Starting phenix.real_space_refine on Wed Mar 20 05:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7g_23712/03_2024/7m7g_23712.pdb" } resolution = 4.1 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= 0.077 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 94 5.16 5 C 16523 2.51 5 N 4758 2.21 5 O 5105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1356, 10046 Classifications: {'peptide': 1356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 70, 'TRANS': 1285} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 10220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10220 Classifications: {'peptide': 1379} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 73, 'TRANS': 1305} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Time building chain proxies: 13.89, per 1000 atoms: 0.52 Number of scatterers: 26480 At special positions: 0 Unit cell: (138, 156, 150, 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 94 16.00 O 5105 8.00 N 4758 7.00 C 16523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.00 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.06 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " distance=2.02 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: 9.98 Conformation dependent library (CDL) restraints added in 5.2 seconds 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6412 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 42 sheets defined 31.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 50 through 59 removed outlier: 3.859A pdb=" N TRP A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.678A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.763A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 5.497A 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 221 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.586A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.578A pdb=" N ILE A 334 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.577A pdb=" N ILE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 4.032A pdb=" N ARG A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.407A 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 384 through 398 removed outlier: 3.611A pdb=" N ILE A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.596A pdb=" N LEU A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.119A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 578' Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 623 through 642 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 657 through 666 removed outlier: 3.820A pdb=" N CYS A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 688 removed outlier: 3.972A 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: 3.875A pdb=" N CYS A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.933A 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 822 Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.926A pdb=" N VAL A 887 " --> pdb=" O ASP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.676A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 998 removed outlier: 3.524A pdb=" N ARG A 993 " --> pdb=" O GLU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1020 Processing helix chain 'A' and resid 1021 through 1038 removed outlier: 3.570A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.805A pdb=" N GLY A1065 " --> pdb=" O ASN A1061 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1105 removed outlier: 3.594A pdb=" N ALA A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.970A 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 1153 Processing helix chain 'A' and resid 1154 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 1215 Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1248 through 1263 removed outlier: 3.657A pdb=" N VAL A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1303 removed outlier: 3.508A pdb=" N ASN A1292 " --> pdb=" O TYR A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 removed outlier: 3.844A pdb=" N ARG A1333 " --> pdb=" O ASP A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1354 removed outlier: 5.101A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 removed outlier: 4.808A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.673A pdb=" N PHE A1382 " --> pdb=" O THR A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1389 removed outlier: 3.565A pdb=" N ALA A1388 " --> pdb=" O ILE A1385 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A1389 " --> pdb=" O ASP A1386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1385 through 1389' Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.655A pdb=" N ARG B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 removed outlier: 3.619A pdb=" N SER B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.553A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.648A pdb=" N LEU B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 181 through 192 removed outlier: 4.189A pdb=" N SER B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.550A 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 220 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.790A 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 389 through 394 Processing helix chain 'B' and resid 481 through 489 removed outlier: 3.742A pdb=" N ARG B 486 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.678A pdb=" N THR B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 removed outlier: 3.789A pdb=" N SER B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.678A pdb=" N ALA B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 602 through 608 Processing helix chain 'B' and resid 609 through 614 removed outlier: 3.607A pdb=" N GLU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 667 removed outlier: 3.637A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 686 Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.862A pdb=" N VAL B 704 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 Processing helix chain 'B' and resid 801 through 807 Processing helix chain 'B' and resid 812 through 823 removed outlier: 3.532A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.704A pdb=" N ALA B 840 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 843 