Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 04:18:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/04_2023/6b6h_7059_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.022 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 183 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 22425 2.51 5 N 6502 2.21 5 O 7408 1.98 5 H 35400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 72070 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 21010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21010 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 8105 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "G" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3219 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 196} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3223 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 196} Chain: "I" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1198 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain: "1" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2796 Classifications: {'DNA': 88} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 87} Chain: "2" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2805 Classifications: {'DNA': 88} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 87} Chain: "3" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 137.197 63.206 64.179 1.00 20.00 S ATOM 29236 SG CYS D 72 139.792 65.051 62.894 1.00 20.00 S ATOM 29466 SG CYS D 85 140.409 61.675 63.220 1.00 20.00 S ATOM 29513 SG CYS D 88 141.285 62.722 66.424 1.00 20.00 S ATOM 41046 SG CYS D 814 116.790 25.113 117.696 1.00 20.00 S ATOM 42183 SG CYS D 888 119.056 27.662 117.182 1.00 20.00 S ATOM 42312 SG CYS D 898 115.608 27.633 120.215 1.00 20.00 S Time building chain proxies: 23.28, per 1000 atoms: 0.32 Number of scatterers: 72070 At special positions: 0 Unit cell: (221.4, 164.7, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 149 16.00 P 183 15.00 Mg 1 11.99 O 7408 8.00 N 6502 7.00 C 22425 6.00 H 35400 1.00 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 50.05 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 36 sheets defined 37.2% alpha, 9.1% beta 65 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 31.15 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.808A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.589A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 232 removed outlier: 5.736A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.586A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 480 removed outlier: 4.469A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.576A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 824 No H-bonds generated for 'chain 'C' and resid 821 through 824' Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.765A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 977 removed outlier: 3.563A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1037 removed outlier: 3.650A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.772A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C1133 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1262 through 1264 No H-bonds generated for 'chain 'C' and resid 1262 through 1264' Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 4.145A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1333 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.740A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 265 through 283 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 454 Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.837A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 651 through 670 Processing helix chain 'D' and resid 676 through 700 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 788 removed outlier: 4.406A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 5.699A pdb=" N ASP D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 916 through 924 Processing helix chain 'D' and resid 927 through 929 No H-bonds generated for 'chain 'D' and resid 927 through 929' Processing helix chain 'D' and resid 1139 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.626A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.930A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 3.649A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1336 Processing helix chain 'D' and resid 1348 through 1352 Processing helix chain 'D' and resid 1360 through 1374 removed outlier: 3.987A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN D1367 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 81 through 90 removed outlier: 3.501A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 115 through 135 Processing helix chain 'F' and resid 138 through 152 removed outlier: 3.608A pdb=" N TYR F 143 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 147 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR F 148 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 152 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 214 through 236 removed outlier: 3.869A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 263 through 295 removed outlier: 3.906A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 308 removed outlier: 3.557A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.982A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 393 removed outlier: 4.559A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.381A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 3.871A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 531 through 550 removed outlier: 4.295A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 563 removed outlier: 4.270A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 585 through 598 Processing helix chain 'F' and resid 604 through 610 removed outlier: 3.535A pdb=" N ARG F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER F 609 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 15 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 99 through 108 removed outlier: 4.026A pdb=" N GLN G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 135 Processing helix chain 'G' and resid 139 through 152 removed outlier: 3.776A pdb=" N LYS G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 176 Processing helix chain 'G' and resid 180 through 192 Processing helix chain 'H' and resid 10 through 17 removed outlier: 4.106A pdb=" N HIS H 17 " --> pdb=" O TRP H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 108 Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 139 through 152 Processing helix chain 'H' and resid 