Starting phenix.real_space_refine on Thu Mar 5 15:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7j_23715/03_2026/7m7j_23715.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 14488 2.51 5 N 4159 2.21 5 O 4491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23224 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 6741 Classifications: {'peptide': 912} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 859} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 10277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10277 Classifications: {'peptide': 1390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 74, 'TRANS': 1315} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'TRP:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 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: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1564 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1564 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.12, per 1000 atoms: 0.22 Number of scatterers: 23224 At special positions: 0 Unit cell: (111, 155, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 4491 8.00 N 4159 7.00 C 14488 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=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5642 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 32.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 5 through 32 removed outlier: 4.208A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 removed outlier: 3.762A pdb=" N GLU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.665A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 4.258A pdb=" N LEU B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.626A pdb=" N LEU B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.460A pdb=" N THR B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.801A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 222 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.918A pdb=" N LEU B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.522A pdb=" N ILE B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.840A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 4.164A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.237A pdb=" N ASN B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.516A pdb=" N VAL B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.272A pdb=" N LEU B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 609 through 613 removed outlier: 4.034A pdb=" N ARG B 612 " --> pdb=" O GLU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 644 Proline residue: B 629 - end of helix removed outlier: 3.956A pdb=" N ALA B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 664 Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 670 through 688 removed outlier: 4.017A pdb=" N MET B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 731 through 741 removed outlier: 3.752A pdb=" N CYS B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.567A pdb=" N THR B 762 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 808 Processing helix chain 'B' and resid 812 through 823 Processing helix chain 'B' and resid 837 through 847 Processing helix chain 'B' and resid 868 through 877 removed outlier: 3.574A pdb=" N LEU B 872 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 874 " --> pdb=" O GLU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 888 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.677A pdb=" N GLU A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.989A pdb=" N ALA A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.838A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 138 removed outlier: 3.590A pdb=" N LEU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.680A pdb=" N LEU A 144 " --> pdb=" O PRO A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 removed outlier: 4.285A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.752A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.751A pdb=" N ARG A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.630A pdb=" N SER A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 359 removed outlier: 4.768A pdb=" N GLU A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.093A pdb=" N ASN A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.143A pdb=" N VAL A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 removed outlier: 3.963A pdb=" N ALA A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.944A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 removed outlier: 3.703A pdb=" N THR A 579 " --> pdb=" O LEU A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 579' Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 601 through 608 removed outlier: 4.348A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.693A pdb=" N GLN A 615 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 644 Proline residue: A 629 - end of helix removed outlier: 3.813A pdb=" N MET A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 671 through 688 removed outlier: 3.979A pdb=" N MET A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 731 through 741 removed outlier: 3.796A pdb=" N CYS A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.772A pdb=" N THR A 762 " --> pdb=" O HIS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 808 Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.511A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.704A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 