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 879 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.803A pdb=" N VAL B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 888 " --> pdb=" O TRP B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 888' Processing helix chain 'B' and resid 959 through 967 removed outlier: 3.676A pdb=" N THR B 963 " --> pdb=" O ASP B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 998 Processing helix chain 'B' and resid 1021 through 1038 removed outlier: 3.535A pdb=" N ALA B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1078 removed outlier: 3.806A pdb=" N GLY B1065 " --> pdb=" O ASN B1061 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B1066 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP B1068 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B1075 " --> pdb=" O GLY B1071 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B1076 " --> pdb=" O ARG B1072 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1105 removed outlier: 3.594A pdb=" N ALA B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA B1102 " --> pdb=" O ARG B1098 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1153 Processing helix chain 'B' and resid 1154 through 1164 Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'B' and resid 1204 through 1215 Processing helix chain 'B' and resid 1240 through 1248 Processing helix chain 'B' and resid 1248 through 1262 removed outlier: 3.717A pdb=" N VAL B1252 " --> pdb=" O SER B1248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B1254 " --> pdb=" O ALA B1250 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1304 removed outlier: 3.508A pdb=" N ASN B1292 " --> pdb=" O TYR B1288 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B1304 " --> pdb=" O GLN B1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1333 removed outlier: 3.844A pdb=" N ARG B1333 " --> pdb=" O ASP B1329 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1354 removed outlier: 5.101A pdb=" N ARG B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1365 through 1374 removed outlier: 4.808A pdb=" N LEU B1371 " --> pdb=" O ASP B1367 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B1372 " --> pdb=" O ARG B1368 " (cutoff:3.500A) Processing helix chain 'B' and resid 1379 through 1383 removed outlier: 3.674A pdb=" N PHE B1382 " --> pdb=" O THR B1379 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1389 removed outlier: 3.564A pdb=" N ALA B1388 " --> pdb=" O ILE B1385 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B1389 " --> pdb=" O ASP B1386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1385 through 1389' Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.551A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 150 removed outlier: 3.575A pdb=" N LEU D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.859A pdb=" N TYR D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) 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 209 removed outlier: 3.848A pdb=" N TYR F 208 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.597A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 276 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET A 40 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET A 274 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS A 42 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 272 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 199 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 200 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 437 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP B 335 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY B 370 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 337 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.863A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.730A pdb=" N PHE A 524 " --> pdb=" O TRP A 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA7, first strand: chain 'A' and resid 693 through 695 removed outlier: 5.600A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 935 through 936 removed outlier: 6.196A pdb=" N LEU A1043 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A1086 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A1045 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1088 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N THR A1047 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A1007 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLU A1048 " --> pdb=" O LEU A1007 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 948 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A1004 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 950 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A1006 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA A 952 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A1008 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 979 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1145 through 1146 removed outlier: 6.783A pdb=" N PHE A1225 " --> pdb=" O THR A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1172 removed outlier: 6.269A pdb=" N LEU A1168 " --> pdb=" O THR A1196 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA A1198 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A1170 " --> pdb=" O ALA A1198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1272 through 1275 removed outlier: 6.592A pdb=" N LEU A1272 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A1314 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A1361 " --> pdb=" O ALA A1311 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A1313 " --> pdb=" O VAL A1361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1336 through 1337 removed outlier: 4.185A pdb=" N ASP A1363 " --> pdb=" O ILE A1337 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 479 Processing sheet with id=AB6, first strand: chain 'B' and resid 649 through 654 removed outlier: 7.291A pdb=" N ALA B 558 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 652 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 560 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY B 654 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE B 562 " --> pdb=" O GLY B 654 