Starting phenix.real_space_refine on Sun Sep 29 12:08:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eok_28378/09_2024/8eok_28378.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 117 5.16 5 C 14068 2.51 5 N 3784 2.21 5 O 4263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22233 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4926 Classifications: {'peptide': 629} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 592} Chain breaks: 5 Chain: "H" Number of atoms: 7146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7146 Classifications: {'peptide': 895} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 855} Chain breaks: 3 Chain: "D" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5545 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 665} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2278 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 268} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "C" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1863 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.02, per 1000 atoms: 0.59 Number of scatterers: 22233 At special positions: 0 Unit cell: (139.84, 150.88, 170.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 Mg 1 11.99 O 4263 8.00 N 3784 7.00 C 14068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS G 537 " - pdb=" SG CYS H 794 " distance=2.04 Simple disulfide: pdb=" SG CYS G 605 " - pdb=" SG CYS G 640 " distance=2.04 Simple disulfide: pdb=" SG CYS H 851 " - pdb=" SG CYS H1491 " distance=2.03 Simple disulfide: pdb=" SG CYS H1079 " - pdb=" SG CYS H1136 " distance=2.03 Simple disulfide: pdb=" SG CYS H1336 " - pdb=" SG CYS H1467 " distance=2.03 Simple disulfide: pdb=" SG CYS H1367 " - pdb=" SG CYS H1436 " distance=2.04 Simple disulfide: pdb=" SG CYS H1484 " - pdb=" SG CYS H1489 " distance=2.03 Simple disulfide: pdb=" SG CYS H1496 " - pdb=" SG CYS H1568 " distance=2.03 Simple disulfide: pdb=" SG CYS H1515 " - pdb=" SG CYS H1639 " distance=2.03 Simple disulfide: pdb=" SG CYS H1615 " - pdb=" SG CYS H1624 " distance=2.04 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 120 " distance=2.03 Simple disulfide: pdb=" SG CYS D 106 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS D 453 " - pdb=" SG CYS D 571 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 574 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 631 " - pdb=" SG CYS D 657 " distance=2.03 Simple disulfide: pdb=" SG CYS D 670 " - pdb=" SG CYS D 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG CYS L 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 96 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 111 " - pdb=" SG CYS L 124 " distance=2.03 Simple disulfide: pdb=" SG CYS L 132 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 301 " - " ASN A 239 " " NAG B 1 " - " ASN A 40 " " NAG D 802 " - " ASN D 353 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 3.1 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5214 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 39 sheets defined 17.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 281 through 289 removed outlier: 3.627A pdb=" N LEU G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 289 " --> pdb=" O LEU G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 removed outlier: 3.699A pdb=" N VAL G 298 " --> pdb=" O GLU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 504 removed outlier: 3.590A pdb=" N PHE G 503 " --> pdb=" O THR G 500 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 504 " --> pdb=" O THR G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 500 through 504' Processing helix chain 'G' and resid 579 through 584 removed outlier: 3.942A pdb=" N LEU G 583 " --> pdb=" O GLY G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 601 removed outlier: 3.906A pdb=" N ALA G 601 " --> pdb=" O VAL G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 619 Processing helix chain 'H' and resid 988 through 1009 Proline residue: H 998 - end of helix Processing helix chain 'H' and resid 1011 through 1015 Processing helix chain 'H' and resid 1019 through 1037 Processing helix chain 'H' and resid 1053 through 1067 removed outlier: 3.658A pdb=" N THR H1057 " --> pdb=" O SER H1053 " (cutoff:3.500A) Processing helix chain 'H' and resid 1074 through 1089 Processing helix chain 'H' and resid 1116 through 1134 removed outlier: 3.675A pdb=" N ALA H1120 " --> pdb=" O GLU H1116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP H1134 " --> pdb=" O GLN H1130 " (cutoff:3.500A) Processing helix chain 'H' and resid 1142 through 1156 removed outlier: 4.389A pdb=" N ALA H1156 " --> pdb=" O ASP H1152 " (cutoff:3.500A) Processing helix chain 'H' and resid 1163 through 1177 removed outlier: 3.633A pdb=" N VAL H1167 " --> pdb=" O ARG H1163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET H1177 " --> pdb=" O ALA H1173 " (cutoff:3.500A) Processing helix chain 'H' and resid 1182 through 1192 