892 removed outlier: 3.685A pdb=" N VAL A 887 " --> pdb=" O ASP A 883 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 removed outlier: 4.129A pdb=" N VAL A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 968 removed outlier: 4.129A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 973 Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1017 through 1020 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.547A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 4.027A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 5.814A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1180 through 1192 Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.938A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1280 Processing helix chain 'A' and resid 1288 through 1305 Processing helix chain 'A' and resid 1325 through 1334 Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 4.289A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 removed outlier: 4.475A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1390 removed outlier: 3.718A pdb=" N ARG A1389 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 removed outlier: 4.048A pdb=" N LYS C 69 " --> pdb=" O ALA C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.749A pdb=" N TYR D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 209' Processing helix chain 'E' and resid 66 through 69 removed outlier: 4.049A pdb=" N LYS E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 69' Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.749A pdb=" N TYR F 208 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU F 209 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS F 210 " --> pdb=" O ASP F 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 205 through 210' Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 201 removed outlier: 7.884A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 276 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA B 39 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU B 278 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 37 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 337 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AA3, first strand: chain 'B' and resid 648 through 652 removed outlier: 4.431A pdb=" N GLN B 556 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 650 " --> pdb=" O GLN B 556 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 558 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 652 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE B 560 " --> pdb=" O VAL B 652 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 693 through 697 removed outlier: 5.804A pdb=" N ALA B 726 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 714 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 201 removed outlier: 7.795A pdb=" N ILE A 199 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 39 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL A 337 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.889A pdb=" N GLN A 556 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 650 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 558 " --> pdb=" O ALA A 650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 697 removed outlier: 5.612A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 930 through 935 removed outlier: 3.647A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU A1113 " --> pdb=" O GLY A1083 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A1085 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A1115 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP A1087 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A1043 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A1086 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR A1045 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A1088 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR A1047 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 950 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 979 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1195 through 1199 removed outlier: 5.873A pdb=" N LEU A1168 " --> pdb=" O THR A1196 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA A1198 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A1170 " --> pdb=" O ALA A1198 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A1143 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1171 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A1145 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR A1142 " --> pdb=" O ALA A1223 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A1225 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A1144 " --> pdb=" O PHE A1225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1271 through 1275 removed outlier: 6.352A pdb=" N LEU A1272 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP A1314 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.609A pdb=" N THR C 73 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.546A pdb=" N GLY C 12 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 117 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.819A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 157 through 161 removed outlier: 3.791A pdb=" N THR C 158 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 206 