Starting phenix.real_space_refine on Mon Feb 19 00:03:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_23715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_23715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_23715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_23715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/02_2024/7m7j_23715.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'ARG:plan': 2, 'TRP:plan': 1, 'HIS: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: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 3, 'HIS: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: 11.76, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.91 Conformation dependent library (CDL) restraints added in 4.8 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: 2.70 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: 10.07 Time building geometry restraints manager: 10.41 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: 95.59 - 104.62: 475 104.62 - 113.64: 13314 113.64 - 122.67: 15296 122.67 - 131.70: 3100 131.70 - 140.73: 46 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 2.440 nonbonded pdb=" OG SER D 42 " pdb=" OE1 GLN D 43 " model vdw 2.117 2.440 nonbonded pdb=" OG SER A 3 " pdb=" OH TYR C 58 " model vdw 2.161 2.440 nonbonded pdb=" O ARG A 318 " pdb=" NE2 GLN A 322 " model vdw 2.233 2.520 nonbonded pdb=" NE1 TRP A 74 " pdb=" O PRO A 236 " model vdw 2.246 2.520 ... (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 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: 2.800 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: 9.320 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 65.240 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.780 ------------------------------------------------------------------------------- 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 23692 Z= 0.337 Angle : 0.928 19.137 32231 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 : 19.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (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 TRP 0.035 0.002 TRP C 49 HIS 0.009 0.001 HIS A1334 PHE 0.025 0.002 PHE B 868 TYR 0.014 0.002 TYR B 901 ARG 0.017 0.000 ARG B 905 *********************** 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 fitting. rotamer outliers: 121 poor density : 137 time to evaluate : 2.761 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: B 29 GLU cc_start: 0.8857 (pt0) cc_final: 0.8435 (tm-30) REVERT: B 126 MET cc_start: 0.9147 (mmt) cc_final: 0.8470 (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: 0.6810 (mtm180) REVERT: B 641 MET cc_start: -0.0922 (ptm) cc_final: -0.1549 (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: 0.9011 (mm) REVERT: A 631 MET cc_start: -0.0103 (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: 0.7885 (m-30) REVERT: D 197 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7739 (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: 0.6505 (tp) outliers start: 121 outliers final: 21 residues processed: 231 average time/residue: 0.3836 time to fit residues: 136.8461 Evaluate side-chains 128 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 300 ASN B 316 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS F 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23692 Z= 0.375 Angle : 0.762 10.259 32231 Z= 0.395 Chirality : 0.044 0.169 3644 Planarity : 0.007 0.157 4271 Dihedral : 5.124 29.342 3401 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 0.29 % Allowed : 7.21 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 3096 helix: -0.59 (0.18), residues: 847 sheet: -1.58 (0.21), residues: 540 loop : -1.46 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A1317 HIS 0.014 0.002 HIS D 220 PHE 0.026 0.003 PHE D 92 TYR 0.020 0.002 TYR E 183 ARG 0.026 0.001 ARG B 905 *********************** 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 120 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8323 (tpt) cc_final: 0.8102 (mmm) REVERT: A 214 LEU cc_start: 0.9581 (tp) cc_final: 0.9375 (tp) REVERT: D 110 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8485 (tpp) outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.3496 time to fit residues: 68.8230 Evaluate side-chains 82 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 279 optimal weight: 40.0000 chunk 96 optimal weight: 0.0070 chunk 226 optimal weight: 10.0000 overall best weight: 3.3804 ------------------------------------------------------------------------------- 