removed outlier: 4.255A pdb=" N ALA H1192 " --> pdb=" O PHE H1188 " (cutoff:3.500A) Processing helix chain 'H' and resid 1193 through 1196 Processing helix chain 'H' and resid 1203 through 1205 No H-bonds generated for 'chain 'H' and resid 1203 through 1205' Processing helix chain 'H' and resid 1206 through 1222 removed outlier: 3.943A pdb=" N THR H1211 " --> pdb=" O ASN H1207 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER H1212 " --> pdb=" O VAL H1208 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA H1214 " --> pdb=" O ALA H1210 " (cutoff:3.500A) Processing helix chain 'H' and resid 1226 through 1235 Processing helix chain 'H' and resid 1248 through 1264 Processing helix chain 'H' and resid 1392 through 1402 Processing helix chain 'H' and resid 1409 through 1414 removed outlier: 3.718A pdb=" N LYS H1414 " --> pdb=" O GLU H1411 " (cutoff:3.500A) Processing helix chain 'H' and resid 1475 through 1479 removed outlier: 3.854A pdb=" N GLY H1478 " --> pdb=" O LYS H1475 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS H1479 " --> pdb=" O GLU H1476 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1475 through 1479' Processing helix chain 'H' and resid 1506 through 1514 removed outlier: 3.610A pdb=" N ALA H1514 " --> pdb=" O ARG H1510 " (cutoff:3.500A) Processing helix chain 'H' and resid 1565 through 1567 No H-bonds generated for 'chain 'H' and resid 1565 through 1567' Processing helix chain 'H' and resid 1568 through 1573 removed outlier: 3.723A pdb=" N LYS H1573 " --> pdb=" O ARG H1569 " (cutoff:3.500A) Processing helix chain 'H' and resid 1611 through 1615 removed outlier: 3.512A pdb=" N CYS H1615 " --> pdb=" O GLU H1612 " (cutoff:3.500A) Processing helix chain 'H' and resid 1620 through 1637 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 263 through 277 removed outlier: 3.529A pdb=" N CYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.607A pdb=" N VAL D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 342 removed outlier: 3.683A pdb=" N ALA D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.598A pdb=" N ILE D 377 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 418 removed outlier: 3.800A pdb=" N LEU D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.051A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 437 " --> pdb=" O MET D 433 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER D 447 " --> pdb=" O MET D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 removed outlier: 3.640A pdb=" N LYS D 467 " --> pdb=" O THR D 463 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 463 through 468' Processing helix chain 'D' and resid 508 through 512 Processing helix chain 'D' and resid 575 through 581 Processing helix chain 'D' and resid 589 through 598 Processing helix chain 'D' and resid 627 through 633 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 646 through 651 removed outlier: 4.420A pdb=" N VAL D 650 " --> pdb=" O ASP D 646 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 651 " --> pdb=" O ILE D 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 646 through 651' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.768A pdb=" N TYR A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.667A pdb=" N ASP A 191 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 192 " --> pdb=" O ALA A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 192' Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 124A through 131 Processing helix chain 'C' and resid 164 through 172 removed outlier: 4.302A pdb=" N SER C 172 " --> pdb=" O CYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing sheet with id=AA1, first strand: chain 'G' and resid 61 through 68 removed outlier: 3.562A pdb=" N SER G 16 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N THR G 19 " --> pdb=" O PRO G 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.813A pdb=" N LEU G 12 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER G 102 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS G 82 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER G 48 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 107 through 112 removed outlier: 3.813A pdb=" N VAL G 130 " --> pdb=" O TYR G 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR G 125 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 116 through 117 removed outlier: 3.786A pdb=" N LYS G 154 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 210 through 216 Processing sheet with id=AA6, first strand: chain 'G' and resid 258 through 272 removed outlier: 10.954A pdb=" N SER G 261 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 11.672A pdb=" N ASP G 255 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N ILE G 253 " --> pdb=" O PRO G 263 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER G 265 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE G 251 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR G 303 