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS C 203 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 212 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.627A pdb=" N PHE D 92 " --> pdb=" O CYS D 39 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 84 " --> pdb=" O LYS D 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 74 through 75 removed outlier: 5.990A pdb=" N LEU D 67 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 58 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 69 " --> pdb=" O TRP D 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 105 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.518A pdb=" N ALA D 152 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 156 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 200 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 140 removed outlier: 5.836A pdb=" N TYR D 195 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'E' and resid 8 through 9 removed outlier: 3.608A pdb=" N THR E 73 " --> pdb=" O GLN E 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.546A pdb=" N GLY E 12 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR E 117 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.818A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.767A pdb=" N CYS E 203 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS E 207 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 212 " --> pdb=" O HIS E 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.627A pdb=" N PHE F 92 " --> pdb=" O CYS F 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER F 84 " --> pdb=" O LYS F 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 74 through 75 removed outlier: 6.005A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 69 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.519A pdb=" N ALA F 152 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS F 156 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER F 199 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 200 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 136 through 140 removed outlier: 5.837A pdb=" N TYR F 195 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 169 through 170 813 hydrogen bonds defined for protein. 2259 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: 4.83 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3976 1.31 - 1.43: 6023 1.43 - 1.56: 13553 1.56 - 1.69: 5 1.69 - 1.81: 135 Bond restraints: 23692 Sorted by residual: bond pdb=" C ARG A 966 " pdb=" O ARG A 966 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.19e-02 7.06e+03 2.38e+01 bond pdb=" N LEU C 47 " pdb=" CA LEU C 47 " ideal model delta sigma weight residual 1.453 1.499 -0.046 1.22e-02 6.72e+03 1.42e+01 bond pdb=" N GLN B 657 " pdb=" CA GLN B 657 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" N ILE A 653 " pdb=" CA ILE A 653 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N GLN A 628 " pdb=" CA GLN A 628 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.13e+01 ... (remaining 23687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 31973 3.83 - 7.65: 235 7.65 - 11.48: 20 11.48 - 15.31: 2 15.31 - 19.14: 1 Bond angle restraints: 32231 Sorted by residual: angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 112.96 105.57 7.39 1.00e+00 1.00e+00 5.47e+01 angle pdb=" N ASP B 867 " pdb=" CA ASP B 867 " pdb=" C ASP B 867 " ideal model delta sigma weight residual 113.19 105.47 7.72 1.19e+00 7.06e-01 4.21e+01 angle pdb=" CA GLU E 155 " pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 117.47 123.41 -5.94 9.90e-01 1.02e+00 3.60e+01 angle pdb=" N ALA B 866 " pdb=" CA ALA B 866 " pdb=" C ALA B 866 " ideal model delta sigma weight residual 112.68 104.81 7.87 1.33e+00 5.65e-01 3.50e+01 angle pdb=" C ARG B 124 " pdb=" CA ARG B 124 " pdb=" CB ARG B 124 " ideal model delta sigma weight residual 110.79 120.37 -9.58 1.66e+00 3.63e-01 3.33e+01 ... (remaining 32226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12749 17.92 - 35.83: 1046 35.83 - 53.75: 270 53.75 - 71.66: 100 71.66 - 89.58: 23 Dihedral angle restraints: 14188 sinusoidal: 5370 harmonic: 8818 Sorted by residual: dihedral pdb=" CB CYS C 147 " pdb=" SG CYS C 147 " pdb=" SG CYS C 203 " pdb=" CB CYS C 203 " ideal model delta sinusoidal sigma weight residual 93.00 153.25 -60.25 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 203 " pdb=" CB CYS E 203 " ideal model delta sinusoidal sigma weight residual 93.00 153.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA MET A 391 " pdb=" C MET A 391 " pdb=" N VAL A 392 " pdb=" CA VAL A 392 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 14185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3172 0.081 - 0.161: 392 0.161 - 0.242: 58 0.242 - 0.323: 19 0.323 - 0.404: 3 Chirality restraints: 3644 Sorted by residual: chirality pdb=" CA GLN B 657 " pdb=" N GLN B 657 " pdb=" C GLN B 657 " pdb=" CB GLN B 657 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA TYR A 825 " pdb=" N TYR A 825 " pdb=" C TYR A 825 " pdb=" CB TYR A 825 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA MET A 228 " pdb=" N MET A 228 " pdb=" C MET A 228 " pdb=" CB MET A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3641 not shown) Planarity restraints: 4271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 905 " 0.302 9.50e-02 1.11e+02 1.35e-01 1.22e+01 pdb=" NE ARG B 905 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 905 