169 through 176 Processing helix chain 'H' and resid 180 through 192 Processing helix chain 'I' and resid 257 through 260 Processing helix chain 'I' and resid 264 through 273 removed outlier: 3.507A pdb=" N GLU I 273 " --> pdb=" O CYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 283 removed outlier: 3.510A pdb=" N GLN I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 290 No H-bonds generated for 'chain 'I' and resid 287 through 290' Processing helix chain 'I' and resid 298 through 310 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 5.988A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.004A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.796A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 116 through 123 removed outlier: 3.914A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 154 through 161 Processing sheet with id= K, first strand: chain 'C' and resid 333 through 336 removed outlier: 4.843A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 588 through 592 Processing sheet with id= M, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= N, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.289A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1227 through 1232 removed outlier: 6.836A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 876 through 878 Processing sheet with id= Q, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= R, first strand: chain 'C' and resid 930 through 935 removed outlier: 3.645A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= T, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= U, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= V, first strand: chain 'D' and resid 365 through 369 removed outlier: 6.488A pdb=" N GLU D 438 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU D 368 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL D 440 " --> pdb=" O LEU D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 548 through 552 Processing sheet with id= X, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= Y, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= Z, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.659A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 1105 through 1107 Processing sheet with id= AB, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.753A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 950 through 952 removed outlier: 6.600A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 981 through 985 Processing sheet with id= AE, first strand: chain 'G' and resid 19 through 23 removed outlier: 6.353A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 85 through 88 removed outlier: 6.287A pdb=" N ILE G 51 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE G 60 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 157 through 159 Processing sheet with id= AH, first strand: chain 'H' and resid 21 through 23 Processing sheet with id= AI, first strand: chain 'H' and resid 85 through 87 removed outlier: 6.199A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 157 through 159 1173 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 159 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 31.81 Time building geometry restraints manager: 52.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 35369 1.03 - 1.23: 397 1.23 - 1.43: 15238 1.43 - 1.63: 21738 1.63 - 1.83: 260 Bond restraints: 73002 Sorted by residual: bond pdb=" C5 GTP 3 1 " pdb=" C6 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 GTP 3 1 " pdb=" C5 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1' DC 1 18 " pdb=" N1 DC 1 18 " ideal model delta sigma weight residual 1.490 1.565 -0.075 3.00e-02 1.11e+03 6.20e+00 bond pdb=" CA VAL F 166 " pdb=" CB VAL F 166 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.36e-02 5.41e+03 6.01e+00 bond pdb=" C4 GTP 3 1 " pdb=" N9 GTP 3 1 " ideal model delta sigma weight residual 1.375 1.326 0.049 2.00e-02 2.50e+03 5.97e+00 ... (remaining 72997 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.39: 1158 104.39 - 112.52: 85336 112.52 - 120.64: 27072 120.64 - 128.76: 18482 128.76 - 136.88: 378 Bond angle restraints: 132426 Sorted by residual: angle pdb=" N SER F 602 " pdb=" CA SER F 602 " pdb=" C SER F 602 " ideal model delta sigma weight residual 114.04 107.14 6.90 1.24e+00 6.50e-01 3.10e+01 angle pdb=" N VAL D1017 " pdb=" CA VAL D1017 " pdb=" C VAL D1017 " ideal model delta sigma weight residual 110.82 106.12 4.70 9.70e-01 1.06e+00 2.35e+01 angle pdb=" N GLU C1005 " pdb=" CA GLU C1005 " pdb=" C GLU C1005 " ideal model delta sigma weight residual 110.80 120.84 -10.04 2.13e+00 2.20e-01 2.22e+01 angle pdb=" C THR F 112 " pdb=" N ARG F 113 " pdb=" CA ARG F 113 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ILE D 619 " pdb=" N PHE D 620 " pdb=" CA PHE D 620 " ideal model delta sigma weight residual 120.82 127.36 -6.54 1.50e+00 4.44e-01 1.90e+01 ... (remaining 132421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 27459 35.63 - 71.26: 925 71.26 - 106.89: 30 106.89 - 142.51: 5 142.51 - 178.14: 7 Dihedral angle restraints: 28426 sinusoidal: 15034 harmonic: 13392 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -113.91 -66.09 0 5.00e+00 4.00e-02 1.75e+02 dihedral pdb=" CA PHE F 165 " pdb=" C PHE F 165 " pdb=" N VAL F 166 " pdb=" CA VAL F 166 " ideal model delta harmonic sigma weight residual -180.00 -125.67 -54.33 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ASP C1004 " pdb=" C ASP C1004 " pdb=" N GLU C1005 " pdb=" CA GLU C1005 " ideal model delta harmonic sigma weight residual -180.00 -133.02 -46.98 0 5.00e+00 4.00e-02 8.83e+01 ... (remaining 28423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3896 0.045 - 0.090: 1473 0.090 - 0.134: 436 0.134 - 0.179: 60 0.179 - 0.224: 6 Chirality restraints: 5871 Sorted by residual: chirality pdb=" C2' GTP 3 1 " pdb=" C1' GTP 3 1 " pdb=" C3' GTP 3 1 " pdb=" O2' GTP 3 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 754 " pdb=" CA ILE D 754 " pdb=" CG1 ILE D 754 " pdb=" CG2 ILE D 754 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE H 106 " pdb=" CA ILE H 106 " pdb=" CG1 ILE H 106 " pdb=" CG2 ILE H 106 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 5868 not shown) Planarity restraints: 10222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 568 " 0.228 2.00e-02 2.50e+03 3.77e-01 2.14e+03 pdb=" CG ASN C 568 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 568 " -0.220 2.00e-02 2.50e+03 pdb=" ND2 ASN C 568 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 568 " -0.613 2.00e-02 2.50e+03 pdb="HD22 ASN C 568 " 0.615 