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL G 304 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER G 322 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA G 306 " --> pdb=" O GLU G 320 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU G 320 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL G 308 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN G 318 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 333 through 334 removed outlier: 3.514A pdb=" N PHE G 353 " --> pdb=" O HIS G 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 377 removed outlier: 3.676A pdb=" N SER G 377 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 367 " --> pdb=" O SER G 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 448 through 454 removed outlier: 4.058A pdb=" N VAL G 493 " --> pdb=" O PHE G 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 477 through 485 removed outlier: 5.141A pdb=" N LEU G 478 " --> pdb=" O ASN G 474 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN G 474 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS G 480 " --> pdb=" O ILE G 472 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR G 470 " --> pdb=" O GLY G 482 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR G 467 " --> pdb=" O THR G 514 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR G 514 " --> pdb=" O TYR G 467 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 542 through 545 Processing sheet with id=AB3, first strand: chain 'H' and resid 748 through 749 removed outlier: 4.074A pdb=" N ARG G 570 " --> pdb=" O MET H 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 753 through 755 removed outlier: 4.074A pdb=" N ARG G 570 " --> pdb=" O MET H 787 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 807 through 812 removed outlier: 3.853A pdb=" N ARG H 812 " --> pdb=" O ARG H 826 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG H 826 " --> pdb=" O ARG H 812 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 879 " --> pdb=" O CYS H 851 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 816 through 818 removed outlier: 6.492A pdb=" N VAL H 817 " --> pdb=" O VAL H 910 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H 838 " --> pdb=" O ILE H 866 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 914 through 925 removed outlier: 3.558A pdb=" N MET H 916 " --> pdb=" O TYR H1326 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL H1322 " --> pdb=" O VAL H 920 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL H 922 " --> pdb=" O LEU H1320 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H1320 " --> pdb=" O VAL H 922 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR H 924 " --> pdb=" O GLY H1318 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY H1318 " --> pdb=" O THR H 924 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 936 through 937 removed outlier: 3.574A pdb=" N THR H1309 " --> pdb=" O GLN H1277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 1342 through 1346 removed outlier: 3.618A pdb=" N ILE H1366 " --> pdb=" O LEU H1437 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H1437 " --> pdb=" O ILE H1366 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR H1368 " --> pdb=" O ASP H1435 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP H1435 " --> pdb=" O THR H1368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 1405 through 1406 Processing sheet with id=AC2, first strand: chain 'H' and resid 1598 through 1599 removed outlier: 7.088A pdb=" N GLU H1538 " --> pdb=" O VAL H1530 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL H1530 " --> pdb=" O GLU H1538 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE H1540 " --> pdb=" O VAL H1528 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS H1524 " --> pdb=" O GLU H1544 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR H1546 " --> pdb=" O VAL H1522 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL H1522 " --> pdb=" O THR H1546 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR H1521 " --> pdb=" O GLY H1584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY H1584 " --> pdb=" O TYR H1521 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS H1579 " --> pdb=" O TRP H1609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.985A pdb=" N CYS D 73 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D 72 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 23 through 27 Processing sheet with id=AC5, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AC6, first strand: chain 'D' and resid 111 through 113 Processing sheet with id=AC7, first strand: chain 'D' and resid 149 through 152 Processing sheet with id=AC8, first strand: chain 'D' and resid 293 through 297 removed outlier: 6.623A pdb=" N LEU D 286 " --> pdb=" O TRP D 296 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 250 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 289 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER D 243 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL D 358 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN D 245 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE D 360 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 247 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET D 362 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL D 249 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP D 399 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS D 357 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR D 401 " --> pdb=" O HIS D 357 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE D 359 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE D 403 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 361 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL D 405 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE D 428 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 402 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL D 430 " --> pdb=" O VAL D 402 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY D 404 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 471 through 477 Processing sheet with id=AD1, first strand: chain 'D' and resid 495 through 498 Processing sheet with id=AD2, first strand: chain 'D' and resid 602 through 611 Processing sheet with id=AD3, first strand: chain 'D' and resid 655 through 658 removed outlier: 5.776A pdb=" N ILE D 718 " --> pdb=" O ILE D 692 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE D 692 " --> pdb=" O ILE D 718 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU D 678 " --> pdb=" O VAL D 689 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 3 through 8 removed outlier: 7.008A pdb=" N TYR A 107 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE A 59 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 105 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 61 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A 103 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A 63 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA A 101 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 102 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER A 21 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 104 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A 19 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 106 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 15 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.215A pdb=" N LYS A 36 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.908A pdb=" N PHE A 151 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 162 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 169 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A 215 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 212 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 216 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 254 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA A 255 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU A 186 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 257 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA A 184 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 259 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 182 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.908A pdb=" N PHE A 151 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 162 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 169 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A 215 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 212 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 216 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 254 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 260 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 197 through 201 removed outlier: 3.932A pdb=" N VAL A 245 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 230 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 100 through 103 Processing sheet with id=AE1, first strand: chain 'L' and resid 115 through 117 Processing sheet with id=AE2, first strand: chain 'C' and resid 20 through 21 removed outlier: 7.343A pdb=" N THR C 135 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG C 202 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS C 199 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 30 through 34 removed outlier: 4.112A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.93 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7288 1.34 - 1.46: 5128 1.46 - 1.58: 10106 1.58 - 1.71: 0 1.71 - 1.83: 166 Bond restraints: 22688 Sorted by residual: bond pdb=" C1 NAG D 802 " pdb=" O5 NAG D 802 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C SER G 1 " pdb=" N PRO G 2 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.04e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 22683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 