Starting phenix.real_space_refine on Wed Dec 13 00:28:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/12_2023/7m7j_23715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/12_2023/7m7j_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_23715/12_2023/7m7j_23715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/12_2023/7m7j_23715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/12_2023/7m7j_23715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7j_23715/12_2023/7m7j_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-1.21rc1-5172/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: 11.98, per 1000 atoms: 0.52 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: 8.99 Conformation dependent library (CDL) restraints added in 4.4 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: 2.91 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: 9.31 Time building geometry restraints manager: 9.72 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.000 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 62.210 Find NCS groups from input model: 0.930 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.130 ------------------------------------------------------------------------------- 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 outliers start: 121 outliers final: 21 residues processed: 231 average time/residue: 0.3900 time to fit residues: 139.2632 Evaluate side-chains 117 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3980 time to fit residues: 16.0007 ------------------------------------------------------------------------------- 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: 0.1980 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 HIS A 300 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23692 Z= 0.291 Angle : 0.690 8.350 32231 Z= 0.354 Chirality : 0.043 0.163 3644 Planarity : 0.006 0.151 4271 Dihedral : 4.968 29.481 3401 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 0.29 % Allowed : 7.13 % Favored : 92.58 % 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: -1.77 (0.15), residues: 3096 helix: -0.49 (0.18), residues: 841 sheet: -1.35 (0.22), residues: 510 loop : -1.46 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A1314 HIS 0.007 0.001 HIS A1334 PHE 0.020 0.002 PHE A 784 TYR 0.021 0.002 TYR E 183 ARG 0.024 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 121 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 121 average time/residue: 0.3438 time to fit residues: 70.7629 Evaluate side-chains 85 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2052 time to fit residues: 4.5828 ------------------------------------------------------------------------------- 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: 0.0470 chunk 87 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- 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 322 GLN B 375 ASN ** B 380 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 217 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23692 Z= 0.221 Angle : 0.612 12.391 32231 Z= 0.311 Chirality : 0.042 0.189 3644 Planarity : 0.005 0.157 4271 Dihedral : 4.799 28.103 3401 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -1.66 (0.15), residues: 3096 helix: -0.27 (0.18), residues: 858 sheet: -1.45 (0.21), residues: 539 loop : -1.40 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 55 HIS 0.007 0.001 HIS B 213 PHE 0.029 0.002 PHE D 92 TYR 0.022 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: 0 poor density : 113 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.3391 time to fit residues: 63.9725 Evaluate side-chains 79 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6640 ------------------------------------------------------------------------------- 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: 10.0000 chunk 212 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 299 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 268 optimal weight: 0.3980 chunk 80 optimal weight: 30.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 316 GLN B 322 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** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23692 Z= 0.301 Angle : 0.661 7.570 32231 Z= 0.341 Chirality : 0.042 0.180 3644 Planarity : 0.006 0.167 4271 Dihedral : 4.923 33.586 3401 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.62 % 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: -1.67 (0.15), residues: 3096 helix: -0.22 (0.18), residues: 874 sheet: -1.50 (0.20), residues: 552 loop : -1.42 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 55 HIS 0.006 0.001 HIS B 91 PHE 0.028 0.002 PHE F 92 TYR 0.022 0.002 TYR E 183 ARG 0.025 0.001 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 113 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.3459 time to fit residues: 65.2335 Evaluate side-chains 81 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2228 time to fit residues: 3.8106 ------------------------------------------------------------------------------- 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: 3.9990 chunk 170 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 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** D 59 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3661 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= 0.209 Angle : 0.597 6.959 32231 Z= 0.303 Chirality : 0.042 0.177 3644 Planarity : 0.005 0.165 4271 Dihedral : 4.764 27.113 3401 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -1.45 (0.15), residues: 3096 helix: 0.01 (0.18), residues: 883 sheet: -1.28 (0.21), residues: 544 loop : -1.36 (0.15), residues: 1669 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 0.020 0.002 PHE F 92 TYR 0.017 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 106 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3499 time to fit residues: 62.6080 Evaluate side-chains 83 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4344 ------------------------------------------------------------------------------- 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: 10.0000 chunk 269 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 25 GLN A 158 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23692 Z= 0.188 Angle : 0.586 7.463 32231 Z= 0.296 Chirality : 0.042 0.174 