Starting phenix.real_space_refine (version: dev) on Thu Dec 15 04:37:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/12_2022/7m7f_23711_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.138 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 799": "OD1" <-> "OD2" Residue "B GLU 1413": "OE1" <-> "OE2" Residue "B GLU 1418": "OE1" <-> "OE2" Residue "B ARG 1421": "NH1" <-> "NH2" Residue "B GLU 1434": "OE1" <-> "OE2" Residue "B ASP 1439": "OD1" <-> "OD2" Residue "B GLU 1444": "OE1" <-> "OE2" Residue "B ASP 1448": "OD1" <-> "OD2" Residue "B ARG 1456": "NH1" <-> "NH2" Residue "B ASP 1477": "OD1" <-> "OD2" Residue "B GLU 1488": "OE1" <-> "OE2" Residue "A TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1303": "NH1" <-> "NH2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23971 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7417 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 57, 'TRANS': 941} Chain breaks: 1 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10319 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 74, 'TRANS': 1315} Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 13.35, per 1000 atoms: 0.56 Number of scatterers: 23971 At special positions: 0 Unit cell: (136, 159, 149, 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 87 16.00 P 1 15.00 O 4621 8.00 N 4302 7.00 C 14960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.00 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.06 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 3.9 seconds 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 31 sheets defined 24.7% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'B' and resid 13 through 16 No H-bonds generated for 'chain 'B' and resid 13 through 16' Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.705A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 175 through 178 No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 183 through 191 removed outlier: 5.498A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 220 removed outlier: 5.803A pdb=" N SER B 208 " --> pdb=" O CYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.971A pdb=" N LEU B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.596A pdb=" N LEU B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 583 through 594 removed outlier: 3.562A pdb=" N LEU B 587 " --> pdb=" O PHE B 583 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 624 through 644 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 658 through 665 Processing helix chain 'B' and resid 671 through 688 removed outlier: 3.569A pdb=" N THR B 687 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 5.360A pdb=" N ALA B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 4.194A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 769 removed outlier: 4.957A pdb=" N ASP B 765 " --> pdb=" O THR B 762 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 767 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS B 768 " --> pdb=" O ASP B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.579A pdb=" N GLU B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 877 Processing helix chain 'B' and resid 884 through 887 No H-bonds generated for 'chain 'B' and resid 884 through 887' Processing helix chain 'B' and resid 1410 through 1427 Processing helix chain 'B' and resid 1449 through 1462 Processing helix chain 'B' and resid 1471 through 1474 No H-bonds generated for 'chain 'B' and resid 1471 through 1474' Processing helix chain 'B' and resid 1478 through 1487 Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.654A pdb=" N ARG A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 181 through 191 removed outlier: 4.143A pdb=" N SER A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 187 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 188 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.620A pdb=" N SER A 207 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.742A pdb=" N ARG A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.624A pdb=" N ARG A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 No H-bonds generated for 'chain 'A' and resid 576 through 579' Processing helix chain 'A' and resid 581 through 597 removed outlier: 4.071A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Proline residue: A 596 - end of helix Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 610 through 613 No H-bonds generated for 'chain 'A' and resid 610 through 613' Processing helix chain 'A' and resid 624 through 644 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 671 through 687 removed outlier: 4.780A pdb=" N THR A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 837 through 844 removed outlier: 3.638A pdb=" N GLU A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 884 through 887 No H-bonds generated for 'chain 'A' and resid 884 through 887' Processing helix chain 'A' and resid 922 through 926 Processing helix chain 'A' and resid 960 through 968 removed outlier: 4.221A pdb=" N ALA A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 997 Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1062 through 1077 removed outlier: 3.754A pdb=" N ALA A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 removed outlier: 5.616A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 4.199A pdb=" N ILE A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1181 through 1191 Processing helix chain 