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 380 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 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** 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** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23692 Z= 0.250 Angle : 0.633 12.229 32231 Z= 0.325 Chirality : 0.043 0.178 3644 Planarity : 0.006 0.168 4271 Dihedral : 4.963 31.965 3401 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 3096 helix: -0.28 (0.18), residues: 860 sheet: -1.49 (0.21), residues: 530 loop : -1.44 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 56 HIS 0.007 0.001 HIS B 91 PHE 0.026 0.002 PHE D 92 TYR 0.021 0.002 TYR E 183 ARG 0.024 0.001 ARG B 905 *********************** 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 113 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9518 (mmt) cc_final: 0.8828 (mmm) REVERT: B 192 LEU cc_start: 0.9787 (tp) cc_final: 0.9465 (tp) REVERT: B 194 LEU cc_start: 0.9518 (mt) cc_final: 0.9257 (mt) REVERT: B 212 VAL cc_start: 0.9848 (m) cc_final: 0.9551 (p) REVERT: B 235 MET cc_start: 0.8325 (tpt) cc_final: 0.8068 (mmm) REVERT: B 631 MET cc_start: -0.0154 (mmm) cc_final: -0.1299 (mmt) REVERT: A 126 MET cc_start: 0.8695 (mmt) cc_final: 0.8429 (mmt) REVERT: A 214 LEU cc_start: 0.9523 (tp) cc_final: 0.9293 (tp) REVERT: A 395 MET cc_start: 0.8963 (mmt) cc_final: 0.8727 (mmt) REVERT: A 572 MET cc_start: 0.1091 (OUTLIER) cc_final: 0.0571 (tmm) REVERT: A 631 MET cc_start: -0.1334 (ptt) cc_final: -0.1821 (ptt) REVERT: D 95 LYS cc_start: 0.9158 (tmtt) cc_final: 0.8941 (tptt) REVERT: D 183 GLU cc_start: 0.8495 (tp30) cc_final: 0.8077 (tp30) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.3244 time to fit residues: 60.6165 Evaluate side-chains 83 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 283 optimal weight: 30.0000 chunk 299 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 380 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 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23692 Z= 0.166 Angle : 0.573 7.260 32231 Z= 0.289 Chirality : 0.042 0.166 3644 Planarity : 0.005 0.154 4271 Dihedral : 4.660 26.819 3401 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3096 helix: -0.01 (0.18), residues: 860 sheet: -1.30 (0.21), residues: 563 loop : -1.35 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 55 HIS 0.006 0.001 HIS A1334 PHE 0.016 0.001 PHE F 92 TYR 0.017 0.001 TYR A 190 ARG 0.019 0.000 ARG B 905 *********************** 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 110 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 3.117 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: B 192 LEU cc_start: 0.9753 (tp) cc_final: 0.9372 (tp) REVERT: B 194 LEU cc_start: 0.9492 (mt) cc_final: 0.9177 (mt) REVERT: B 212 VAL cc_start: 0.9843 (m) cc_final: 0.9522 (p) REVERT: B 235 MET cc_start: 0.8284 (tpt) cc_final: 0.8032 (mmm) REVERT: B 274 MET cc_start: 0.9453 (tpp) cc_final: 0.9080 (tpp) REVERT: B 277 LEU cc_start: 0.9315 (mm) cc_final: 0.9076 (mm) REVERT: B 694 MET cc_start: 0.2075 (mmm) cc_final: 0.1704 (mmm) REVERT: A 214 LEU cc_start: 0.9506 (tp) cc_final: 0.9233 (tp) REVERT: A 274 MET cc_start: 0.8498 (tpt) cc_final: 0.8203 (tpt) REVERT: A 395 MET cc_start: 0.8909 (mmt) cc_final: 0.8618 (mmt) REVERT: A 462 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 631 MET cc_start: -0.1310 (ptt) cc_final: -0.2059 (ptt) REVERT: D 95 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8880 (tptt) REVERT: D 110 MET cc_start: 0.8503 (tpt) cc_final: 0.8093 (tmm) REVERT: D 183 GLU cc_start: 0.8535 (tp30) cc_final: 0.8125 (tp30) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.3933 time to fit residues: 72.4413 Evaluate side-chains 88 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 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 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23692 Z= 0.204 Angle : 0.580 7.223 32231 Z= 0.294 Chirality : 0.041 0.172 3644 Planarity : 0.005 0.152 4271 Dihedral : 4.647 33.954 3401 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3096 helix: 0.06 (0.18), residues: 881 sheet: -1.43 (0.21), residues: 568 loop : -1.30 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.007 0.001 HIS B 213 PHE 0.016 0.001 PHE F 92 TYR 0.019 0.002 TYR C 183 ARG 0.021 0.000 ARG B 905 *********************** 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 109 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9084 (tpp) cc_final: 0.8756 (tpp) REVERT: B 126 MET cc_start: 0.9623 (mmt) cc_final: 0.8966 (mmm) REVERT: B 192 LEU cc_start: 0.9748 (tp) cc_final: 0.9360 (tp) REVERT: B 194 LEU cc_start: 0.9518 (mt) cc_final: 0.9200 (mt) REVERT: B 212 VAL cc_start: 0.9850 (m) cc_final: 0.9541 (p) REVERT: B 274 MET cc_start: 0.9183 (tpp) cc_final: 0.8847 (tpp) REVERT: A 214 LEU cc_start: 0.9529 (tp) cc_final: 0.9228 (tp) REVERT: A 395 MET cc_start: 0.8914 (mmt) cc_final: 0.8545 (mmt) REVERT: A 462 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 631 MET cc_start: 0.0225 (ptt) cc_final: -0.0392 (ptt) REVERT: D 95 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8879 (tptt) REVERT: D 183 GLU cc_start: 0.8600 (tp30) cc_final: 0.8244 (tp30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3451 time to fit residues: 62.9713 Evaluate side-chains 87 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 175 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 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 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23692 Z= 0.162 Angle : 0.563 7.708 32231 Z= 0.282 Chirality : 0.042 0.153 3644 Planarity : 0.005 0.144 4271 Dihedral : 4.535 28.679 3401 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3096 helix: 0.20 (0.18), residues: 881 sheet: -1.24 (0.21), residues: 571 loop : -1.25 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 110 HIS 0.005 0.001 HIS A1334 PHE 0.015 0.001 PHE C 173 TYR 0.017 0.001 TYR C 183 ARG 0.018 0.000 ARG B 905 *********************** 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 115 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.690 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: B 192 LEU cc_start: 0.9741 (tp) cc_final: 0.9338 (tp) REVERT: B 194 LEU cc_start: 0.9510 (mt) cc_final: 0.9194 (mt) REVERT: B 212 VAL cc_start: 0.9850 (m) cc_final: 0.9522 (p) REVERT: B 274 MET cc_start: 0.9134 (tpp) cc_final: 0.8807 (tpp) REVERT: A 214 LEU cc_start: 0.9525 (tp) cc_final: 0.9205 (tp) REVERT: A 395 MET cc_start: 0.8894 (mmt) cc_final: 0.8527 (mmt) REVERT: A 462 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8141 (tm-30) REVERT: D 95 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8830 (tptt) REVERT: D 107 TYR cc_start: 0.8757 (m-10) cc_final: 0.8532 (m-10) REVERT: D 183 GLU cc_start: 0.8580 (tp30) cc_final: 0.8179 (tm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3469 time to fit residues: 66.9392 Evaluate side-chains 88 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 170 optimal weight: 40.0000 chunk 219 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 0.0470 chunk 137 optimal weight: 10.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23692 Z= 0.251 Angle : 0.611 8.358 32231 Z= 0.310 Chirality : 0.042 0.187 3644 Planarity : 0.005 0.148 4271 Dihedral : 4.661 25.894 3401 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3096 helix: 0.21 (0.18), residues: 896 sheet: -1.28 (0.21), residues: 564 loop : -1.25 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 110 HIS 0.007 0.001 HIS B 213 PHE 0.019 0.002 PHE F 92 TYR 0.014 0.002 TYR E 183 ARG 0.022 0.001 ARG B 905 *********************** 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 fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 LEU cc_start: 0.9725 (tp) cc_final: 0.9309 (tp) REVERT: B 194 LEU cc_start: 0.9537 (mt) cc_final: 0.9211 (mt) REVERT: B 274 MET cc_start: 0.9212 (tpp) cc_final: 0.8940 (tpp) REVERT: B 391 MET cc_start: 0.9023 (mmm) cc_final: 0.8653 (mmm) REVERT: D 95 LYS cc_start: 0.9227 (tmtt) cc_final: 0.8915 (tptt) REVERT: D 107 TYR cc_start: 0.8820 (m-10) cc_final: 0.8433 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3530 time to fit residues: 61.8822 Evaluate side-chains 81 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 40.0000 chunk 189 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23692 Z= 0.318 Angle : 0.720 11.325 32231 Z= 0.367 Chirality : 0.044 0.232 3644 Planarity : 0.006 0.172 4271 Dihedral : 5.175 24.035 3401 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 34.