Starting phenix.real_space_refine on Sat Mar 16 02:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/03_2024/6b6h_7059_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/03_2024/6b6h_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_7059/03_2024/6b6h_7059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/03_2024/6b6h_7059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/03_2024/6b6h_7059_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b6h_7059/03_2024/6b6h_7059_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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-dev-5265/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: 22.78, 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: 46.69 Conformation dependent library (CDL) restraints added in 5.5 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: 33.99 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: 27.45 Time building geometry restraints manager: 49.14 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: 31772 35.63 - 71.26: 1402 71.26 - 106.89: 30 106.89 - 142.51: 5 142.51 - 178.14: 7 Dihedral angle restraints: 33216 sinusoidal: 19824 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 33213 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: 0.310 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: 0.780 Extract box with map and model: 4.600 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 219.550 Find NCS groups from input model: 1.440 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: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.520 ------------------------------------------------------------------------------- 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 : 16.110 178.143 14889 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 % Allowed : 1.84 % Favored : 98.13 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 85 HIS 0.014 0.003 HIS B 132 PHE 0.043 0.003 PHE D 620 TYR 0.029 0.003 TYR C1229 ARG 0.015 0.002 ARG C1301 *********************** 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 : 4.008 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: F 297 MET cc_start: 0.2476 (ptt) cc_final: 0.0090 (mtt) REVERT: H 51 ILE cc_start: 0.5139 (tp) cc_final: 0.4919 (tt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 1.1944 time to fit residues: 462.0689 Evaluate side-chains 186 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.050 ------------------------------------------------------------------------------- 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: 40.0000 chunk 181 optimal weight: 8.9990 chunk 111 optimal weight: 0.3980 chunk 220 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 337 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 391 optimal weight: 50.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.4764 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37602 Z= 0.220 Angle : 0.661 9.884 51553 Z= 0.364 Chirality : 0.042 0.182 5871 Planarity : 0.005 0.065 6078 Dihedral : 20.473 178.145 6597 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 0.50 % Allowed : 4.02 % Favored : 95.48 % 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: -3.15 (0.11), residues: 4164 helix: -1.51 (0.11), residues: 1592 sheet: -2.59 (0.20), residues: 446 loop : -2.43 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.026 0.002 PHE D 620 TYR 0.014 0.001 TYR D 679 ARG 0.008 0.001 ARG D1036 *********************** 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 211 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 4.039 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: D 1095 MET cc_start: 0.3061 (mtm) cc_final: 0.2283 (mtt) REVERT: F 297 MET cc_start: 0.1732 (ptt) cc_final: 0.0550 (tmm) REVERT: G 59 MET cc_start: 0.0557 (tpt) cc_final: 0.0099 (tpt) REVERT: G 72 GLU cc_start: 0.0148 (pm20) cc_final: -0.0639 (mp0) outliers start: 18 outliers final: 10 residues processed: 206 average time/residue: 1.0375 time to fit residues: 338.1919 Evaluate side-chains 195 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 190 LEU 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: 10.0000 chunk 325 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 392 optimal weight: 50.0000 chunk 423 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 388 