'A' and resid 1205 through 1214 Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'A' and resid 1241 through 1264 removed outlier: 6.086A pdb=" N ALA A1250 " --> pdb=" O ARG A1246 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A1264 " --> pdb=" O GLU A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1302 Proline residue: A1290 - end of helix Processing helix chain 'A' and resid 1326 through 1333 removed outlier: 3.844A pdb=" N ARG A1333 " --> pdb=" O ASP A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1353 removed outlier: 5.101A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1373 removed outlier: 4.808A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'F' and resid 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing sheet with id= A, first strand: chain 'B' and resid 198 through 201 removed outlier: 7.939A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 226 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE B 152 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET B 228 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY B 154 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY B 230 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 39 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 278 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL B 37 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 453 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 297 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS B 451 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 299 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 449 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 336 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER B 441 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 338 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE B 443 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 367 through 369 Processing sheet with id= C, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.730A pdb=" N PHE B 524 " --> pdb=" O TRP B 475 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 652 through 654 removed outlier: 9.233A pdb=" N ILE B 653 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE B 560 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR B 827 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 561 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 829 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER B 853 " --> pdb=" O PHE B 828 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU B 830 " --> pdb=" O SER B 853 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE B 855 " --> pdb=" O GLU B 830 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 746 through 748 removed outlier: 3.617A pdb=" N VAL B 725 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ALA B 726 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE B 714 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.920A pdb=" N LEU A 226 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE A 152 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 228 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY A 154 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A 230 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 420 through 422 removed outlier: 5.939A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ARG A 437 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 337 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A 439 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 521 through 524 Processing sheet with id= I, first strand: chain 'A' and resid 828 through 830 removed outlier: 6.185A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE A 560 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL A 652 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 562 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY A 654 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 695 through 697 removed outlier: 5.613A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1359 through 1361 removed outlier: 3.621A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU A1113 " --> pdb=" O GLY A1083 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A1085 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1115 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP A1087 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A1043 " --> pdb=" O GLY A1083 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU A1085 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR A1045 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASP A1087 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR A1047 " --> pdb=" O ASP A1087 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 948 through 953 removed outlier: 6.069A pdb=" N ARG A 975 " --> pdb=" O TRP A 949 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 951 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG A 977 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS A 953 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU A 979 " --> pdb=" O LYS A 953 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 1272 through 1275 Processing sheet with id= N, first strand: chain 'C' and resid 5 through 9 Processing sheet with id= O, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.643A pdb=" N GLY C 12 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 