Starting phenix.real_space_refine on Mon Feb 19 07:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_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_23711/02_2024/7m7f_23711_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7f_23711/02_2024/7m7f_23711_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.138 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 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. 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-5238/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: 12.70, per 1000 atoms: 0.53 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: 9.84 Conformation dependent library (CDL) restraints added in 4.8 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: 6.45 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: 11.02 Time building geometry restraints manager: 10.56 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: 13033 22.06 - 44.11: 1099 44.11 - 66.17: 460 66.17 - 88.22: 36 88.22 - 110.28: 8 Dihedral angle restraints: 14636 sinusoidal: 5568 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 14633 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 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: 1.830 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: 9.400 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 68.260 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 84.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 18.865 110.281 8806 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 16.06 % Allowed : 5.61 % Favored : 78.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP A 642 HIS 0.015 0.002 HIS F 220 PHE 0.100 0.004 PHE B 266 TYR 0.040 0.003 TYR E 99 ARG 0.018 0.001 ARG E 21 *********************** 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 : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 123 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: B 197 PRO cc_start: 0.8852 (OUTLIER) cc_final: 0.8563 (Cg_exo) REVERT: B 268 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6917 (ttp) REVERT: B 391 MET cc_start: 0.7959 (mmm) cc_final: 0.7479 (mmp) REVERT: B 865 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5959 (tp) REVERT: B 901 TYR cc_start: 0.8235 (t80) cc_final: 0.7846 (t80) REVERT: A 43 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8084 (mpt180) REVERT: A 62 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7614 (ttm170) REVERT: A 124 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6994 (ptp-170) REVERT: A 391 MET cc_start: 0.7403 (mmt) cc_final: 0.7183 (mmt) REVERT: A 601 GLU cc_start: 0.2165 (OUTLIER) cc_final: 0.1771 (mm-30) REVERT: A 631 MET cc_start: 0.4097 (mmm) cc_final: 0.3777 (mtt) REVERT: A 694 MET cc_start: 0.3212 (mmm) cc_final: 0.2920 (mmm) REVERT: A 703 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.2216 (pm20) REVERT: A 745 ARG cc_start: 0.1270 (OUTLIER) cc_final: 0.1002 (ptt180) REVERT: A 799 ASP cc_start: 0.3297 (OUTLIER) cc_final: 0.2642 (p0) REVERT: A 841 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6191 (mm) REVERT: A 894 ARG cc_start: 0.7661 (ptp90) cc_final: 0.7369 (mtm-85) REVERT: A 1300 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: C 106 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 108 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: E 34 TYR cc_start: 0.7364 (m-80) cc_final: 0.7155 (m-80) REVERT: E 97 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8769 (t) REVERT: F 127 ASP cc_start: 0.6655 (m-30) cc_final: 0.6418 (m-30) outliers start: 398 outliers final: 83 residues processed: 643 average time/residue: 0.4280 time to fit residues: 408.8172 Evaluate side-chains 333 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 233 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 197 PRO Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 PRO Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 859 ARG Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 162 PRO Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 977 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 217 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 213 HIS B 657 GLN A 378 HIS A 459 GLN A 488 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** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24460 Z= 0.271 Angle : 0.697 8.465 33273 Z= 0.359 Chirality : 0.045 0.238 3754 Planarity : 0.007 0.129 4402 Dihedral : 10.053 85.816 3719 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 5.21 % Allowed : 12.79 % Favored : 82.00 % 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: -3.36 (0.13), residues: 3181 helix: -2.28 (0.15), residues: 932 sheet: -2.14 (0.19), residues: 589 loop : -2.20 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 642 HIS 0.007 0.001 HIS A1259 PHE 0.033 0.002 PHE A1369 TYR 0.025 0.002 