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 905 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 905 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 21 " -0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR D 21 " 0.056 2.00e-02 2.50e+03 pdb=" O THR D 21 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN D 22 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 21 " -0.014 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C THR F 21 " 0.052 2.00e-02 2.50e+03 pdb=" O THR F 21 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN F 22 " -0.017 2.00e-02 2.50e+03 ... (remaining 4268 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 575 2.67 - 3.23: 22950 3.23 - 3.79: 40004 3.79 - 4.34: 54423 4.34 - 4.90: 85454 Nonbonded interactions: 203406 Sorted by model distance: nonbonded pdb=" OG SER F 42 " pdb=" OE1 GLN F 43 " model vdw 2.117 3.040 nonbonded pdb=" OG SER D 42 " pdb=" OE1 GLN D 43 " model vdw 2.117 3.040 nonbonded pdb=" OG SER A 3 " pdb=" OH TYR C 58 " model vdw 2.161 3.040 nonbonded pdb=" O ARG A 318 " pdb=" NE2 GLN A 322 " model vdw 2.233 3.120 nonbonded pdb=" NE1 TRP A 74 " pdb=" O PRO A 236 " model vdw 2.246 3.120 ... (remaining 203401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.005 0.098 23700 Z= 0.328 Angle : 0.928 19.137 32247 Z= 0.574 Chirality : 0.058 0.404 3644 Planarity : 0.006 0.135 4271 Dihedral : 15.467 89.579 8522 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 5.04 % Allowed : 1.88 % Favored : 93.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 3096 helix: -1.01 (0.18), residues: 827 sheet: -1.28 (0.22), residues: 509 loop : -1.67 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 905 TYR 0.014 0.002 TYR B 901 PHE 0.025 0.002 PHE B 868 TRP 0.035 0.002 TRP C 49 HIS 0.009 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00499 (23692) covalent geometry : angle 0.92753 (32231) SS BOND : bond 0.00437 ( 8) SS BOND : angle 1.18698 ( 16) hydrogen bonds : bond 0.20813 ( 801) hydrogen bonds : angle 8.83205 ( 2259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 137 time to evaluate : 0.567 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: B 29 GLU cc_start: 0.8857 (pt0) cc_final: 0.8435 (tm-30) REVERT: B 125 LEU cc_start: 0.9312 (mm) cc_final: 0.9101 (mm) REVERT: B 126 MET cc_start: 0.9147 (mmt) cc_final: 0.8472 (mmt) REVERT: B 153 VAL cc_start: 0.9608 (t) cc_final: 0.9268 (p) REVERT: B 553 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6817 (mtm180) REVERT: B 641 MET cc_start: -0.0922 (ptm) cc_final: -0.1543 (ptm) REVERT: A 205 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7511 (m) REVERT: A 275 LEU cc_start: 0.9394 (mm) cc_final: 0.9012 (mm) REVERT: A 631 MET cc_start: -0.0102 (ptp) cc_final: -0.0777 (ptm) REVERT: C 171 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7599 (m-70) REVERT: D 20 MET cc_start: 0.8596 (mmp) cc_final: 0.8327 (mmm) REVERT: D 55 ASP cc_start: 0.8116 (m-30) cc_final: 0.7884 (m-30) REVERT: D 197 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7740 (tt) REVERT: E 36 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8099 (tpp) REVERT: E 91 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (pttm) REVERT: E 120 SER cc_start: 0.0812 (OUTLIER) cc_final: 0.0522 (p) REVERT: F 55 ASP cc_start: 0.8421 (m-30) cc_final: 0.7995 (t0) REVERT: F 74 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8729 (t0) REVERT: F 197 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6504 (tp) outliers start: 121 outliers final: 21 residues processed: 231 average time/residue: 0.1680 time to fit residues: 59.7592 Evaluate side-chains 128 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 300 ASN B 316 GLN B 628 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 300 ASN A 322 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS F 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.082165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.056583 restraints weight = 251096.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056822 restraints weight = 178216.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.057072 restraints weight = 132482.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.056655 restraints weight = 119791.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.056694 restraints weight = 116402.266| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 23700 Z= 0.294 Angle : 0.805 10.687 32247 Z= 0.414 Chirality : 0.045 0.170 3644 Planarity : 0.007 0.147 4271 Dihedral : 5.282 29.322 3401 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 0.38 % Allowed : 6.92 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.14), residues: 3096 helix: -0.63 (0.18), residues: 842 sheet: -1.67 (0.20), residues: 559 loop : -1.56 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 905 TYR 0.024 0.003 TYR E 183 PHE 0.029 0.003 PHE D 92 TRP 0.034 0.003 TRP A1314 HIS 0.009 0.002 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00607 (23692) covalent geometry : angle 0.80429 (32231) SS BOND : bond 0.00618 ( 8) SS BOND : angle 1.42652 ( 16) hydrogen bonds : bond 0.05135 ( 801) hydrogen bonds : angle 6.74479 ( 2259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9427 (mmt) cc_final: 0.8595 (mmt) REVERT: B 235 MET cc_start: 0.8578 (tpt) cc_final: 0.7895 (mmm) REVERT: A 13 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9329 (mm) REVERT: D 183 GLU cc_start: 0.8246 (tp30) cc_final: 0.7941 (tp30) REVERT: E 36 MET cc_start: 0.9242 (mmp) cc_final: 0.9019 (tpp) outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 0.1459 time to fit residues: 28.7051 Evaluate side-chains 86 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 232 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 289 optimal weight: 30.0000 chunk 309 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 219 optimal weight: 40.0000 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.071667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043113 restraints weight = 175872.