30259 2.08 - 4.16: 374 4.16 - 6.24: 59 6.24 - 8.32: 7 8.32 - 10.40: 1 Bond angle restraints: 30700 Sorted by residual: angle pdb=" C ASP H1512 " pdb=" N LYS H1513 " pdb=" CA LYS H1513 " ideal model delta sigma weight residual 122.38 116.58 5.80 1.81e+00 3.05e-01 1.03e+01 angle pdb=" C PHE H 807 " pdb=" N PHE H 808 " pdb=" CA PHE H 808 " ideal model delta sigma weight residual 122.10 117.17 4.93 1.66e+00 3.63e-01 8.83e+00 angle pdb=" CA LEU H 981 " pdb=" CB LEU H 981 " pdb=" CG LEU H 981 " ideal model delta sigma weight residual 116.30 126.70 -10.40 3.50e+00 8.16e-02 8.82e+00 angle pdb=" CA CYS A 114 " pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " ideal model delta sigma weight residual 114.40 120.97 -6.57 2.30e+00 1.89e-01 8.17e+00 angle pdb=" C LEU G 45 " pdb=" CA LEU G 45 " pdb=" CB LEU G 45 " ideal model delta sigma weight residual 110.42 115.97 -5.55 1.99e+00 2.53e-01 7.78e+00 ... (remaining 30695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.54: 12900 23.54 - 47.09: 866 47.09 - 70.63: 77 70.63 - 94.18: 33 94.18 - 117.72: 3 Dihedral angle restraints: 13879 sinusoidal: 5776 harmonic: 8103 Sorted by residual: dihedral pdb=" CB CYS H1079 " pdb=" SG CYS H1079 " pdb=" SG CYS H1136 " pdb=" CB CYS H1136 " ideal model delta sinusoidal sigma weight residual 93.00 -178.83 -88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS C 168 " pdb=" SG CYS C 168 " pdb=" SG CYS C 182 " pdb=" CB CYS C 182 " ideal model delta sinusoidal sigma weight residual -86.00 -169.57 83.57 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS H1484 " pdb=" SG CYS H1484 " pdb=" SG CYS H1489 " pdb=" CB CYS H1489 " ideal model delta sinusoidal sigma weight residual -86.00 -11.23 -74.77 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 13876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2961 0.067 - 0.134: 437 0.134 - 0.200: 14 0.200 - 0.267: 1 0.267 - 0.334: 1 Chirality restraints: 3414 Sorted by residual: chirality pdb=" C1 NAG A 301 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG A 301 " pdb=" O5 NAG A 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE G 233 " pdb=" N ILE G 233 " pdb=" C ILE G 233 " pdb=" CB ILE G 233 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 3411 not shown) Planarity restraints: 3964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 31 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO G 32 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H1278 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO H1279 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO H1279 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H1279 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 847 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO H 848 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 848 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 848 " 0.032 5.00e-02 4.00e+02 ... (remaining 3961 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 309 2.66 - 3.22: 19680 3.22 - 3.78: 30002 3.78 - 4.34: 39805 4.34 - 4.90: 68048 Nonbonded interactions: 157844 Sorted by model distance: nonbonded pdb=" OG1 THR D 201 " pdb=" OE1 GLU D 204 " model vdw 2.102 3.040 nonbonded pdb=" OXT ASN H1641 " pdb="MG MG D 801 " model vdw 2.124 2.170 nonbonded pdb=" OG1 THR D 291 " pdb=" O SER D 326 " model vdw 2.164 3.040 nonbonded pdb=" OG SER H1533 " pdb=" O PHE H1536 " model vdw 2.174 3.040 nonbonded pdb=" O LEU D 572 " pdb=" OG1 THR D 578 " model vdw 2.176 3.040 ... (remaining 157839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.190 Process input model: 51.940 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.003 0.080 22688 Z= 0.185 Angle : 0.600 10.395 30700 Z= 0.319 Chirality : 0.045 0.334 3414 Planarity : 0.005 0.084 3961 Dihedral : 14.891 117.720 8566 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2754 helix: 0.73 (0.27), residues: 382 sheet: 0.25 (0.19), residues: 802 loop : -1.71 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 90 HIS 0.007 0.001 HIS G 435 PHE 0.033 0.001 PHE H1630 TYR 0.021 0.001 TYR H1005 ARG 0.003 0.000 ARG G 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: G 346 MET cc_start: 0.8288 (mtm) cc_final: 0.7910 (mtm) REVERT: H 1089 LYS cc_start: 0.2491 (mtmm) cc_final: 0.1957 (tptm) REVERT: H 1177 MET cc_start: 0.5755 (pmm) cc_final: 0.4691 (mpp) REVERT: C 116 MET cc_start: 0.7185 (ttt) cc_final: 0.6750 (tpp) REVERT: C 228 TYR cc_start: 0.7426 (m-80) cc_final: 0.7223 (m-80) REVERT: C 242 MET cc_start: 0.8140 (mmp) cc_final: 0.7731 (mmm) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.3447 time to fit residues: 80.2478 Evaluate side-chains 108 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.0010 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 71 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H1139 GLN H1157 ASN D 181 GLN D 565 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22688 Z= 0.166 Angle : 0.564 