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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 832 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D1279 GLN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4944 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 37602 Z= 0.370 Angle : 0.748 10.156 51553 Z= 0.413 Chirality : 0.044 0.253 5871 Planarity : 0.006 0.064 6078 Dihedral : 20.348 177.047 6597 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.00 % Favored : 88.93 % Rotamer: Outliers : 1.17 % Allowed : 4.68 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.07 % 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: -3.01 (0.12), residues: 4164 helix: -1.26 (0.12), residues: 1597 sheet: -2.46 (0.22), residues: 443 loop : -2.51 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 85 HIS 0.010 0.002 HIS D 80 PHE 0.030 0.002 PHE D 620 TYR 0.019 0.002 TYR D 772 ARG 0.008 0.001 ARG C1301 *********************** 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 222 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 4.162 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: C 488 MET cc_start: 0.6567 (mmt) cc_final: 0.6261 (mmt) REVERT: C 922 ASN cc_start: 0.5450 (t0) cc_final: 0.5194 (t0) REVERT: D 505 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7842 (t0) REVERT: D 1095 MET cc_start: 0.3880 (mtm) cc_final: 0.3153 (mtt) REVERT: F 297 MET cc_start: 0.3116 (ptt) cc_final: 0.1152 (tmm) REVERT: F 561 MET cc_start: 0.4728 (mmm) cc_final: 0.4494 (mmm) REVERT: G 72 GLU cc_start: 0.1043 (pm20) cc_final: 0.0507 (mm-30) outliers start: 42 outliers final: 26 residues processed: 210 average time/residue: 1.0052 time to fit residues: 334.0197 Evaluate side-chains 197 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 387 optimal weight: 50.0000 chunk 294 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 393 optimal weight: 30.0000 chunk 416 optimal weight: 60.0000 chunk 205 optimal weight: 8.9990 chunk 372 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 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 894 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D1108 GLN D1259 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4956 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37602 Z= 0.298 Angle : 0.661 9.847 51553 Z= 0.366 Chirality : 0.043 0.239 5871 Planarity : 0.005 0.063 6078 Dihedral : 20.169 172.437 6597 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.93 % Favored : 91.02 % Rotamer: Outliers : 1.28 % Allowed : 5.52 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.07 % 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: -2.62 (0.12), residues: 4164 helix: -0.86 (0.12), residues: 1622 sheet: -2.18 (0.22), residues: 443 loop : -2.38 (0.12), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 85 HIS 0.010 0.002 HIS D 80 PHE 0.023 0.002 PHE D 620 TYR 0.014 0.002 TYR C 301 ARG 0.010 0.001 ARG C 268 *********************** 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 219 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 4.067 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: B 68 TYR cc_start: 0.5073 (OUTLIER) cc_final: 0.3263 (m-80) REVERT: C 488 MET cc_start: 0.6966 (mmt) cc_final: 0.6659 (mmt) REVERT: C 800 MET cc_start: 0.7843 (pmm) cc_final: 0.7466 (pmm) REVERT: D 1095 MET cc_start: 0.4043 (mtm) cc_final: 0.3457 (mtt) REVERT: E 71 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.4683 (pm20) REVERT: F 297 MET cc_start: 0.3216 (ptt) cc_final: 0.1753 (tmm) REVERT: H 114 MET cc_start: 0.2949 (mtp) cc_final: 0.2452 (mtm) outliers start: 46 outliers final: 29 residues processed: 204 average time/residue: 0.9684 time to fit residues: 315.7382 Evaluate side-chains 198 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 346 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 373 optimal weight: 50.0000 chunk 105 optimal weight: 0.