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.043153 restraints weight = 148925.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.043153 restraints weight = 147177.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.043153 restraints weight = 147177.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.043153 restraints weight = 147177.979| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23700 Z= 0.258 Angle : 0.745 13.850 32247 Z= 0.386 Chirality : 0.046 0.205 3644 Planarity : 0.007 0.166 4271 Dihedral : 5.418 34.171 3401 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3096 helix: -0.60 (0.17), residues: 887 sheet: -1.77 (0.21), residues: 539 loop : -1.61 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 905 TYR 0.029 0.003 TYR E 183 PHE 0.039 0.003 PHE F 92 TRP 0.022 0.002 TRP F 56 HIS 0.008 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00531 (23692) covalent geometry : angle 0.74451 (32231) SS BOND : bond 0.00672 ( 8) SS BOND : angle 1.76899 ( 16) hydrogen bonds : bond 0.04739 ( 801) hydrogen bonds : angle 6.40568 ( 2259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8725 (tpp) cc_final: 0.8435 (tpp) REVERT: B 126 MET cc_start: 0.9667 (mmt) cc_final: 0.9062 (mmm) REVERT: B 192 LEU cc_start: 0.9762 (tp) cc_final: 0.9425 (tp) REVERT: B 194 LEU cc_start: 0.9631 (mt) cc_final: 0.9415 (mt) REVERT: B 391 MET cc_start: 0.9195 (mmm) cc_final: 0.8953 (mmm) REVERT: B 631 MET cc_start: 0.0813 (mmm) cc_final: -0.0147 (mmm) REVERT: A 126 MET cc_start: 0.8932 (mmt) cc_final: 0.8431 (mmt) REVERT: A 214 LEU cc_start: 0.9773 (tp) cc_final: 0.9558 (tp) REVERT: D 95 LYS cc_start: 0.9496 (tmtt) cc_final: 0.9226 (tptt) REVERT: F 55 ASP cc_start: 0.8748 (p0) cc_final: 0.8227 (p0) outliers start: 6 outliers final: 0 residues processed: 109 average time/residue: 0.1445 time to fit residues: 26.3431 Evaluate side-chains 81 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 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 = 0.3805 r_free = 0.3805 target = 0.069130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.040209 restraints weight = 178333.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040403 restraints weight = 150969.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040737 restraints weight = 141449.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.040778 restraints weight = 130622.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.040856 restraints weight = 128666.287| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 23700 Z= 0.281 Angle : 0.766 10.099 32247 Z= 0.392 Chirality : 0.045 0.184 3644 Planarity : 0.007 0.172 4271 Dihedral : 5.519 23.239 3401 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3096 helix: -0.48 (0.17), residues: 892 sheet: -1.91 (0.21), residues: 539 loop : -1.71 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 905 TYR 0.029 0.003 TYR E 183 PHE 0.036 0.003 PHE B 775 TRP 0.022 0.002 TRP A 55 HIS 0.009 0.002 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00578 (23692) covalent geometry : angle 0.76514 (32231) SS BOND : bond 0.00607 ( 8) SS BOND : angle 1.74418 ( 16) hydrogen bonds : bond 0.04475 ( 801) hydrogen bonds : angle 6.41175 ( 2259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8982 (tpp) cc_final: 0.8715 (tpp) REVERT: B 126 MET cc_start: 0.9817 (mmt) cc_final: 0.9063 (mmm) REVERT: B 176 MET cc_start: 0.9658 (tpp) cc_final: 0.9419 (tpp) REVERT: B 192 LEU cc_start: 0.9733 (tp) cc_final: 0.9408 (tp) REVERT: B 274 MET cc_start: 0.9334 (tpp) cc_final: 0.9015 (tpp) REVERT: B 391 MET cc_start: 0.9377 (mmm) cc_final: 0.8942 (mmm) REVERT: B 635 MET cc_start: -0.4902 (ptm) cc_final: -0.5168 (tpt) REVERT: A 126 MET cc_start: 0.9192 (mmt) cc_final: 0.8650 (mmt) REVERT: A 395 MET cc_start: 0.8968 (mmt) cc_final: 0.8719 (mmt) REVERT: D 95 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9108 (tptt) REVERT: E 177 LEU cc_start: 0.9432 (mp) cc_final: 0.9160 (mp) REVERT: E 183 TYR cc_start: 0.8855 (m-80) cc_final: 0.8120 (m-80) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.1578 time to fit residues: 25.1020 Evaluate side-chains 74 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 166 optimal weight: 50.0000 chunk 138 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 304 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 246 optimal weight: 0.3980 chunk 60 optimal weight: 0.0060 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.071836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.043430 restraints weight = 170715.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.044088 restraints weight = 144601.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.044127 restraints weight = 117733.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.044127 restraints weight = 116106.