loop : -2.58 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1226 time to fit residues: 19.8022 Evaluate side-chains 77 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 210 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 252 optimal weight: 20.0000 chunk 273 optimal weight: 0.6980 chunk 225 optimal weight: 40.0000 chunk 250 optimal weight: 40.0000 chunk 86 optimal weight: 40.0000 chunk 202 optimal weight: 50.0000 overall best weight: 22.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 14169 Z= 0.516 Angle : 0.987 17.270 19760 Z= 0.630 Chirality : 0.057 0.290 2697 Planarity : 0.007 0.027 2824 Dihedral : 11.617 89.293 3039 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.71 % Favored : 84.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.14), residues: 2800 helix: -1.10 (0.13), residues: 1200 sheet: -1.15 (0.35), residues: 202 loop : -3.30 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.545 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1270 time to fit residues: 21.0731 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 131 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 169 optimal weight: 0.0070 chunk 253 optimal weight: 8.9990 chunk 268 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14169 Z= 0.134 Angle : 0.495 13.163 19760 Z= 0.298 Chirality : 0.047 0.255 2697 Planarity : 0.003 0.020 2824 Dihedral : 9.714 85.475 3039 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.16), residues: 2800 helix: 0.80 (0.15), residues: 1231 sheet: -0.85 (0.37), residues: 193 loop : -2.81 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.579 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1310 time to fit residues: 21.7299 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 200 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 chunk 229 optimal weight: 50.0000 chunk 185 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14169 Z= 0.131 Angle : 0.453 9.475 19760 Z= 0.273 Chirality : 0.046 0.296 2697 Planarity : 0.002 0.019 2824 Dihedral : 9.252 88.506 3039 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2800 helix: 1.38 (0.15), residues: 1243 sheet: -0.97 (0.35), residues: 210 loop : -2.62 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1354 time to fit residues: 21.3791 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.6980 chunk 241 optimal weight: 0.0000 chunk 53 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 268 optimal weight: 40.0000 chunk 223 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 overall best weight: 4.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14169 Z= 0.137 Angle : 0.450 9.720 19760 Z= 0.272 Chirality : 0.046 0.289 2697 Planarity : 0.002 0.019 2824 Dihedral : 8.909 84.726 3039 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.16), residues: 2800 helix: 1.45 (0.15), residues: 1246 sheet: -0.99 (0.35), residues: 212 loop : -2.58 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.733 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1463 time to fit residues: 23.6011 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 196 optimal weight: 40.0000 chunk 152 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 267 optimal weight: 0.0470 chunk 167 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14169 Z= 0.128 Angle : 0.435 9.477 19760 Z= 0.263 Chirality : 0.046 0.289 2697 Planarity : 0.002 0.018 2824 Dihedral : 8.630 81.501 3039 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.17), residues: 2800 helix: 1.60 (0.15), residues: 1244 sheet: -0.96 (0.36), residues: 210 loop : -2.49 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1327 time to fit residues: 22.2250 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14169 Z= 0.292 Angle : 0.654 9.759 19760 Z= 0.414 Chirality : 0.050 0.294 2697 Planarity : 0.004 0.027 2824 Dihedral : 9.642 88.606 3039 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.15), residues: 2800 helix: 0.32 (0.14), residues: 1231 sheet: -1.18 (0.37), residues: 197 loop : -2.94 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.625 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1215 time to fit residues: 20.2598 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 40.0000 chunk 256 optimal weight: 50.0000 chunk 234 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14169 Z= 0.229 Angle : 0.576 11.197 19760 Z= 0.352 Chirality : 0.048 0.314 2697 Planarity : 0.003 0.035 2824 Dihedral : 9.421 89.635 3039 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.16), residues: 2800 helix: 0.54 (0.15), residues: 1239 sheet: -1.46 (0.36), residues: 207 loop : -2.94 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.467 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1254 time to fit residues: 21.0234 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 chunk 276 optimal weight: 10.0000 chunk 254 optimal weight: 0.0970 chunk 220 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 overall best weight: 3.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14169 Z= 0.117 Angle : 0.436 8.468 19760 Z= 0.259 Chirality : 0.047 0.477 2697 Planarity : 0.002 0.021 2824 Dihedral : 8.755 86.872 3039 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.17), residues: 2800 helix: 1.57 (0.15), residues: 1238 sheet: -1.29 (0.36), residues: 207 loop : -2.69 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.615 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1457 time to fit residues: 23.8224 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 0.8980 chunk 234 optimal weight: 20.0000 chunk 67 optimal weight: 40.0000 chunk 203 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 0.0670 chunk 220 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 226 optimal weight: 40.0000 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.238922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.236620 restraints weight = 23578.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.217222 restraints weight = 56583.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.215714 restraints weight = 65784.486| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 14169 Z= 0.102 Angle : 0.402 8.425 19760 Z= 0.239 Chirality : 0.045 0.206 2697 Planarity : 0.002 0.017 2824 Dihedral : 8.270 86.055 3039 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.17), residues: 2800 helix: 1.94 (0.15), residues: 1244 sheet: -1.17 (0.36), residues: 214 loop : -2.52 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 =============================================================================== Job complete usr+sys time: 1892.70 seconds wall clock time: 34 minutes 30.55 seconds (2070.55 seconds total)