9.233 30700 Z= 0.291 Chirality : 0.045 0.337 3414 Planarity : 0.004 0.057 3961 Dihedral : 6.898 102.140 3126 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.45 % Allowed : 5.86 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2754 helix: 0.67 (0.27), residues: 396 sheet: 0.39 (0.19), residues: 804 loop : -1.69 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 749 HIS 0.006 0.001 HIS G 435 PHE 0.015 0.001 PHE H1630 TYR 0.024 0.001 TYR H1213 ARG 0.013 0.000 ARG D 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 346 MET cc_start: 0.8287 (mtm) cc_final: 0.7930 (mtm) REVERT: H 1089 LYS cc_start: 0.2636 (mtmm) cc_final: 0.2052 (tptm) REVERT: H 1177 MET cc_start: 0.5866 (pmm) cc_final: 0.5070 (mpp) REVERT: C 51 TYR cc_start: 0.5358 (m-80) cc_final: 0.4941 (m-80) REVERT: C 242 MET cc_start: 0.7989 (mmp) cc_final: 0.7583 (mmm) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.3637 time to fit residues: 75.6500 Evaluate side-chains 115 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1184 LEU Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 624 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22688 Z= 0.184 Angle : 0.544 9.279 30700 Z= 0.281 Chirality : 0.045 0.353 3414 Planarity : 0.004 0.058 3961 Dihedral : 6.427 95.131 3126 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.73 % Allowed : 9.76 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2754 helix: 0.77 (0.27), residues: 396 sheet: 0.43 (0.19), residues: 804 loop : -1.66 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 127 HIS 0.007 0.001 HIS G 435 PHE 0.017 0.001 PHE A 18 TYR 0.019 0.001 TYR H1213 ARG 0.003 0.000 ARG H1232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: H 1089 LYS cc_start: 0.2672 (mtmm) cc_final: 0.2133 (tptm) REVERT: H 1177 MET cc_start: 0.5945 (pmm) cc_final: 0.5658 (ptp) REVERT: H 1209 GLU cc_start: -0.1297 (OUTLIER) cc_final: -0.1716 (pt0) REVERT: C 241 SER cc_start: 0.8613 (m) cc_final: 0.8408 (m) REVERT: C 242 MET cc_start: 0.7889 (mmp) cc_final: 0.7498 (mmm) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.3387 time to fit residues: 69.3881 Evaluate side-chains 116 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1209 GLU Chi-restraints excluded: chain H residue 1311 THR Chi-restraints excluded: chain H residue 1315 LYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 HIS D 565 GLN D 668 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 22688 Z= 0.466 Angle : 0.696 9.579 30700 Z= 0.364 Chirality : 0.049 0.384 3414 Planarity : 0.005 0.062 3961 Dihedral : 6.663 92.503 3126 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.67 % Allowed : 12.44 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2754 helix: 0.69 (0.27), residues: 392 sheet: 0.10 (0.19), residues: 823 loop : -1.87 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 127 HIS 0.010 0.001 HIS G 435 PHE 0.033 0.002 PHE A 18 TYR 0.021 0.002 TYR A 231 ARG 0.005 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (pp) REVERT: G 164 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8451 (tt) REVERT: H 1089 LYS cc_start: 0.2592 (mtmm) cc_final: 0.1954 (tptm) REVERT: D 570 ILE cc_start: 0.7280 (tt) cc_final: 0.7054 (tt) REVERT: A 113 LYS cc_start: 0.7606 (pptt) cc_final: 0.7226 (ptmt) REVERT: C 242 MET cc_start: 0.7949 (mmp) cc_final: 0.7493 (mmm) outliers start: 41 outliers final: 27 residues processed: 152 average time/residue: 0.3314 time to fit residues: 81.8338 Evaluate side-chains 135 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 435 HIS Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 598 VAL Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1310 VAL Chi-restraints excluded: chain H residue 1311 THR Chi-restraints excluded: chain H residue 1366 ILE Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 198 optimal weight: 40.0000 chunk 110 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 GLN D 565 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22688 Z= 0.371 Angle : 0.645 9.992 30700 Z= 0.338 Chirality : 0.047 0.376 3414 Planarity : 0.005 0.062 3961 Dihedral : 6.298 88.740 3126 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.99 % Allowed : 14.72 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2754 helix: 0.65 (0.27), residues: 391 sheet: -0.04 (0.19), residues: 805 loop : -1.90 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 127 HIS 0.008 0.001 HIS G 435 PHE 0.026 0.002 PHE A 18 TYR 0.025 0.002 TYR A 231 ARG 0.004 0.000 ARG G 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 MET cc_start: 0.7808 (mtt) cc_final: 0.7569 (mtt) REVERT: G 164 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8516 (tt) REVERT: G 375 VAL cc_start: 0.8299 (t) cc_final: 0.7979 (m) REVERT: H 1089 LYS cc_start: 0.2302 (mtmm) cc_final: 0.1681 (tptm) REVERT: C 242 MET cc_start: 0.7909 (mmp) cc_final: 0.7433 (mmm) outliers start: 49 outliers final: 32 residues processed: 153 average time/residue: 0.3339 time to fit residues: 