99 through 101 removed outlier: 5.797A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 144 through 148 Processing sheet with id= R, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.722A pdb=" N SER C 160 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 204 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 201 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 218 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 21 through 23 Processing sheet with id= T, first strand: chain 'D' and resid 105 through 111 removed outlier: 6.408A pdb=" N LEU D 58 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU D 67 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS D 60 " --> pdb=" O PRO D 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 138 through 140 removed outlier: 3.944A pdb=" N VAL D 154 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.678A pdb=" N GLU D 217 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 5 through 9 Processing sheet with id= X, first strand: chain 'E' and resid 99 through 101 removed outlier: 6.145A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= Z, first strand: chain 'E' and resid 144 through 148 Processing sheet with id= AA, first strand: chain 'E' and resid 159 through 161 removed outlier: 4.339A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 218 " --> pdb=" O TYR E 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS E 207 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= AC, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.838A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 136 through 140 removed outlier: 4.451A pdb=" N VAL F 154 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER F 199 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.630A pdb=" N GLU F 217 " --> pdb=" O GLN F 169 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1671 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: 9.25 Time building geometry restraints manager: 11.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 182 1.21 - 1.36: 8217 1.36 - 1.52: 8228 1.52 - 1.67: 7697 1.67 - 1.82: 136 Bond restraints: 24460 Sorted by residual: bond pdb=" CA SER A 442 " pdb=" CB SER A 442 " ideal model delta sigma weight residual 1.532 1.304 0.228 1.58e-02 4.01e+03 2.08e+02 bond pdb=" C ARG A 43 " pdb=" O ARG A 43 " ideal model delta sigma weight residual 1.236 1.073 0.163 1.14e-02 7.69e+03 2.05e+02 bond pdb=" CA SER A 207 " pdb=" CB SER A 207 " ideal model delta sigma weight residual 1.530 1.283 0.248 1.75e-02 3.27e+03 2.00e+02 bond pdb=" C PRO B 197 " pdb=" O PRO B 197 " ideal model delta sigma weight residual 1.235 1.062 0.173 1.30e-02 5.92e+03 1.77e+02 bond pdb=" C SER A 442 " pdb=" O SER A 442 " ideal model delta sigma weight residual 1.235 1.094 0.141 1.12e-02 7.97e+03 1.59e+02 ... (remaining 24455 not shown) Histogram of bond angle deviations from ideal: 78.12 - 89.45: 9 89.45 - 100.79: 104 100.79 - 112.12: 12023 112.12 - 123.46: 19049 123.46 - 134.79: 2088 Bond angle restraints: 33273 Sorted by residual: angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.32 83.45 19.87 8.40e-01 1.42e+00 5.59e+02 angle pdb=" C GLU A 159 " pdb=" CA GLU A 159 " pdb=" CB GLU A 159 " ideal model delta sigma weight residual 110.19 78.12 32.07 1.62e+00 3.81e-01 3.92e+02 angle pdb=" C ASP B 883 " pdb=" CA ASP B 883 " pdb=" CB ASP B 883 " ideal model delta sigma weight residual 109.75 78.51 31.24 1.65e+00 3.67e-01 3.59e+02 angle pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " pdb=" CG PHE B 266 " ideal model delta sigma weight residual 113.80 131.55 -17.75 1.00e+00 1.00e+00 3.15e+02 angle pdb=" C ARG A 43 " pdb=" CA ARG A 43 " pdb=" CB ARG A 43 " ideal model delta sigma weight residual 110.74 83.20 27.54 1.61e+00 3.86e-01 2.93e+02 ... (remaining 33268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 13034 22.06 - 44.11: 1097 44.11 - 66.17: 458 66.17 - 88.22: 37 88.22 - 110.28: 8 Dihedral angle restraints: 14634 sinusoidal: 5566 harmonic: 9068 Sorted by residual: dihedral pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta harmonic sigma weight residual 180.00 69.72 110.28 0 5.00e+00 4.00e-02 4.86e+02 dihedral pdb=" CA GLU E 155 " pdb=" C GLU E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual 180.00 78.77 101.23 0 5.00e+00 4.00e-02 4.10e+02 dihedral pdb=" CA THR F 115 " pdb=" C THR F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 180.00 85.75 94.25 0 5.00e+00 4.00e-02 3.55e+02 ... (remaining 14631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 3361 0.149 - 0.297: 331 0.297 - 0.446: 49 0.446 - 0.595: 9 0.595 - 0.743: 4 Chirality restraints: 3754 Sorted by residual: chirality pdb=" CB VAL A 232 " pdb=" CA VAL A 232 " pdb=" CG1 VAL A 232 " pdb=" CG2 VAL A 232 " both_signs ideal model delta sigma weight residual False -2.63 -1.89 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CB VAL B 385 " pdb=" CA VAL B 385 " pdb=" CG1 VAL B 385 " pdb=" CG2 VAL B 385 " both_signs ideal model delta sigma weight residual False -2.63 -1.97 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA ARG A1303 " pdb=" N ARG A1303 " pdb=" C ARG A1303 " pdb=" CB ARG A1303 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 ... (remaining 3751 not shown) Planarity restraints: 4402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1301 " 0.050 2.00e-02 2.50e+03 1.05e-01 1.10e+02 pdb=" C GLN A1301 " -0.181 2.00e-02 2.50e+03 pdb=" O GLN A1301 " 0.070 2.00e-02 2.50e+03 pdb=" N ARG A1302 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 96 " -0.031 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ALA E 96 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA E 96 " -0.038 2.00e-02 2.50e+03 pdb=" N VAL E 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " -0.046 2.00e-02 2.50e+03 4.32e-02 3.26e+01 pdb=" CG PHE B 266 " 0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " -0.010 2.00e-02 2.50e+03 ... (remaining 4399 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 59 2.38 - 3.01: 13720 3.01 - 3.64: 37918 3.64 - 4.27: 61559 4.27 - 4.90: 99618 Nonbonded interactions: 212874 Sorted by model distance: nonbonded pdb=" O GLU A 159 " pdb=" CB GLU A 159 " model vdw 1.751 2.752 nonbonded pdb=" O ARG A 43 " pdb=" CB ARG A 43 " model vdw 1.811 2.752 nonbonded pdb=" O PRO B 902 " pdb=" CB PRO B 902 " model vdw 1.948 2.752 nonbonded pdb=" N THR C 101 " pdb=" OG1 THR C 101 " model vdw 1.954 2.496 nonbonded pdb=" O ARG C 102 " pdb=" CB ARG C 102 " model vdw 2.022 2.752 ... (remaining 212869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 through 209 or resid 215 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 87 5.16 5 C 14960 2.51 5 N 4302 2.21 5 O 4621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.030 Extract box with map and model: 10.860 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 63.550 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.012 0.248 24460 Z= 0.826 Angle : 1.705 32.071 33273 Z= 1.171 Chirality : 0.095 0.743 3754 Planarity : 0.009 0.139 4402 Dihedral : 18.861 110.281 8804 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer Outliers : 16.06 % Cbeta Deviations : 2.20 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -4.26 (0.13), residues: 3181 helix: -3.24 (0.13), residues: 915 sheet: -2.66 (0.19), residues: 555 loop : -2.64 (0.14), residues: 1711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 335 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 398 outliers final: 83 residues processed: 643 average time/residue: 0.4038 time to fit residues: 387.5880 Evaluate side-chains 316 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 233 time to evaluate : 3.064 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 2 residues processed: 83 average time/residue: 0.3106 time to fit residues: 45.5498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 488 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 GLN C 88 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN D 180 ASN E 171 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 24460 Z= 0.273 Angle : 0.699 8.644 33273 Z= 0.360 Chirality : 0.045 0.234 3754 Planarity : 0.007 0.130 4402 Dihedral : 5.931 58.174 3504 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -3.37 (0.13), residues: 3181 helix: -2.32 (0.15), residues: 932 sheet: -2.14 (0.19), residues: 581 loop : -2.19 (0.14), residues: 1668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 307 average time/residue: 0.3649 time to fit residues: 178.2170 Evaluate side-chains 250 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2380 time to fit residues: 18.4968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN B 657 GLN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 GLN C 15 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 180 ASN E 15 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 24460 Z= 0.363 Angle : 0.676 7.977 33273 Z= 0.346 Chirality : 0.044 0.186 3754 Planarity : 0.006 0.100 4402 Dihedral : 5.700 54.808 3504 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -2.93 (0.14), residues: 3181 helix: -1.96 (0.15), residues: 939 sheet: -1.93 (0.19), residues: 573 loop : -1.89 (0.15), residues: 1669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 238 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 19 residues processed: 284 average time/residue: 0.3520 time to fit residues: 161.5749 Evaluate side-chains 227 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2573 time to fit residues: 12.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 150 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 856 HIS A 459 GLN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN E 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24460 Z= 0.226 Angle : 0.600 7.861 33273 Z= 0.305 Chirality : 0.042 0.167 3754 Planarity : 0.006 0.099 4402 Dihedral : 5.380 47.107 3504 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -2.58 (0.14), residues: 3181 helix: -1.57 (0.16), residues: 932 sheet: -1.86 (0.19), residues: 628 loop : -1.65 (0.15), residues: 1621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 32 residues processed: 279 average time/residue: 0.3485 time to fit residues: 156.2332 Evaluate side-chains 243 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2275 time to fit residues: 17.3144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 174 optimal weight: 50.0000 chunk 4 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 212 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1423 HIS A 368 HIS A 459 GLN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN E 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24460 Z= 0.237 Angle : 0.593 8.246 33273 Z= 0.301 Chirality : 0.042 0.173 3754 Planarity : 0.006 0.101 4402 Dihedral : 5.183 45.586 3504 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -2.30 (0.14), residues: 