3644 Planarity : 0.005 0.156 4271 Dihedral : 4.686 27.470 3401 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.18), residues: 903 sheet: -1.14 (0.21), residues: 542 loop : -1.33 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 110 HIS 0.006 0.001 HIS A1259 PHE 0.016 0.001 PHE F 92 TYR 0.016 0.002 TYR C 183 ARG 0.020 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 105 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3567 time to fit residues: 63.6736 Evaluate side-chains 82 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4784 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 169 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 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 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: 0.7636 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23692 Z= 0.283 Angle : 0.662 8.550 32231 Z= 0.338 Chirality : 0.043 0.188 3644 Planarity : 0.006 0.167 4271 Dihedral : 4.904 23.118 3401 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.50 (0.15), residues: 3096 helix: -0.01 (0.18), residues: 904 sheet: -1.35 (0.21), residues: 520 loop : -1.41 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 110 HIS 0.008 0.001 HIS B 213 PHE 0.022 0.002 PHE F 92 TYR 0.026 0.002 TYR C 34 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 100 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3701 time to fit residues: 62.8609 Evaluate side-chains 77 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7540 ------------------------------------------------------------------------------- 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: 1.9990 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 147 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 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** B 834 HIS ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23692 Z= 0.315 Angle : 0.705 10.997 32231 Z= 0.360 Chirality : 0.044 0.244 3644 Planarity : 0.006 0.168 4271 Dihedral : 5.237 38.478 3401 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 33.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -1.68 (0.15), residues: 3096 helix: -0.17 (0.17), residues: 902 sheet: -1.58 (0.22), residues: 507 loop : -1.48 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 110 HIS 0.015 0.002 HIS A 213 PHE 0.025 0.002 PHE F 92 TYR 0.021 0.002 TYR C 183 ARG 0.021 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 95 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.752 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3659 time to fit residues: 59.3480 Evaluate side-chains 72 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6658 ------------------------------------------------------------------------------- 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: 0.0270 chunk 286 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 121 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 0.1980 overall best weight: 3.2444 ------------------------------------------------------------------------------- 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 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 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: 0.7673 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23692 Z= 0.245 Angle : 0.642 8.724 32231 Z= 0.326 Chirality : 0.043 0.237 3644 Planarity : 0.006 0.153 4271 Dihedral : 5.060 33.182 3401 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.55 (0.15), residues: 3096 helix: 0.05 (0.18), residues: 889 sheet: -1.56 (0.22), residues: 512 loop : -1.44 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 110 HIS 0.008 0.001 HIS B 213 PHE 0.024 0.002 PHE F 92 TYR 0.025 0.002 TYR C 201 ARG 0.019 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 97 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.606 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3636 time to fit residues: 60.1848 Evaluate side-chains 74 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5651 ------------------------------------------------------------------------------- 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: 4.9990 chunk 294 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 308 optimal weight: 0.0980 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 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: 0.7654 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23692 Z= 0.204 Angle : 0.618 9.847 32231 Z= 0.311 Chirality : 0.043 0.210 3644 Planarity : 0.005 0.123 4271 Dihedral : 4.912 30.902 3401 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.44 % 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: -1.46 (0.15), residues: 3096 helix: 0.12 (0.18), residues: 896 sheet: -1.53 (0.21), residues: 523 loop : -1.37 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 110 HIS 0.006 0.001 HIS B 213 PHE 0.022 0.002 PHE F 92 TYR 0.020 0.002 TYR C 34 ARG 0.015 0.000 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 101 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.813 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3587 time to fit residues: 61.3823 Evaluate side-chains 81 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7884 ------------------------------------------------------------------------------- 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: 8.9990 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.068054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.039604 restraints weight = 180684.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.040402 restraints weight = 154985.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.040412 restraints weight = 124326.307| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23692 Z= 0.298 Angle : 0.685 16.105 32231 Z= 0.348 Chirality : 0.043 0.236 3644 Planarity : 0.006 0.115 4271 Dihedral : 5.083 31.625 3401 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.55 (0.15), residues: 3096 helix: 0.03 (0.18), residues: 897 sheet: -1.65 (0.21), residues: 533 loop : -1.38 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 110 HIS 0.009 0.001 HIS B 213 PHE 0.021 0.002 PHE B 775 TYR 0.020 0.002 TYR C 34 ARG 0.016 0.001 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.80 seconds wall clock time: 71 minutes 27.66 seconds (4287.66 seconds total)