TYR E 183 ARG 0.019 0.001 ARG B 721 *********************** 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 389 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 260 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 123 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 159 GLU cc_start: 0.6448 (pm20) cc_final: 0.6236 (pm20) REVERT: B 244 PHE cc_start: 0.8125 (m-80) cc_final: 0.7898 (m-10) REVERT: B 268 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6791 (mtm) REVERT: B 1427 VAL cc_start: 0.8549 (p) cc_final: 0.8307 (m) REVERT: A 202 ASP cc_start: 0.7546 (t0) cc_final: 0.7132 (t70) REVERT: C 106 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8075 (tp) REVERT: D 145 GLU cc_start: 0.5457 (pp20) cc_final: 0.4929 (pp20) REVERT: E 112 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: F 195 TYR cc_start: 0.7392 (m-80) cc_final: 0.6617 (m-10) outliers start: 129 outliers final: 68 residues processed: 363 average time/residue: 0.3858 time to fit residues: 219.5811 Evaluate side-chains 295 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 222 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 859 ARG Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 chunk 196 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 289 optimal weight: 0.7980 chunk 312 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 232 optimal weight: 0.2980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 375 ASN B 794 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN ** A 597 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 15 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN E 15 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24460 Z= 0.318 Angle : 0.658 7.714 33273 Z= 0.339 Chirality : 0.044 0.203 3754 Planarity : 0.006 0.099 4402 Dihedral : 7.857 59.822 3590 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.12 % Allowed : 15.42 % Favored : 80.47 % 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: -2.83 (0.14), residues: 3181 helix: -1.80 (0.16), residues: 937 sheet: -1.89 (0.19), residues: 582 loop : -1.87 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 170 HIS 0.006 0.001 HIS A1259 PHE 0.037 0.002 PHE A1369 TYR 0.019 0.002 TYR E 84 ARG 0.015 0.001 ARG B 721 *********************** 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 341 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 239 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 THR cc_start: 0.6759 (OUTLIER) cc_final: 0.6516 (t) REVERT: B 112 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 268 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7190 (ttp) REVERT: B 350 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 901 TYR cc_start: 0.8217 (t80) cc_final: 0.7717 (t80) REVERT: A 87 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 631 MET cc_start: 0.4195 (mmm) cc_final: 0.3913 (mtt) REVERT: A 1334 HIS cc_start: 0.5093 (p-80) cc_final: 0.4802 (p90) REVERT: C 106 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8211 (tp) REVERT: D 139 ILE cc_start: 0.7756 (tp) cc_final: 0.7424 (tp) REVERT: E 112 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: F 209 GLU cc_start: 0.5932 (mp0) cc_final: 0.5241 (mm-30) outliers start: 102 outliers final: 61 residues processed: 325 average time/residue: 0.3624 time to fit residues: 185.8818 Evaluate side-chains 285 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 217 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 5.9990 chunk 217 optimal weight: 30.0000 chunk 150 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 290 optimal weight: 0.4980 chunk 307 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3178 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= 0.213 Angle : 0.588 9.376 33273 Z= 0.299 Chirality : 0.042 0.168 3754 Planarity : 0.006 0.104 4402 Dihedral : 6.869 58.565 3561 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.79 % Allowed : 17.15 % Favored : 79.06 % 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: -2.41 (0.14), residues: 3181 helix: -1.41 (0.16), residues: 934 sheet: -1.67 (0.19), residues: 599 loop : -1.62 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1125 HIS 0.007 0.001 HIS A1099 PHE 0.025 0.002 PHE A1369 TYR 0.020 0.001 TYR F 195 ARG 0.015 0.000 ARG B 721 *********************** 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 332 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 238 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6939 (ttp) REVERT: B 350 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 572 MET cc_start: 0.4215 (mpp) cc_final: 0.3822 (mtm) REVERT: A 87 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7405 (t) REVERT: A 642 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.3122 (m-90) REVERT: A 1334 HIS cc_start: 0.5149 (p-80) cc_final: 0.4838 (p90) REVERT: D 139 ILE cc_start: 0.7661 (tp) cc_final: 0.7300 (tp) REVERT: D 145 GLU cc_start: 0.5322 (pp20) cc_final: 0.4847 (pp20) REVERT: E 82 ILE cc_start: 0.6814 (tp) cc_final: 0.6571 (tp) REVERT: F 110 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: F 209 GLU cc_start: 0.5831 (mp0) cc_final: 0.5349 (mm-30) outliers start: 94 outliers final: 60 residues processed: 316 average time/residue: 0.3796 time to fit residues: 188.0467 Evaluate side-chains 276 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 211 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN B1423 HIS A 368 HIS A 459 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24460 Z= 0.312 Angle : 0.615 7.968 33273 Z= 0.314 Chirality : 0.043 0.174 3754 Planarity : 0.006 0.099 4402 Dihedral : 6.258 57.226 3538 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.20 % Allowed : 17.64 % Favored : 78.17 % 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: -2.22 (0.14), residues: 3181 helix: -1.25 (0.16), residues: 935 sheet: -1.51 (0.20), residues: 598 loop : -1.53 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 170 HIS 0.007 0.001 HIS A1099 PHE 0.025 0.002 PHE A 266 TYR 0.017 0.002 TYR F 195 ARG 0.012 0.000 ARG B 721 *********************** 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 327 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 223 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7153 (ttp) REVERT: B 350 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 572 MET cc_start: 0.4449 (mpp) cc_final: 0.4159 (mtm) REVERT: A 87 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7467 (t) REVERT: A 202 ASP cc_start: 0.7546 (t0) cc_final: 0.6945 (t0) REVERT: A 266 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8209 (p90) REVERT: A 560 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 642 TRP cc_start: 0.5682 (OUTLIER) cc_final: 0.3019 (m-90) REVERT: A 1334 HIS cc_start: 0.5214 (p-80) cc_final: 0.4933 (p90) REVERT: D 139 ILE cc_start: 0.7730 (tp) cc_final: 0.7328 (tp) REVERT: E 82 ILE cc_start: 0.6958 (tp) cc_final: 0.6624 (tp) REVERT: F 110 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6943 (tmm) REVERT: F 130 ARG cc_start: 0.6355 (ptm160) cc_final: 0.6034 (ptm160) REVERT: F 209 GLU cc_start: 0.5841 (mp0) cc_final: 0.5340 (mm-30) outliers start: 104 outliers final: 73 residues processed: 305 average time/residue: 0.3508 time to fit residues: 170.4601 Evaluate side-chains 292 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 212 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 405 HIS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.7980 chunk 276 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 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** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3678 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= 0.196 Angle : 0.558 8.680 33273 Z= 0.284 Chirality : 0.041 0.166 3754 Planarity : 0.005 0.096 4402 Dihedral : 5.842 57.439 3534 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.27 % Allowed : 19.09 % Favored : 77.64 % 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: -1.99 (0.15), residues: 3181 helix: -0.98 (0.17), residues: 940 sheet: -1.39 (0.20), residues: 610 loop : -1.42 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1125 HIS 0.008 0.001 HIS A1099 PHE 0.020 0.002 PHE A1270 TYR 0.015 0.001 TYR E 84 ARG 0.011 0.000 ARG B 721 *********************** 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 308 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 227 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.7357 (tmm) cc_final: 0.6930 (tmm) REVERT: B 350 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8134 (mp) REVERT: B 572 MET cc_start: 0.4304 (mpp) cc_final: 0.4095 (mtm) REVERT: B 694 MET cc_start: 0.4383 (mpp) cc_final: 0.4178 (mpp) REVERT: B 901 TYR cc_start: 0.8106 (t80) cc_final: 0.7639 (t80) REVERT: A 202 ASP cc_start: 0.7673 (t0) cc_final: 0.7302 (t0) REVERT: A 560 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6148 (t80) REVERT: A 642 TRP cc_start: 0.5594 (OUTLIER) cc_final: 0.2946 (m-90) REVERT: A 1068 TRP cc_start: 0.8004 (m100) cc_final: 0.7664 (m100) REVERT: A 1285 LEU cc_start: 0.6122 (mp) cc_final: 0.5793 (mt) REVERT: A 1334 HIS cc_start: 0.5255 (p-80) cc_final: 0.5028 (p90) REVERT: D 139 ILE cc_start: 0.7696 (tp) cc_final: 0.7314 (tp) REVERT: D 145 GLU cc_start: 0.5212 (pp20) cc_final: 0.4688 (pp20) REVERT: E 82 ILE cc_start: 0.6816 (tp) cc_final: 0.6565 (tp) REVERT: F 110 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6927 (tmm) REVERT: F 209 GLU cc_start: 0.5827 (mp0) cc_final: 0.5375 (mm-30) outliers start: 81 outliers final: 57 residues processed: 290 average time/residue: 0.3648 time to fit residues: 168.8282 Evaluate side-chains 270 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 