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4947 moved from start: 0.3592 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= 0.231 Angle : 0.608 10.370 51553 Z= 0.337 Chirality : 0.041 0.233 5871 Planarity : 0.004 0.058 6078 Dihedral : 20.008 172.941 6597 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 1.28 % Allowed : 6.00 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.07 % 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: -2.22 (0.12), residues: 4164 helix: -0.45 (0.12), residues: 1611 sheet: -2.10 (0.23), residues: 426 loop : -2.18 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 85 HIS 0.009 0.001 HIS D 80 PHE 0.019 0.001 PHE D 620 TYR 0.013 0.001 TYR C 756 ARG 0.004 0.000 ARG C 678 *********************** 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 217 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 4.082 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: B 68 TYR cc_start: 0.4875 (OUTLIER) cc_final: 0.3004 (m-80) REVERT: C 488 MET cc_start: 0.6797 (mmt) cc_final: 0.6496 (mmt) REVERT: C 800 MET cc_start: 0.7734 (pmm) cc_final: 0.7121 (pmm) REVERT: D 1095 MET cc_start: 0.3674 (mtm) cc_final: 0.2970 (mtt) REVERT: D 1174 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5789 (mtt90) REVERT: E 71 GLU cc_start: 0.5410 (OUTLIER) cc_final: 0.4692 (pm20) REVERT: F 297 MET cc_start: 0.2642 (ptt) cc_final: 0.1234 (tmm) outliers start: 46 outliers final: 32 residues processed: 202 average time/residue: 0.9871 time to fit residues: 319.4459 Evaluate side-chains 198 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU 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: 40.0000 chunk 82 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 417 optimal weight: 30.0000 chunk 346 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 0.0050 chunk 137 optimal weight: 9.9990 chunk 218 optimal weight: 0.0770 overall best weight: 4.6158 ------------------------------------------------------------------------------- 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 760 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.4945 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37602 Z= 0.212 Angle : 0.586 10.081 51553 Z= 0.324 Chirality : 0.041 0.225 5871 Planarity : 0.004 0.055 6078 Dihedral : 19.885 172.856 6597 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer: Outliers : 1.12 % Allowed : 6.78 % Favored : 92.11 % 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: -1.89 (0.12), residues: 4164 helix: -0.11 (0.13), residues: 1603 sheet: -1.92 (0.23), residues: 452 loop : -2.04 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.018 0.001 PHE D 620 TYR 0.011 0.001 TYR C 756 ARG 0.008 0.000 ARG C 268 *********************** 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 203 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 4.021 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: B 68 TYR cc_start: 0.4933 (OUTLIER) cc_final: 0.3018 (m-80) REVERT: C 247 ARG cc_start: 0.3379 (ptt90) cc_final: 0.3004 (ptt-90) REVERT: C 488 MET cc_start: 0.6850 (mmt) cc_final: 0.6550 (mmt) REVERT: C 800 MET cc_start: 0.7722 (pmm) cc_final: 0.7077 (pmm) REVERT: D 932 MET cc_start: 0.4954 (mpp) cc_final: 0.4154 (mpp) REVERT: D 1095 MET cc_start: 0.3664 (mtm) cc_final: 0.3075 (mtt) REVERT: D 1174 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5798 (mtt90) REVERT: E 71 GLU cc_start: 0.5722 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: F 297 MET cc_start: 0.2626 (ptt) cc_final: 0.0988 (tmm) outliers start: 40 outliers final: 32 residues processed: 192 average time/residue: 0.9447 time to fit residues: 295.1136 Evaluate side-chains 198 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain I residue 259 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 402 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 304 optimal weight: 0.3980 chunk 235 optimal weight: 0.0980 chunk 351 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 415 optimal weight: 70.0000 chunk 259 optimal weight: 20.0000 chunk 253 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 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: 0.4918 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37602 Z= 0.174 Angle : 0.559 10.176 51553 Z= 0.309 Chirality : 0.041 0.208 5871 Planarity : 0.004 0.051 6078 Dihedral : 19.772 173.000 6597 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.27 % Rotamer: Outliers : 1.12 % Allowed : 7.00 % Favored : 91.89 % 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: -1.54 (0.13), residues: 4164 helix: 0.20 (0.13), residues: 1610 sheet: -1.85 (0.23), residues: 460 loop : -1.83 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.017 0.001 PHE D 620 TYR 0.011 0.001 TYR F 430 ARG 0.004 0.000 ARG C 268 *********************** 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 208 