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.044127 restraints weight = 116106.667| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23700 Z= 0.145 Angle : 0.632 7.912 32247 Z= 0.322 Chirality : 0.044 0.196 3644 Planarity : 0.006 0.153 4271 Dihedral : 5.193 30.736 3401 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3096 helix: -0.14 (0.18), residues: 893 sheet: -1.71 (0.21), residues: 530 loop : -1.56 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 905 TYR 0.017 0.002 TYR A 190 PHE 0.022 0.002 PHE F 92 TRP 0.018 0.001 TRP A 55 HIS 0.008 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00316 (23692) covalent geometry : angle 0.63071 (32231) SS BOND : bond 0.00520 ( 8) SS BOND : angle 1.56897 ( 16) hydrogen bonds : bond 0.03611 ( 801) hydrogen bonds : angle 5.97722 ( 2259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9032 (tpp) cc_final: 0.8777 (tpp) REVERT: B 126 MET cc_start: 0.9811 (mmt) cc_final: 0.9174 (mmm) REVERT: B 176 MET cc_start: 0.9674 (tpp) cc_final: 0.9256 (tpp) REVERT: B 212 VAL cc_start: 0.9870 (m) cc_final: 0.9624 (p) REVERT: B 216 CYS cc_start: 0.9638 (m) cc_final: 0.9404 (m) REVERT: B 391 MET cc_start: 0.9397 (mmm) cc_final: 0.8876 (mmm) REVERT: B 631 MET cc_start: -0.0918 (mmm) cc_final: -0.1596 (mmm) REVERT: A 25 GLN cc_start: 0.9570 (tt0) cc_final: 0.9217 (tp-100) REVERT: A 126 MET cc_start: 0.8938 (mmt) cc_final: 0.8448 (mmt) REVERT: A 631 MET cc_start: -0.2789 (ptp) cc_final: -0.3839 (ptm) REVERT: A 635 MET cc_start: -0.0574 (tpt) cc_final: -0.0848 (tpt) REVERT: D 95 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9100 (tptt) REVERT: E 177 LEU cc_start: 0.9379 (mp) cc_final: 0.9132 (mt) REVERT: E 183 TYR cc_start: 0.8729 (m-80) cc_final: 0.7859 (m-80) REVERT: F 110 MET cc_start: 0.8461 (mmm) cc_final: 0.8206 (mmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1570 time to fit residues: 25.9318 Evaluate side-chains 83 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 132 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 266 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.073353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.045186 restraints weight = 165678.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.044969 restraints weight = 142823.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.045571 restraints weight = 130960.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.045593 restraints weight = 114244.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.045594 restraints weight = 110774.600| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23700 Z= 0.117 Angle : 0.610 8.726 32247 Z= 0.308 Chirality : 0.043 0.202 3644 Planarity : 0.006 0.125 4271 Dihedral : 4.947 25.251 3401 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 3096 helix: 0.01 (0.18), residues: 882 sheet: -1.57 (0.21), residues: 527 loop : -1.44 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 905 TYR 0.023 0.001 TYR C 34 PHE 0.015 0.001 PHE B 876 TRP 0.017 0.001 TRP A 55 HIS 0.008 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00262 (23692) covalent geometry : angle 0.60953 (32231) SS BOND : bond 0.00433 ( 8) SS BOND : angle 1.35356 ( 16) hydrogen bonds : bond 0.03259 ( 801) hydrogen bonds : angle 5.69190 ( 2259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9101 (tpp) cc_final: 0.8771 (tpp) REVERT: B 126 MET cc_start: 0.9815 (mmt) cc_final: 0.9106 (mmm) REVERT: B 176 MET cc_start: 0.9657 (tpp) cc_final: 0.9196 (tpp) REVERT: B 192 LEU cc_start: 0.9749 (tp) cc_final: 0.9464 (tp) REVERT: B 212 VAL cc_start: 0.9878 (m) cc_final: 0.9634 (p) REVERT: B 216 CYS cc_start: 0.9688 (m) cc_final: 0.9466 (m) REVERT: B 274 MET cc_start: 0.9569 (tpp) cc_final: 0.8870 (tpp) REVERT: B 391 MET cc_start: 0.9410 (mmm) cc_final: 0.8846 (mmm) REVERT: B 694 MET cc_start: 0.3105 (mmm) cc_final: 0.2660 (mmm) REVERT: A 25 GLN cc_start: 0.9559 (tt0) cc_final: 0.9201 (tp-100) REVERT: A 126 MET cc_start: 0.9130 (mmt) cc_final: 0.8496 (mmt) REVERT: A 228 MET cc_start: 0.8730 (tpp) cc_final: 0.8423 (tpp) REVERT: A 631 MET cc_start: -0.2243 (ptp) cc_final: -0.3299 (ptm) REVERT: A 635 MET cc_start: -0.0824 (tpt) cc_final: -0.1127 (tpt) REVERT: D 95 LYS cc_start: 0.9342 (tmtt) cc_final: 0.8995 (tptt) REVERT: E 87 MET cc_start: 0.8780 (mpp) cc_final: 0.8525 (mmp) REVERT: E 177 LEU cc_start: 0.9289 (mp) cc_final: 0.9016 (mt) REVERT: E 183 TYR cc_start: 0.8642 (m-80) cc_final: 0.7786 (m-80) REVERT: F 110 MET cc_start: 0.8435 (mmm) cc_final: 0.8114 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1537 time to fit residues: 27.5518 Evaluate side-chains 89 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 68 optimal weight: 40.0000 chunk 293 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 205 optimal weight: 0.0030 chunk 142 optimal weight: 5.9990 chunk 134 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 overall best weight: 2.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.072124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043576 restraints weight = 167871.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043576 restraints weight = 140695.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043576 restraints weight = 140695.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043576 restraints weight = 140695.