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 424 " 0.246 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN D 424 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN D 424 " -0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN D 424 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN D 424 " -0.508 2.00e-02 2.50e+03 pdb="HD22 ASN D 424 " 0.539 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 400 " 0.232 2.00e-02 2.50e+03 2.88e-01 1.24e+03 pdb=" CD GLN F 400 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN F 400 " -0.219 2.00e-02 2.50e+03 pdb=" NE2 GLN F 400 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN F 400 " -0.436 2.00e-02 2.50e+03 pdb="HE22 GLN F 400 " 0.451 2.00e-02 2.50e+03 ... (remaining 10219 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 6016 2.22 - 2.81: 157855 2.81 - 3.41: 187188 3.41 - 4.00: 252837 4.00 - 4.60: 389698 Nonbonded interactions: 993594 Sorted by model distance: nonbonded pdb=" O ARG D1371 " pdb=" H ALA D1375 " model vdw 1.621 1.850 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.643 1.850 nonbonded pdb=" O LEU C 699 " pdb=" H ILE C1182 " model vdw 1.644 1.850 nonbonded pdb=" O GLU F 114 " pdb=" H ASP F 118 " model vdw 1.650 1.850 nonbonded pdb=" H VAL D1035 " pdb=" O VAL D1113 " model vdw 1.653 1.850 ... (remaining 993589 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 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = (chain 'H' and ((resid 9 and (name CA or name C or name O or name CB or name CG \ or name CD or name HB2 or name HB3 or name HG2 or name HG3)) or resid 10 through \ 209 or resid 301)) } 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: 0.720 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: 0.810 Extract box with map and model: 6.920 Check model and map are aligned: 0.760 Set scattering table: 0.500 Process input model: 225.880 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.210 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4724 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 0.084 37602 Z= 0.544 Angle : 0.958 11.668 51553 Z= 0.530 Chirality : 0.050 0.224 5871 Planarity : 0.006 0.075 6078 Dihedral : 15.909 178.143 14691 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.86 % Favored : 90.97 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.10), residues: 4164 helix: -3.00 (0.09), residues: 1587 sheet: -3.27 (0.19), residues: 419 loop : -2.87 (0.12), residues: 2158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 1.1946 time to fit residues: 463.5102 Evaluate side-chains 186 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 363 optimal weight: 8.9990 chunk 326 optimal weight: 30.0000 chunk 181 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 391 optimal weight: 50.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1264 GLN C1313 HIS D 341 ASN D 665 GLN D 700 ASN D 805 GLN D 910 ASN G 80 GLN H 21 HIS H 125 GLN I 268 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4777 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 37602 Z= 0.245 Angle : 0.673 9.989 51553 Z= 0.370 Chirality : 0.042 0.198 5871 Planarity : 0.005 0.067 6078 Dihedral : 20.374 179.364 6399 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.07 % Favored : 91.81 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.10 % 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: -3.26 (0.11), residues: 4164 helix: -1.63 (0.11), residues: 1592 sheet: -2.70 (0.20), residues: 438 loop : -2.47 (0.12), residues: 2134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 205 average time/residue: 1.0719 time to fit residues: 351.1932 Evaluate side-chains 196 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 4.249 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.7410 time to fit residues: 20.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 217 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 392 optimal weight: 40.0000 chunk 423 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 133 optimal weight: 0.1980 chunk 314 optimal weight: 20.0000 overall best weight: 6.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 83 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4864 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 37602 Z= 0.279 Angle : 0.659 9.813 51553 Z= 0.362 Chirality : 0.042 0.228 5871 Planarity : 0.004 0.066 6078 Dihedral : 20.129 174.927 6399 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.37 % Favored : 90.59 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.10 % 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: -2.63 (0.12), residues: 4164 helix: -0.89 (0.12), residues: 1615 sheet: -2.38 (0.21), residues: 442 loop : -2.31 (0.12), residues: 2107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 199 average time/residue: 1.0473 time to fit residues: 330.4629 Evaluate side-chains 190 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.7271 time to fit residues: 20.0181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 387 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 393 optimal weight: 8.9990 chunk 416 optimal weight: 60.0000 chunk 205 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D1326 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4946 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 37602 Z= 0.318 Angle : 0.678 9.334 51553 Z= 0.373 Chirality : 0.043 0.260 5871 Planarity : 0.005 0.064 6078 Dihedral : 20.033 173.411 6399 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.94 % Favored : 90.01 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.10 % 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: -2.52 (0.12), residues: 4164 helix: -0.73 (0.12), residues: 1613 sheet: -2.24 (0.21), residues: 460 loop : -2.32 (0.12), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 204 average time/residue: 1.0202 time to fit residues: 331.9404 Evaluate side-chains 183 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 4.284 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.8789 time to fit residues: 28.