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 4.073 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: B 68 TYR cc_start: 0.5078 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: C 488 MET cc_start: 0.6814 (mmt) cc_final: 0.6541 (mmt) REVERT: C 800 MET cc_start: 0.7700 (pmm) cc_final: 0.7067 (pmm) REVERT: D 204 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5518 (tm-30) REVERT: D 932 MET cc_start: 0.5134 (mpp) cc_final: 0.4309 (mpp) REVERT: D 1095 MET cc_start: 0.3602 (mtm) cc_final: 0.3057 (mtt) REVERT: D 1189 MET cc_start: 0.6521 (mtt) cc_final: 0.6226 (mtp) REVERT: E 71 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4905 (pm20) REVERT: F 297 MET cc_start: 0.2534 (ptt) cc_final: 0.1002 (tmm) REVERT: G 72 GLU cc_start: 0.0961 (pm20) cc_final: 0.0313 (mm-30) REVERT: H 114 MET cc_start: 0.2309 (mtp) cc_final: 0.1822 (mtm) outliers start: 40 outliers final: 29 residues processed: 197 average time/residue: 0.9329 time to fit residues: 296.8785 Evaluate side-chains 197 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 73 LEU 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: 10.0000 chunk 248 optimal weight: 0.1980 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 326 optimal weight: 50.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 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: 0.4960 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37602 Z= 0.237 Angle : 0.585 9.954 51553 Z= 0.324 Chirality : 0.041 0.221 5871 Planarity : 0.004 0.085 6078 Dihedral : 19.752 173.122 6597 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.65 % Favored : 91.31 % Rotamer: Outliers : 1.12 % Allowed : 7.36 % Favored : 91.52 % 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: -1.58 (0.13), residues: 4164 helix: 0.17 (0.13), residues: 1604 sheet: -1.82 (0.23), residues: 462 loop : -1.85 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 85 HIS 0.031 0.001 HIS D 651 PHE 0.014 0.001 PHE D 620 TYR 0.011 0.001 TYR B 68 ARG 0.011 0.000 ARG D1174 *********************** 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 206 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 4.039 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: B 68 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.3326 (m-80) REVERT: C 370 MET cc_start: 0.7143 (mmm) cc_final: 0.6749 (tpp) REVERT: C 488 MET cc_start: 0.7418 (mmt) cc_final: 0.7022 (mmt) REVERT: D 204 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5588 (tm-30) REVERT: D 932 MET cc_start: 0.4947 (mpp) cc_final: 0.4191 (mpp) REVERT: D 1095 MET cc_start: 0.3661 (mtm) cc_final: 0.3120 (mtt) REVERT: D 1189 MET cc_start: 0.6513 (mtt) cc_final: 0.6290 (mtp) REVERT: E 71 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5064 (pm20) REVERT: F 297 MET cc_start: 0.2593 (ptt) cc_final: 0.1314 (tmm) REVERT: G 72 GLU cc_start: 0.1069 (pm20) cc_final: 0.0342 (mm-30) REVERT: H 114 MET cc_start: 0.2377 (mtp) cc_final: 0.1887 (mtm) outliers start: 40 outliers final: 35 residues processed: 195 average time/residue: 0.9196 time to fit residues: 290.5555 Evaluate side-chains 203 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 377 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 363 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 385 optimal weight: 50.0000 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** 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: 0.5004 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37602 Z= 0.308 Angle : 0.630 9.816 51553 Z= 0.348 Chirality : 0.042 0.232 5871 Planarity : 0.005 0.153 6078 Dihedral : 19.788 172.666 6597 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.65 % Favored : 90.30 % Rotamer: Outliers : 1.28 % Allowed : 7.25 % Favored : 91.47 % 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: 1606 sheet: -1.92 (0.23), residues: 464 loop : -1.95 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 85 HIS 0.030 0.002 HIS D 651 PHE 0.015 0.002 PHE D 620 TYR 0.013 0.002 TYR B 68 ARG 0.020 0.001 ARG D1290 *********************** 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 206 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 4.037 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: B 68 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.3503 (m-80) REVERT: C 488 MET cc_start: 0.7544 (mmt) cc_final: 0.7139 (mmt) REVERT: D 204 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5662 (tm-30) REVERT: D 932 MET cc_start: 0.5097 (mpp) cc_final: 0.4286 (mpp) REVERT: D 1095 MET cc_start: 0.3747 (mtm) cc_final: 0.3191 (mtt) REVERT: E 71 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5063 (pm20) REVERT: F 297 MET cc_start: 0.2484 (ptt) cc_final: 0.1302 (tmm) REVERT: G 72 GLU cc_start: 0.1238 (pm20) cc_final: 0.0398 (mm-30) REVERT: G 157 MET cc_start: 0.1187 (mmm) cc_final: 0.0802 (mmm) REVERT: H 114 MET cc_start: 0.2445 (mtp) cc_final: 0.1956 (mtm) outliers start: 46 outliers final: 38 residues processed: 197 average time/residue: 0.9172 time to fit residues: 295.0597 Evaluate side-chains 201 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 73 LEU 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: 50.0000 chunk 249 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 429 optimal weight: 30.0000 chunk 395 optimal weight: 7.9990 chunk 341 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 209 optimal weight: 0.1980 overall best weight: 5.6388 ------------------------------------------------------------------------------- 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** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** 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: 0.4986 moved from start: 0.4595 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= 0.234 Angle : 0.593 9.756 51553 Z= 0.327 Chirality : 0.041 0.225 5871 Planarity : 0.005 0.122 6078 Dihedral : 19.762 172.378 6597 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.65 % Favored : 91.31 % Rotamer: Outliers : 1.14 % Allowed : 7.50 % Favored : 91.36 % 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: -1.65 (0.13), residues: 4164 helix: 0.08 (0.13), residues: 1611 sheet: -1.87 (0.23), residues: 471 loop : -1.87 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.015 0.001 PHE D 620 TYR 0.012 0.001 TYR B 68 ARG 0.021 0.000 ARG D1290 ********************** 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 201 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 4.050 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: B 68 TYR cc_start: 0.5526 (OUTLIER) cc_final: 0.3575 (m-80) REVERT: C 488 MET cc_start: 0.7544 (mmt) cc_final: 0.7160 (mmt) REVERT: D 204 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5610 (tm-30) REVERT: D 932 MET cc_start: 0.5153 (mpp) cc_final: 0.4366 (mpp) REVERT: D 1095 MET cc_start: 0.3817 (mtm) cc_final: 0.3244 (mtt) REVERT: E 71 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5042 (pm20) REVERT: F 297 MET cc_start: 0.2425 (ptt) cc_final: 0.1285 (tmm) REVERT: G 72 GLU cc_start: 0.1235 (pm20) cc_final: 0.0383 (mm-30) REVERT: G 157 MET cc_start: 0.1188 (mmm) cc_final: 0.0829 (mmm) REVERT: H 114 MET cc_start: 0.2407 (mtp) cc_final: 0.1913 (mtm) outliers start: 41 outliers final: 37 residues processed: 192 average time/residue: 0.9646 time to fit residues: 304.9429 Evaluate side-chains 198 residues out of total 3587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1293 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain H residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 271 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.102431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.081290 restraints weight = 855852.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.077657 restraints weight = 716033.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.077509 restraints weight = 681613.862| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4750 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= 0.264 Angle : 0.607 9.683 51553 Z= 0.335 Chirality : 0.041 0.231 5871 Planarity : 0.005 0.121 6078 Dihedral : 19.757 172.547 6597 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.53 % Favored : 90.42 % Rotamer: Outliers : 1.12 % Allowed : 7.61 % Favored : 91.27 % 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: -1.68 (0.13), residues: 4164 helix: 0.04 (0.13), residues: 1612 sheet: -1.89 (0.23), residues: 471 loop : -1.88 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 85 HIS 0.008 0.001 HIS D 80 PHE 0.015 0.002 PHE D 620 TYR 0.013 0.001 TYR B 68 ARG 0.018 0.001 ARG D1290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9552.73 seconds wall clock time: 168 minutes 11.17 seconds (10091.17 seconds total)