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043576 restraints weight = 140695.498| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23700 Z= 0.140 Angle : 0.603 8.118 32247 Z= 0.305 Chirality : 0.043 0.172 3644 Planarity : 0.005 0.112 4271 Dihedral : 4.880 24.678 3401 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3096 helix: 0.09 (0.18), residues: 887 sheet: -1.54 (0.21), residues: 530 loop : -1.42 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 905 TYR 0.016 0.002 TYR C 34 PHE 0.016 0.001 PHE B 775 TRP 0.016 0.001 TRP A 55 HIS 0.006 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00305 (23692) covalent geometry : angle 0.60239 (32231) SS BOND : bond 0.00417 ( 8) SS BOND : angle 1.21461 ( 16) hydrogen bonds : bond 0.03302 ( 801) hydrogen bonds : angle 5.64723 ( 2259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9039 (tpp) cc_final: 0.8739 (tpp) REVERT: B 126 MET cc_start: 0.9772 (mmt) cc_final: 0.9072 (mmm) REVERT: B 176 MET cc_start: 0.9626 (tpp) cc_final: 0.9262 (tpp) REVERT: B 212 VAL cc_start: 0.9885 (m) cc_final: 0.9647 (p) REVERT: B 216 CYS cc_start: 0.9701 (m) cc_final: 0.9485 (m) REVERT: B 391 MET cc_start: 0.9425 (mmm) cc_final: 0.8898 (mmm) REVERT: B 635 MET cc_start: -0.3057 (tpt) cc_final: -0.5617 (ptm) REVERT: A 25 GLN cc_start: 0.9593 (tt0) cc_final: 0.9260 (tp-100) REVERT: A 126 MET cc_start: 0.9276 (mmt) cc_final: 0.8498 (mmt) REVERT: A 631 MET cc_start: -0.2485 (ptp) cc_final: -0.3248 (ptm) REVERT: A 1322 MET cc_start: 0.5941 (tpp) cc_final: 0.5698 (tpp) REVERT: D 95 LYS cc_start: 0.9413 (tmtt) cc_final: 0.9073 (tptt) REVERT: E 177 LEU cc_start: 0.9345 (mp) cc_final: 0.9040 (mt) REVERT: E 183 TYR cc_start: 0.8743 (m-80) cc_final: 0.7831 (m-80) REVERT: F 110 MET cc_start: 0.8482 (mmm) cc_final: 0.8131 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1570 time to fit residues: 27.4048 Evaluate side-chains 85 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 85 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 305 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.071794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.043394 restraints weight = 169028.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.043895 restraints weight = 146737.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044295 restraints weight = 123283.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044295 restraints weight = 114466.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044295 restraints weight = 114465.884| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23700 Z= 0.141 Angle : 0.605 9.147 32247 Z= 0.306 Chirality : 0.043 0.170 3644 Planarity : 0.005 0.085 4271 Dihedral : 4.886 25.471 3401 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3096 helix: 0.12 (0.18), residues: 894 sheet: -1.64 (0.20), residues: 572 loop : -1.39 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 905 TYR 0.016 0.002 TYR E 183 PHE 0.016 0.001 PHE B 876 TRP 0.016 0.001 TRP A 55 HIS 0.007 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00308 (23692) covalent geometry : angle 0.60432 (32231) SS BOND : bond 0.00369 ( 8) SS BOND : angle 1.12432 ( 16) hydrogen bonds : bond 0.03332 ( 801) hydrogen bonds : angle 5.66042 ( 2259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9132 (tpp) cc_final: 0.8775 (tpp) REVERT: B 126 MET cc_start: 0.9824 (mmt) cc_final: 0.9045 (mmm) REVERT: B 176 MET cc_start: 0.9630 (tpp) cc_final: 0.9119 (tpp) REVERT: B 235 MET cc_start: 0.9168 (mmm) cc_final: 0.8774 (mmm) REVERT: B 391 MET cc_start: 0.9478 (mmm) cc_final: 0.8972 (mmm) REVERT: B 635 MET cc_start: -0.3132 (tpt) cc_final: -0.5504 (ptm) REVERT: A 25 GLN cc_start: 0.9586 (tt0) cc_final: 0.9247 (tp-100) REVERT: A 126 MET cc_start: 0.9326 (mmt) cc_final: 0.8603 (mmt) REVERT: A 572 MET cc_start: 0.1580 (ppp) cc_final: 0.1333 (ppp) REVERT: A 631 MET cc_start: -0.2242 (ptp) cc_final: -0.3141 (ptm) REVERT: A 635 MET cc_start: -0.0779 (tpt) cc_final: -0.1134 (mmm) REVERT: A 1322 MET cc_start: 0.6055 (tpp) cc_final: 0.5733 (tpp) REVERT: D 95 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9051 (tptt) REVERT: E 177 LEU cc_start: 0.9337 (mp) cc_final: 0.9035 (mt) REVERT: E 183 TYR cc_start: 0.8764 (m-80) cc_final: 0.7858 (m-80) REVERT: F 110 MET cc_start: 0.8515 (mmm) cc_final: 0.8166 (mmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1516 time to fit residues: 25.9532 Evaluate side-chains 86 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 130 optimal weight: 0.4980 chunk 195 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 286 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.069771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.041885 restraints weight = 170872.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.042401 restraints weight = 144800.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.042599 restraints weight = 123464.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.042612 restraints weight = 115734.