82.6470 Evaluate side-chains 144 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 435 HIS Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 598 VAL Chi-restraints excluded: chain H residue 809 ILE Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 996 MET Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1311 THR Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1366 ILE Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1437 LEU Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1630 PHE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22688 Z= 0.156 Angle : 0.550 10.636 30700 Z= 0.284 Chirality : 0.045 0.361 3414 Planarity : 0.004 0.060 3961 Dihedral : 5.429 75.944 3126 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.63 % Allowed : 15.82 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2754 helix: 0.89 (0.27), residues: 391 sheet: 0.26 (0.19), residues: 795 loop : -1.73 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H1583 HIS 0.005 0.001 HIS A 230 PHE 0.014 0.001 PHE H1630 TYR 0.018 0.001 TYR A 231 ARG 0.004 0.000 ARG H 932 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 117 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8513 (pp) REVERT: G 36 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8440 (p) REVERT: G 164 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8549 (tp) REVERT: H 1089 LYS cc_start: 0.2318 (mtmm) cc_final: 0.1669 (tptm) REVERT: D 363 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (t) REVERT: D 570 ILE cc_start: 0.7295 (tt) cc_final: 0.7077 (tt) REVERT: C 242 MET cc_start: 0.7852 (mmp) cc_final: 0.7474 (mmm) outliers start: 40 outliers final: 25 residues processed: 151 average time/residue: 0.3302 time to fit residues: 80.7162 Evaluate side-chains 138 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 739 ILE Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1188 PHE Chi-restraints excluded: chain H residue 1310 VAL Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 152 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1623 GLN D 459 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22688 Z= 0.326 Angle : 0.619 11.321 30700 Z= 0.321 Chirality : 0.046 0.376 3414 Planarity : 0.005 0.060 3961 Dihedral : 5.379 56.093 3126 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.40 % Allowed : 16.47 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2754 helix: 0.87 (0.27), residues: 392 sheet: 0.08 (0.19), residues: 812 loop : -1.79 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 127 HIS 0.008 0.001 HIS G 435 PHE 0.029 0.002 PHE A 18 TYR 0.017 0.002 TYR A 231 ARG 0.004 0.000 ARG H1490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 109 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (pp) REVERT: G 36 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (p) REVERT: G 164 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (tp) REVERT: H 1089 LYS cc_start: 0.2446 (mtmm) cc_final: 0.1682 (tppt) REVERT: C 242 MET cc_start: 0.7805 (mmp) cc_final: 0.7464 (mmm) outliers start: 59 outliers final: 40 residues processed: 157 average time/residue: 0.3220 time to fit residues: 83.2274 Evaluate side-chains 148 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 105 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain H residue 739 ILE Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 883 THR Chi-restraints excluded: chain H residue 899 ILE Chi-restraints excluded: chain H residue 996 MET Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1188 PHE Chi-restraints excluded: chain H residue 1310 VAL Chi-restraints excluded: chain H residue 1311 THR Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1437 LEU Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1630 PHE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 140 CYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 209 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H1130 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22688 Z= 0.144 Angle : 0.539 9.481 30700 Z= 0.277 Chirality : 0.044 0.361 3414 Planarity : 0.004 0.059 3961 Dihedral : 4.724 55.345 3126 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.79 % Allowed : 17.24 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2754 helix: 0.99 (0.28), residues: 391 sheet: 0.29 (0.19), residues: 797 loop : -1.69 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 127 HIS 0.004 0.001 HIS G 435 PHE 0.010 0.001 PHE G 66 TYR 0.015 0.001 TYR H1031 ARG 0.003 0.000 ARG H1232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8510 (pp) REVERT: G 36 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8454 (p) REVERT: G 164 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8577 (tp) REVERT: H 1089 LYS cc_start: 0.2450 (mtmm) cc_final: 0.1915 (tptm) REVERT: D 570 ILE cc_start: 0.7300 (tt) cc_final: 0.7086 (tt) REVERT: C 242 MET cc_start: 0.7724 (mmp) cc_final: 0.7461 (mmm) outliers start: 44 outliers final: 33 residues