3181 helix: -1.35 (0.16), residues: 939 sheet: -1.61 (0.19), residues: 632 loop : -1.50 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 10 residues processed: 251 average time/residue: 0.3695 time to fit residues: 150.3116 Evaluate side-chains 222 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 2.685 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2348 time to fit residues: 8.2136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 307 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN A 776 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN E 171 HIS F 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24460 Z= 0.255 Angle : 0.588 8.754 33273 Z= 0.298 Chirality : 0.042 0.171 3754 Planarity : 0.006 0.100 4402 Dihedral : 5.068 44.545 3504 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -2.13 (0.15), residues: 3181 helix: -1.14 (0.17), residues: 935 sheet: -1.57 (0.19), residues: 633 loop : -1.42 (0.16), residues: 1613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 240 average time/residue: 0.3486 time to fit residues: 134.3760 Evaluate side-chains 223 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.395 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2164 time to fit residues: 10.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 175 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 0.0040 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 459 GLN B 768 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS F 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 24460 Z= 0.334 Angle : 0.623 9.746 33273 Z= 0.316 Chirality : 0.043 0.174 3754 Planarity : 0.006 0.087 4402 Dihedral : 5.120 45.038 3504 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -2.09 (0.15), residues: 3181 helix: -1.11 (0.17), residues: 932 sheet: -1.50 (0.20), residues: 622 loop : -1.43 (0.16), residues: 1627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 240 average time/residue: 0.3611 time to fit residues: 141.7018 Evaluate side-chains 218 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2304 time to fit residues: 8.5376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.0770 chunk 194 optimal weight: 0.0570 chunk 208 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 768 HIS A 459 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN E 171 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24460 Z= 0.194 Angle : 0.574 11.266 33273 Z= 0.289 Chirality : 0.041 0.162 3754 Planarity : 0.005 0.096 4402 Dihedral : 4.905 43.737 3504 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 3181 helix: -0.92 (0.17), residues: 945 sheet: -1.44 (0.19), residues: 649 loop : -1.32 (0.16), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 236 average time/residue: 0.3635 time to fit residues: 137.5043 Evaluate side-chains 221 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2821 time to fit residues: 11.0042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 267 optimal weight: 0.6980 chunk 285 optimal weight: 10.0000 chunk 171 optimal weight: 40.0000 chunk 124 optimal weight: 0.0050 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 768 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24460 Z= 0.207 Angle : 0.574 10.914 33273 Z= 0.288 Chirality : 0.041 0.173 3754 Planarity : 0.005 0.097 4402 Dihedral : 4.824 43.661 3504 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3181 helix: -0.83 (0.17), residues: 943 sheet: -1.33 (0.19), residues: 647 loop : -1.24 (0.16), residues: 1591 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 223 average time/residue: 0.3798 time to fit residues: 134.5923 Evaluate side-chains 213 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3265 time to fit residues: 7.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 768 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24460 Z= 0.236 Angle : 0.587 10.644 33273 Z= 0.294 Chirality : 0.042 0.204 3754 Planarity : 0.005 0.091 4402 Dihedral : 4.829 43.219 3504 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.72 (0.15), residues: 3181 helix: -0.77 (0.17), residues: 944 sheet: -1.30 (0.19), residues: 652 loop : -1.21 (0.16), residues: 1585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 219 average time/residue: 0.3735 time to fit residues: 130.8495 Evaluate side-chains 211 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.417 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2355 time to fit residues: 5.3977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 37 optimal weight: 0.0000 chunk 70 optimal weight: 30.0000 chunk 252 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 768 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.205296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173152 restraints weight = 30848.396| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.58 r_work: 0.3947 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24460 Z= 0.236 Angle : 0.597 20.178 33273 Z= 0.296 Chirality : 0.042 0.199 3754 Planarity : 0.005 0.092 4402 Dihedral : 4.802 42.938 3504 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.67 (0.15), residues: 3181 helix: -0.72 (0.17), residues: 943 sheet: -1.30 (0.20), residues: 637 loop : -1.17 (0.16), residues: 1601 =============================================================================== Job complete usr+sys time: 4925.44 seconds wall clock time: 90 minutes 52.31 seconds (5452.31 seconds total)