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 3096 helix: -0.05 (0.17), residues: 898 sheet: -1.46 (0.22), residues: 525 loop : -1.44 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 110 HIS 0.010 0.002 HIS B 213 PHE 0.026 0.003 PHE F 92 TYR 0.048 0.003 TYR C 34 ARG 0.022 0.001 ARG B 905 *********************** 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 100 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9674 (mmt) cc_final: 0.8976 (mmm) REVERT: B 275 LEU cc_start: 0.9260 (mm) cc_final: 0.9034 (mm) REVERT: B 391 MET cc_start: 0.9176 (mmm) cc_final: 0.8835 (mmm) REVERT: B 631 MET cc_start: -0.2592 (mmm) cc_final: -0.2982 (mmt) REVERT: A 126 MET cc_start: 0.8950 (mmt) cc_final: 0.8634 (mmt) REVERT: A 631 MET cc_start: 0.2918 (ppp) cc_final: 0.2609 (ppp) REVERT: D 95 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8934 (tptt) REVERT: D 144 ASP cc_start: 0.9254 (t70) cc_final: 0.9044 (p0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3836 time to fit residues: 63.1968 Evaluate side-chains 79 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 20.0000 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 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 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23692 Z= 0.300 Angle : 0.672 8.647 32231 Z= 0.343 Chirality : 0.043 0.225 3644 Planarity : 0.006 0.157 4271 Dihedral : 5.161 33.836 3401 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3096 helix: 0.01 (0.17), residues: 883 sheet: -1.53 (0.21), residues: 530 loop : -1.42 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 110 HIS 0.010 0.001 HIS B 213 PHE 0.022 0.002 PHE F 92 TYR 0.019 0.002 TYR C 183 ARG 0.021 0.001 ARG B 905 *********************** 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 98 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.916 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: B 126 MET cc_start: 0.9655 (mmt) cc_final: 0.9145 (mmm) REVERT: B 176 MET cc_start: 0.9345 (tpp) cc_final: 0.9049 (mmm) REVERT: B 391 MET cc_start: 0.9210 (mmm) cc_final: 0.8863 (mmm) REVERT: A 126 MET cc_start: 0.8776 (mmt) cc_final: 0.8435 (mmt) REVERT: A 631 MET cc_start: 0.2884 (ppp) cc_final: 0.2631 (ppp) REVERT: D 144 ASP cc_start: 0.9311 (t70) cc_final: 0.9070 (p0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3572 time to fit residues: 59.0704 Evaluate side-chains 80 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.8980 chunk 294 optimal weight: 10.0000 chunk 179 optimal weight: 0.1980 chunk 139 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 308 optimal weight: 0.2980 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 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 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23692 Z= 0.224 Angle : 0.625 9.138 32231 Z= 0.316 Chirality : 0.043 0.208 3644 Planarity : 0.005 0.132 4271 Dihedral : 4.976 30.472 3401 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3096 helix: 0.14 (0.18), residues: 892 sheet: -1.45 (0.22), residues: 517 loop : -1.39 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 110 HIS 0.008 0.001 HIS B 213 PHE 0.027 0.002 PHE A 775 TYR 0.033 0.002 TYR C 201 ARG 0.017 0.001 ARG B 905 ********************** 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 104 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9330 (tpp) cc_final: 0.9105 (tpp) REVERT: B 176 MET cc_start: 0.9363 (tpp) cc_final: 0.9062 (mmm) REVERT: B 391 MET cc_start: 0.9203 (mmm) cc_final: 0.8837 (mmm) REVERT: A 126 MET cc_start: 0.9062 (mmt) cc_final: 0.8569 (mmt) REVERT: A 631 MET cc_start: 0.3284 (ppp) cc_final: 0.3030 (ppp) REVERT: D 95 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8826 (tptt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3582 time to fit residues: 62.0530 Evaluate side-chains 80 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 246 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 380 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 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 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 = 0.3834 r_free = 0.3834 target = 0.070055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.042109 restraints weight = 174551.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042150 restraints weight = 160170.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.042772 restraints weight = 133570.336| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23692 Z= 0.190 Angle : 0.609 10.463 32231 Z= 0.305 Chirality : 0.043 0.223 3644 Planarity : 0.005 0.098 4271 Dihedral : 4.836 30.111 3401 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 3096 helix: 0.25 (0.18), residues: 887 sheet: -1.52 (0.20), residues: 578 loop : -1.29 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 110 HIS 0.008 0.001 HIS B 213 PHE 0.023 0.002 PHE B 775 TYR 0.018 0.002 TYR C 201 ARG 0.012 0.000 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.66 seconds wall clock time: 71 minutes 21.63 seconds (4281.63 seconds total)