processed: 148 average time/residue: 0.3186 time to fit residues: 77.6053 Evaluate side-chains 138 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 883 THR Chi-restraints excluded: chain H residue 899 ILE Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1630 PHE Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 140 CYS Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 232 optimal weight: 0.0270 chunk 247 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 107 optimal weight: 0.0770 chunk 194 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22688 Z= 0.166 Angle : 0.550 10.103 30700 Z= 0.282 Chirality : 0.044 0.361 3414 Planarity : 0.004 0.058 3961 Dihedral : 4.654 55.578 3126 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.63 % Allowed : 17.73 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2754 helix: 0.99 (0.28), residues: 392 sheet: 0.37 (0.19), residues: 798 loop : -1.65 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 127 HIS 0.005 0.001 HIS G 435 PHE 0.014 0.001 PHE A 18 TYR 0.014 0.001 TYR H1031 ARG 0.004 0.000 ARG H1232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8525 (pp) REVERT: G 36 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8456 (p) REVERT: G 164 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8577 (tp) REVERT: H 739 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7657 (tp) REVERT: H 1089 LYS cc_start: 0.2418 (mtmm) cc_final: 0.1865 (tptm) REVERT: D 570 ILE cc_start: 0.7263 (tt) cc_final: 0.7044 (tt) REVERT: C 242 MET cc_start: 0.7675 (mmp) cc_final: 0.7458 (mmm) outliers start: 40 outliers final: 32 residues processed: 137 average time/residue: 0.3204 time to fit residues: 72.0267 Evaluate side-chains 138 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 530 TRP Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 739 ILE Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1310 VAL Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1366 ILE Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 140 CYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22688 Z= 0.265 Angle : 0.595 9.285 30700 Z= 0.308 Chirality : 0.045 0.373 3414 Planarity : 0.004 0.060 3961 Dihedral : 4.875 55.932 3126 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.75 % Allowed : 17.73 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2754 helix: 0.96 (0.28), residues: 392 sheet: 0.26 (0.19), residues: 801 loop : -1.69 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 127 HIS 0.006 0.001 HIS G 435 PHE 0.024 0.002 PHE A 18 TYR 0.017 0.001 TYR A 231 ARG 0.004 0.000 ARG H1232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (pp) REVERT: G 36 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8492 (p) REVERT: G 164 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8593 (tp) REVERT: H 1089 LYS cc_start: 0.2384 (mtmm) cc_final: 0.1882 (tptm) REVERT: D 570 ILE cc_start: 0.7303 (tt) cc_final: 0.7094 (tt) REVERT: C 242 MET cc_start: 0.7847 (mmp) cc_final: 0.7592 (mmm) outliers start: 43 outliers final: 34 residues processed: 140 average time/residue: 0.3165 time to fit residues: 72.8022 Evaluate side-chains 140 residues out of total 2463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 739 ILE Chi-restraints excluded: chain H residue 846 HIS Chi-restraints excluded: chain H residue 883 THR Chi-restraints excluded: chain H residue 899 ILE Chi-restraints excluded: chain H residue 997 THR Chi-restraints excluded: chain H residue 1004 HIS Chi-restraints excluded: chain H residue 1107 MET Chi-restraints excluded: chain H residue 1310 VAL Chi-restraints excluded: chain H residue 1325 MET Chi-restraints excluded: chain H residue 1366 ILE Chi-restraints excluded: chain H residue 1387 THR Chi-restraints excluded: chain H residue 1582 MET Chi-restraints excluded: chain H residue 1621 GLN Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 140 CYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 29 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.131631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091711 restraints weight = 49061.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090417 restraints weight = 31482.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090490 restraints weight = 24341.713| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22688 Z= 0.184 Angle : 0.555 9.407 30700 Z= 0.286 Chirality : 0.044 0.363 3414 Planarity : 0.004 0.059 3961 Dihedral : 4.691 55.654 3126 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.63 % Allowed : 18.06 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2754 helix: 1.00 (0.28), residues: 392 sheet: 0.28 (0.19), residues: 810 loop : -1.65 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 127 HIS 0.004 0.001 HIS G 435 PHE 0.015 0.001 PHE A 18 TYR 0.015 0.001 TYR A 231 ARG 0.004 0.000 ARG H1232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.55 seconds wall clock time: 62 minutes 9.36 seconds (3729.36 seconds total)