209 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL 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: 1.9990 chunk 175 optimal weight: 0.4980 chunk 224 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 259 optimal weight: 0.0000 chunk 171 optimal weight: 8.9990 chunk 306 optimal weight: 0.0470 chunk 191 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.7086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 768 HIS A 459 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** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3851 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= 0.211 Angle : 0.564 7.514 33273 Z= 0.285 Chirality : 0.042 0.192 3754 Planarity : 0.005 0.086 4402 Dihedral : 5.627 58.912 3526 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.35 % Allowed : 18.52 % Favored : 78.13 % 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: -1.83 (0.15), residues: 3181 helix: -0.87 (0.17), residues: 944 sheet: -1.26 (0.20), residues: 592 loop : -1.33 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1044 HIS 0.005 0.001 HIS A1099 PHE 0.019 0.002 PHE A1270 TYR 0.013 0.001 TYR E 183 ARG 0.009 0.000 ARG B 721 *********************** 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 296 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 213 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.7434 (tmm) cc_final: 0.7043 (tmm) REVERT: B 350 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 901 TYR cc_start: 0.8056 (t80) cc_final: 0.7506 (t80) REVERT: A 202 ASP cc_start: 0.7609 (t0) cc_final: 0.7242 (t0) REVERT: A 560 PHE cc_start: 0.6471 (OUTLIER) cc_final: 0.6093 (t80) REVERT: A 642 TRP cc_start: 0.5613 (OUTLIER) cc_final: 0.2880 (m-90) REVERT: A 1285 LEU cc_start: 0.6118 (mp) cc_final: 0.5794 (mt) REVERT: D 139 ILE cc_start: 0.7707 (tp) cc_final: 0.7290 (tp) REVERT: D 145 GLU cc_start: 0.5190 (pp20) cc_final: 0.4620 (pp20) REVERT: F 110 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: F 209 GLU cc_start: 0.5956 (mp0) cc_final: 0.5533 (mm-30) outliers start: 83 outliers final: 62 residues processed: 279 average time/residue: 0.3504 time to fit residues: 156.6692 Evaluate side-chains 273 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 207 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.3980 chunk 122 optimal weight: 0.0030 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 240 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 768 HIS ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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: 0.6992 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24460 Z= 0.175 Angle : 0.545 10.580 33273 Z= 0.274 Chirality : 0.041 0.162 3754 Planarity : 0.005 0.085 4402 Dihedral : 5.409 59.405 3524 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.07 % Allowed : 19.05 % Favored : 77.89 % 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: -1.64 (0.15), residues: 3181 helix: -0.68 (0.17), residues: 950 sheet: -1.15 (0.20), residues: 604 loop : -1.24 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1044 HIS 0.005 0.001 HIS A1099 PHE 0.026 0.001 PHE A1270 TYR 0.027 0.001 TYR E 84 ARG 0.008 0.000 ARG B 721 *********************** 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 292 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.7427 (tmm) cc_final: 0.6997 (tmm) REVERT: B 350 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 901 TYR cc_start: 0.8071 (t80) cc_final: 0.7495 (t80) REVERT: A 202 ASP cc_start: 0.7616 (t0) cc_final: 0.7232 (t0) REVERT: A 560 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5924 (t80) REVERT: A 642 TRP cc_start: 0.5601 (OUTLIER) cc_final: 0.2876 (m-90) REVERT: A 1285 LEU cc_start: 0.5895 (mp) cc_final: 0.5635 (mt) REVERT: C 106 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (tm) REVERT: D 139 ILE cc_start: 0.7773 (tp) cc_final: 0.7379 (tp) REVERT: D 217 GLU cc_start: 0.6111 (pp20) cc_final: 0.5899 (pp20) REVERT: E 36 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6411 (ttm) REVERT: E 112 GLN cc_start: 0.7720 (pm20) cc_final: 0.7377 (pm20) REVERT: F 209 GLU cc_start: 0.5950 (mp0) cc_final: 0.5557 (mm-30) outliers start: 76 outliers final: 60 residues processed: 276 average time/residue: 0.3573 time to fit residues: 158.2898 Evaluate side-chains 271 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 206 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 312 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 171 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24460 Z= 0.268 Angle : 0.586 9.517 33273 Z= 0.295 Chirality : 0.042 0.171 3754 Planarity : 0.005 0.078 4402 Dihedral : 5.414 49.066 3522 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.23 % Allowed : 19.45 % Favored : 77.32 % 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: -1.64 (0.15), residues: 3181 helix: -0.68 (0.17), residues: 951 sheet: -1.17 (0.20), residues: 623 loop : -1.22 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1125 HIS 0.011 0.001 HIS A1259 PHE 0.030 0.002 PHE A1270 TYR 0.011 0.001 TYR A 930 ARG 0.011 0.000 ARG B 221 *********************** 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 293 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 213 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.7498 (tmm) cc_final: 0.6908 (tmm) REVERT: B 350 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8174 (mp) REVERT: B 901 TYR cc_start: 0.8084 (t80) cc_final: 0.7517 (t80) REVERT: A 202 ASP cc_start: 0.7585 (t0) cc_final: 0.7211 (t0) REVERT: A 560 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.5976 (t80) REVERT: A 642 TRP cc_start: 0.5675 (OUTLIER) cc_final: 0.2898 (m-90) REVERT: A 838 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6506 (t) REVERT: A 1285 LEU cc_start: 0.5953 (mp) cc_final: 0.5690 (mt) REVERT: D 139 ILE cc_start: 0.7721 (tp) cc_final: 0.7291 (tp) REVERT: D 145 GLU cc_start: 0.5198 (pp20) cc_final: 0.4598 (pp20) REVERT: D 217 GLU cc_start: 0.6235 (pp20) cc_final: 0.6014 (pp20) REVERT: F 110 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6983 (tmm) REVERT: F 209 GLU cc_start: 0.5882 (mp0) cc_final: 0.5469 (mm-30) outliers start: 80 outliers final: 65 residues processed: 276 average time/residue: 0.3641 time to fit residues: 162.9605 Evaluate side-chains 276 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 206 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.7980 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 768 HIS A 312 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24460 Z= 0.218 Angle : 0.573 9.717 33273 Z= 0.288 Chirality : 0.042 0.200 3754 Planarity : 0.005 0.104 4402 Dihedral : 5.365 49.936 3521 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.70 % Allowed : 20.14 % Favored : 77.16 % 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: -1.58 (0.15), residues: 3181 helix: -0.61 (0.17), residues: 950 sheet: -1.15 (0.20), residues: 632 loop : -1.19 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1125 HIS 0.011 0.001 HIS A1259 PHE 0.032 0.002 PHE A1270 TYR 0.030 0.001 TYR E 84 ARG 0.011 0.000 ARG B 221 ********************** 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 278 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 211 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8147 (mp) REVERT: B 901 TYR cc_start: 0.8055 (t80) cc_final: 0.7482 (t80) REVERT: A 202 ASP cc_start: 0.7586 (t0) cc_final: 0.7146 (t0) REVERT: A 502 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: A 560 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.5951 (t80) REVERT: A 635 MET cc_start: 0.4512 (mtt) cc_final: 0.3984 (mtp) REVERT: A 642 TRP cc_start: 0.5630 (OUTLIER) cc_final: 0.2914 (m-90) REVERT: A 838 THR cc_start: 0.6734 (OUTLIER) cc_final: 0.6496 (t) REVERT: A 1285 LEU cc_start: 0.5929 (mp) cc_final: 0.5683 (mt) REVERT: C 183 TYR cc_start: 0.6543 (m-80) cc_final: 0.6219 (m-80) REVERT: D 139 ILE cc_start: 0.7725 (tp) cc_final: 0.7324 (tp) REVERT: D 145 GLU cc_start: 0.5138 (pp20) cc_final: 0.4563 (pp20) REVERT: D 209 GLU cc_start: 0.4932 (pm20) cc_final: 0.4687 (mm-30) REVERT: D 217 GLU cc_start: 0.6165 (pp20) cc_final: 0.5952 (pp20) REVERT: F 110 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6982 (tmm) REVERT: F 209 GLU cc_start: 0.5805 (mp0) cc_final: 0.5135 (mm-30) outliers start: 67 outliers final: 59 residues processed: 264 average time/residue: 0.3501 time to fit residues: 149.2267 Evaluate side-chains 268 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 203 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 252 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 259 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN B 768 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.206926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179827 restraints weight = 30781.403| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 1.42 r_work: 0.4084 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24460 Z= 0.205 Angle : 0.578 17.168 33273 Z= 0.288 Chirality : 0.042 0.210 3754 Planarity : 0.005 0.099 4402 Dihedral : 5.293 51.092 3519 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.70 % Allowed : 20.30 % Favored : 77.00 % 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: -1.51 (0.15), residues: 3181 helix: -0.54 (0.17), residues: 951 sheet: -1.11 (0.20), residues: 632 loop : -1.15 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1125 HIS 0.011 0.001 HIS A1259 PHE 0.032 0.001 PHE A1270 TYR 0.021 0.001 TYR C 84 ARG 0.010 0.000 ARG B 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5357.12 seconds wall clock time: 98 minutes 34.07 seconds (5914.07 seconds total)