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 346 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 355 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 373 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4904 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 : 0.003 0.047 37602 Z= 0.198 Angle : 0.590 9.911 51553 Z= 0.325 Chirality : 0.041 0.224 5871 Planarity : 0.004 0.061 6078 Dihedral : 19.884 172.780 6399 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.20 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.12), residues: 4164 helix: -0.21 (0.12), residues: 1611 sheet: -2.00 (0.23), residues: 424 loop : -2.05 (0.13), residues: 2129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 188 average time/residue: 1.0132 time to fit residues: 306.2288 Evaluate side-chains 179 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 4.334 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.7117 time to fit residues: 22.3119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 140 optimal weight: 10.0000 chunk 375 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 417 optimal weight: 30.0000 chunk 346 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 137 optimal weight: 0.0470 chunk 218 optimal weight: 7.9990 overall best weight: 6.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS F 131 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4966 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 37602 Z= 0.279 Angle : 0.626 9.938 51553 Z= 0.346 Chirality : 0.042 0.238 5871 Planarity : 0.004 0.059 6078 Dihedral : 19.843 173.156 6399 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.80 % Favored : 90.15 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 4164 helix: -0.24 (0.12), residues: 1618 sheet: -2.07 (0.23), residues: 430 loop : -2.09 (0.13), residues: 2116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 179 average time/residue: 0.9981 time to fit residues: 286.5543 Evaluate side-chains 178 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 4.275 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.7544 time to fit residues: 23.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 402 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 304 optimal weight: 0.6980 chunk 235 optimal weight: 0.0670 chunk 351 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 415 optimal weight: 70.0000 chunk 259 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 overall best weight: 5.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS F 131 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4956 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 37602 Z= 0.233 Angle : 0.597 9.886 51553 Z= 0.329 Chirality : 0.041 0.229 5871 Planarity : 0.004 0.075 6078 Dihedral : 19.804 172.584 6399 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.86 % Favored : 91.09 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.12), residues: 4164 helix: -0.05 (0.13), residues: 1611 sheet: -1.83 (0.23), residues: 443 loop : -2.04 (0.13), residues: 2110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 175 average time/residue: 0.9693 time to fit residues: 275.7357 Evaluate side-chains 171 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 4.346 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.8476 time to fit residues: 22.0067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 256 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 37602 Z= 0.292 Angle : 0.630 9.825 51553 Z= 0.348 Chirality : 0.042 0.235 5871 Planarity : 0.004 0.090 6078 Dihedral : 19.819 172.713 6399 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.25 % Favored : 89.70 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 4164 helix: -0.13 (0.12), residues: 1599 sheet: -1.89 (0.24), residues: 429 loop : -2.10 (0.13), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.9532 time to fit residues: 276.0731 Evaluate side-chains 175 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 4.274 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.6644 time to fit residues: 21.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 349 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 385 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D1326 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5014 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 37602 Z= 0.287 Angle : 0.634 9.776 51553 Z= 0.349 Chirality : 0.042 0.236 5871 Planarity : 0.005 0.097 6078 Dihedral : 19.837 172.243 6399 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.46 % Favored : 90.49 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.12), residues: 4164 helix: -0.18 (0.12), residues: 1609 sheet: -1.80 (0.23), residues: 455 loop : -2.11 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 170 average time/residue: 0.9753 time to fit residues: 269.6124 Evaluate side-chains 167 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 4.275 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.7338 time to fit residues: 12.6637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 254 optimal weight: 10.0000 chunk 409 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 429 optimal weight: 30.0000 chunk 395 optimal weight: 40.0000 chunk 341 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 777 HIS ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5026 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 37602 Z= 0.287 Angle : 0.636 9.578 51553 Z= 0.350 Chirality : 0.042 0.239 5871 Planarity : 0.005 0.098 6078 Dihedral : 19.811 172.415 6399 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.28 % Favored : 89.67 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4164 helix: -0.18 (0.12), residues: 1611 sheet: -1.79 (0.24), residues: 453 loop : -2.12 (0.13), residues: 2100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.9842 time to fit residues: 266.5372 Evaluate side-chains 164 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 4.235 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.6983 time to fit residues: 10.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 271 optimal weight: 9.9990 chunk 364 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 351 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.107269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.094516 restraints weight = 979857.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.094296 restraints weight = 735574.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.094074 restraints weight = 652798.628| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 37602 Z= 0.244 Angle : 0.608 9.554 51553 Z= 0.335 Chirality : 0.041 0.230 5871 Planarity : 0.004 0.094 6078 Dihedral : 19.748 172.214 6399 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.53 % Favored : 91.43 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 4164 helix: -0.04 (0.13), residues: 1619 sheet: -1.79 (0.23), residues: 475 loop : -1.99 (0.13), residues: 2070 =============================================================================== Job complete usr+sys time: 8886.82 seconds wall clock time: 157 minutes 5.17 seconds (9425.17 seconds total)