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.042612 restraints weight = 114843.949| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23700 Z= 0.180 Angle : 0.637 12.184 32247 Z= 0.323 Chirality : 0.043 0.201 3644 Planarity : 0.005 0.065 4271 Dihedral : 4.972 25.731 3401 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 0.04 % Allowed : 0.92 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3096 helix: 0.17 (0.18), residues: 888 sheet: -1.65 (0.21), residues: 550 loop : -1.42 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 14 TYR 0.039 0.002 TYR F 51 PHE 0.018 0.002 PHE B 876 TRP 0.017 0.002 TRP A 55 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00379 (23692) covalent geometry : angle 0.63689 (32231) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.20969 ( 16) hydrogen bonds : bond 0.03499 ( 801) hydrogen bonds : angle 5.70073 ( 2259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9105 (tpp) cc_final: 0.8814 (tpp) REVERT: B 126 MET cc_start: 0.9809 (mmt) cc_final: 0.9092 (mmm) REVERT: B 176 MET cc_start: 0.9651 (tpp) cc_final: 0.9254 (tpp) REVERT: B 212 VAL cc_start: 0.9883 (m) cc_final: 0.9638 (p) REVERT: B 274 MET cc_start: 0.9560 (tpp) cc_final: 0.9260 (tpp) REVERT: B 391 MET cc_start: 0.9483 (mmm) cc_final: 0.8995 (mmm) REVERT: B 635 MET cc_start: -0.3184 (tpt) cc_final: -0.5331 (ptm) REVERT: A 25 GLN cc_start: 0.9601 (tt0) cc_final: 0.9264 (tp-100) REVERT: A 126 MET cc_start: 0.9196 (mmt) cc_final: 0.8716 (mmm) REVERT: A 631 MET cc_start: -0.1666 (ptp) cc_final: -0.2655 (ptm) REVERT: A 635 MET cc_start: -0.0494 (tpt) cc_final: -0.0812 (tpt) REVERT: A 1322 MET cc_start: 0.6093 (tpp) cc_final: 0.5677 (tpp) REVERT: D 95 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9088 (tptt) REVERT: F 110 MET cc_start: 0.8577 (mmm) cc_final: 0.8231 (mmm) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1622 time to fit residues: 26.9973 Evaluate side-chains 85 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 165 optimal weight: 30.0000 chunk 246 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 18 optimal weight: 0.0980 overall best weight: 3.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 HIS ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 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 = 0.3799 r_free = 0.3799 target = 0.068790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.040625 restraints weight = 171438.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.040962 restraints weight = 148814.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.041085 restraints weight = 129277.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.041415 restraints weight = 123848.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.041415 restraints weight = 117140.668| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23700 Z= 0.195 Angle : 0.659 9.568 32247 Z= 0.336 Chirality : 0.043 0.229 3644 Planarity : 0.005 0.067 4271 Dihedral : 5.124 24.197 3401 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 3096 helix: 0.02 (0.18), residues: 898 sheet: -1.78 (0.21), residues: 530 loop : -1.45 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 895 TYR 0.021 0.002 TYR E 183 PHE 0.019 0.002 PHE B 775 TRP 0.018 0.002 TRP A 55 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00408 (23692) covalent geometry : angle 0.65790 (32231) SS BOND : bond 0.00486 ( 8) SS BOND : angle 1.44021 ( 16) hydrogen bonds : bond 0.03645 ( 801) hydrogen bonds : angle 5.80869 ( 2259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9177 (tpp) cc_final: 0.8917 (tpp) REVERT: B 126 MET cc_start: 0.9823 (mmt) cc_final: 0.9098 (mmm) REVERT: B 176 MET cc_start: 0.9643 (tpp) cc_final: 0.9266 (tpp) REVERT: B 194 LEU cc_start: 0.9603 (mt) cc_final: 0.9269 (mp) REVERT: B 235 MET cc_start: 0.9228 (mmm) cc_final: 0.8761 (mmm) REVERT: B 391 MET cc_start: 0.9495 (mmm) cc_final: 0.9002 (mmm) REVERT: B 635 MET cc_start: -0.3453 (tpt) cc_final: -0.5861 (tmm) REVERT: B 694 MET cc_start: 0.3211 (mmm) cc_final: 0.2490 (mmm) REVERT: A 25 GLN cc_start: 0.9584 (tt0) cc_final: 0.9174 (tp-100) REVERT: A 631 MET cc_start: -0.1215 (ptp) cc_final: -0.2131 (ptm) REVERT: A 635 MET cc_start: -0.0615 (tpt) cc_final: -0.0953 (mmm) REVERT: A 1322 MET cc_start: 0.6092 (tpp) cc_final: 0.5679 (tpp) REVERT: D 95 LYS cc_start: 0.9331 (tmtt) cc_final: 0.8964 (tptt) REVERT: E 183 TYR cc_start: 0.8723 (m-80) cc_final: 0.7938 (m-80) REVERT: F 110 MET cc_start: 0.8561 (mmm) cc_final: 0.8214 (mmm) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1536 time to fit residues: 23.9663 Evaluate side-chains 81 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 142 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.069182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.040951 restraints weight = 170524.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041226 restraints weight = 143422.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041227 restraints weight = 124239.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041227 restraints weight = 124217.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041227 restraints weight = 124216.301| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23700 Z= 0.167 Angle : 0.640 9.232 32247 Z= 0.324 Chirality : 0.044 0.233 3644 Planarity : 0.005 0.062 4271 Dihedral : 5.043 24.864 3401 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3096 helix: 0.06 (0.18), residues: 902 sheet: -1.76 (0.21), residues: 509 loop : -1.46 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 98 TYR 0.018 0.002 TYR A1294 PHE 0.019 0.002 PHE B 876 TRP 0.017 0.001 TRP A 55 HIS 0.007 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00359 (23692) covalent geometry : angle 0.63995 (32231) SS BOND : bond 0.00474 ( 8) SS BOND : angle 1.32124 ( 16) hydrogen bonds : bond 0.03414 ( 801) hydrogen bonds : angle 5.71941 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4459.39 seconds wall clock time: 78 minutes 4.09 seconds (4684.09 seconds total)