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL B 559 " --> pdb=" O LEU B 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 719 removed outlier: 5.113A pdb=" N ILE B 714 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ALA B 726 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 696 " --> pdb=" O LYS B 747 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 747 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 935 through 936 removed outlier: 6.196A pdb=" N LEU B1043 " --> pdb=" O GLY B1084 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B1086 " --> pdb=" O LEU B1043 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B1045 " --> pdb=" O VAL B1086 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B1088 " --> pdb=" O THR B1045 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N THR B1047 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B1007 " --> pdb=" O VAL B1046 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU B1048 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR B 948 " --> pdb=" O GLY B1002 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU B1004 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 950 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B1006 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA B 952 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B1008 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 979 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1145 through 1146 removed outlier: 6.783A pdb=" N PHE B1225 " --> pdb=" O THR B1146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1170 through 1172 removed outlier: 6.384A pdb=" N LEU B1170 " --> pdb=" O ALA B1198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 1271 through 1275 removed outlier: 6.483A pdb=" N LEU B1272 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP B1314 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER B1274 " --> pdb=" O TRP B1314 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B1361 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA B1313 " --> pdb=" O VAL B1361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 1336 through 1337 removed outlier: 4.187A pdb=" N ASP B1363 " --> pdb=" O ILE B1337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AC5, first strand: chain 'C' and resid 12 through 14 removed outlier: 5.811A pdb=" N GLY C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.676A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.554A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.720A pdb=" N SER C 160 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 204 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 201 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 218 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AD1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AD2, first strand: chain 'D' and resid 74 through 75 removed outlier: 6.450A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 138 through 140 removed outlier: 5.559A pdb=" N SER D 153 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU D 203 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 155 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU D 201 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU D 157 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 199 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN D 159 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 197 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.678A pdb=" N GLU D 217 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AD7, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.146A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.564A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 159 through 161 removed outlier: 4.338A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 218 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.839A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 46 through 47 removed outlier: 3.760A pdb=" N TYR F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 136 through 140 removed outlier: 5.612A pdb=" N LEU F 157 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER F 199 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN F 159 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU F 197 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER F 196 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.630A pdb=" N GLU F 217 " --> pdb=" O GLN F 169 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 10.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 170 1.21 - 1.36: 9125 1.36 - 1.52: 8928 1.52 - 1.67: 8642 1.67 - 1.82: 146 Bond restraints: 27011 Sorted by residual: bond pdb=" CA SER B 442 " pdb=" CB SER B 442 " ideal model delta sigma weight residual 1.532 1.304 0.227 1.58e-02 4.01e+03 2.07e+02 bond pdb=" CA SER B 207 " pdb=" CB SER B 207 " ideal model delta sigma weight residual 1.530 1.283 0.248 1.75e-02 3.27e+03 2.01e+02 bond pdb=" C PRO A 197 " pdb=" O PRO A 197 " ideal model delta sigma weight residual 1.235 1.062 0.173 1.30e-02 5.92e+03 1.77e+02 bond pdb=" C SER B 442 " pdb=" O SER B 442 " ideal model delta sigma weight residual 1.235 1.094 0.141 1.12e-02 7.97e+03 1.59e+02 bond pdb=" C VAL B 440 " pdb=" O VAL B 440 " ideal model delta sigma weight residual 1.237 1.099 0.138 1.11e-02 8.12e+03 1.55e+02 ... (remaining 27006 not shown) Histogram of bond angle deviations from ideal: 78.14 - 89.46: 7 89.46 - 100.78: 105 100.78 - 112.10: 13220 112.10 - 123.42: 20806 123.42 - 134.74: 2613 Bond angle restraints: 36751 Sorted by residual: angle pdb=" N PRO B 162 " pdb=" CA PRO B 162 " pdb=" CB PRO B 162 " ideal model delta sigma weight residual 103.32 83.47 19.85 8.40e-01 1.42e+00 5.58e+02 angle pdb=" C GLU B 159 " pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " ideal model delta sigma weight residual 110.19 78.14 32.05 1.62e+00 3.81e-01 3.91e+02 angle pdb=" CA PHE A 266 " pdb=" CB PHE A 266 " pdb=" CG PHE A 266 " ideal model delta sigma weight residual 113.80 131.56 -17.76 1.00e+00 1.00e+00 3.15e+02 angle pdb=" C PRO A 902 " pdb=" CA PRO A 902 " pdb=" CB PRO A 902 " ideal model delta sigma weight residual 111.56 86.58 24.98 1.65e+00 3.67e-01 2.29e+02 angle pdb=" C ARG E 102 " pdb=" CA ARG E 102 " pdb=" CB ARG E 102 " ideal model delta sigma weight residual 112.12 89.92 22.20 1.50e+00 4.44e-01 2.19e+02 ... (remaining 36746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 14024 20.25 - 40.50: 1342 40.50 - 60.75: 695 60.75 - 81.01: 49 81.01 - 101.26: 19 Dihedral angle restraints: 16129 sinusoidal: 6106 harmonic: 10023 Sorted by residual: dihedral pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta harmonic sigma weight residual 180.00 78.74 101.26 0 5.00e+00 4.00e-02 4.10e+02 dihedral pdb=" CA GLU E 155 " pdb=" C GLU E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual 180.00 78.83 101.17 0 5.00e+00 4.00e-02 4.09e+02 dihedral pdb=" CA THR F 115 " pdb=" C THR F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 180.00 85.77 94.23 0 5.00e+00 4.00e-02 3.55e+02 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3645 0.148 - 0.297: 448 0.297 - 0.445: 54 0.445 - 0.594: 6 0.594 - 0.742: 2 Chirality restraints: 4155 Sorted by residual: chirality pdb=" CB VAL B 232 " pdb=" CA VAL B 232 " pdb=" CG1 VAL B 232 " pdb=" CG2 VAL B 232 " both_signs ideal model delta sigma weight residual False -2.63 -1.89 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -1.97 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA LYS F 205 " pdb=" N LYS F 205 " pdb=" C LYS F 205 " pdb=" CB LYS F 205 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.97e+00 ... (remaining 4152 not shown) Planarity restraints: 4862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 799 " 0.039 2.00e-02 2.50e+03 8.27e-02 6.84e+01 pdb=" CG ASP B 799 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASP B 799 " 0.052 2.00e-02 2.50e+03 pdb=" OD2 ASP B 799 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 545 " 0.033 2.00e-02 2.50e+03 6.83e-02 4.67e+01 pdb=" C ASP A 545 " -0.118 2.00e-02 2.50e+03 pdb=" O ASP A 545 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY A 546 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 96 " -0.031 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ALA E 96 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA E 96 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL E 97 " -0.036 2.00e-02 2.50e+03 ... (remaining 4859 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 54 2.38 - 3.01: 15033 3.01 - 3.64: 41901 3.64 - 4.27: 68505 4.27 - 4.90: 109971 Nonbonded interactions: 235464 Sorted by model distance: nonbonded pdb=" O GLU B 159 " pdb=" CB GLU B 159 " model vdw 1.751 2.752 nonbonded pdb=" O PRO A 902 " pdb=" CB PRO A 902 " model vdw 1.948 2.752 nonbonded pdb=" N THR C 101 " pdb=" OG1 THR C 101 " model vdw 1.953 2.496 nonbonded pdb=" O ARG C 102 " pdb=" CB ARG C 102 " model vdw 2.022 2.752 nonbonded pdb=" O ARG E 102 " pdb=" CB ARG E 102 " model vdw 2.054 2.752 ... (remaining 235459 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 'A' and (resid 1 through 1125 or resid 1137 through 1390)) selection = (chain 'B' and (resid 1 through 666 or resid 675 through 767 or resid 784 throug \ h 928 or (resid 929 and (name N or name CA or name C or name O or name CB )) or \ resid 930 through 1390)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 through 209 or resid 215 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.230 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 70.810 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.140 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 27011 Z= 0.801 Angle : 1.671 32.047 36751 Z= 1.165 Chirality : 0.097 0.742 4155 Planarity : 0.009 0.139 4862 Dihedral : 19.685 101.257 9693 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.09 % Favored : 90.88 % Rotamer: Outliers : 18.86 % Allowed : 6.73 % Favored : 74.41 % Cbeta Deviations : 1.84 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.12), residues: 3521 helix: -3.08 (0.12), residues: 1005 sheet: -2.48 (0.19), residues: 582 loop : -2.77 (0.12), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP B 642 HIS 0.014 0.002 HIS F 220 PHE 0.100 0.003 PHE A 266 TYR 0.040 0.003 TYR E 99 ARG 0.018 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 513 poor density : 574 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8710 (tp) cc_final: 0.8478 (tp) REVERT: A 97 PHE cc_start: 0.4918 (m-80) cc_final: 0.4480 (m-80) REVERT: A 123 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6099 (mt0) REVERT: A 142 THR cc_start: 0.7297 (p) cc_final: 0.7065 (t) REVERT: A 205 CYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6303 (m) REVERT: A 240 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6361 (mmm) REVERT: A 530 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6597 (p) REVERT: A 549 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6999 (m) REVERT: A 631 MET cc_start: -0.3791 (ttp) cc_final: -0.5090 (ptm) REVERT: A 635 MET cc_start: -0.2974 (ttm) cc_final: -0.4221 (ttt) REVERT: A 643 ARG cc_start: 0.1919 (OUTLIER) cc_final: 0.1313 (ttp80) REVERT: A 826 ARG cc_start: 0.3186 (OUTLIER) cc_final: 0.2857 (mmm160) REVERT: A 853 SER cc_start: 0.4093 (OUTLIER) cc_final: 0.3163 (p) REVERT: A 901 TYR cc_start: 0.6219 (t80) cc_final: 0.5964 (t80) REVERT: A 1010 ASP cc_start: 0.5838 (OUTLIER) cc_final: 0.5311 (m-30) REVERT: A 1237 ASP cc_start: 0.3529 (OUTLIER) cc_final: 0.2401 (t0) REVERT: A 1367 ASP cc_start: 0.5335 (OUTLIER) cc_final: 0.4822 (p0) REVERT: A 1371 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5020 (mt) REVERT: B 214 LEU cc_start: 0.8563 (mt) cc_final: 0.8360 (tp) REVERT: B 290 VAL cc_start: 0.7638 (t) cc_final: 0.7412 (m) REVERT: B 380 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: B 392 VAL cc_start: 0.7444 (t) cc_final: 0.7204 (t) REVERT: B 403 THR cc_start: 0.7218 (m) cc_final: 0.6879 (t) REVERT: B 461 VAL cc_start: 0.6561 (OUTLIER) cc_final: 0.6281 (t) REVERT: B 688 MET cc_start: 0.1746 (mpp) cc_final: 0.1102 (mtt) REVERT: B 694 MET cc_start: -0.1533 (mmm) cc_final: -0.4654 (ttt) REVERT: B 794 GLN cc_start: 0.5810 (OUTLIER) cc_final: 0.5388 (tp40) REVERT: B 1237 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: B 1240 THR cc_start: 0.2119 (OUTLIER) cc_final: 0.1843 (t) REVERT: B 1261 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6324 (tp) REVERT: B 1339 MET cc_start: -0.0001 (OUTLIER) cc_final: -0.0652 (ptt) REVERT: C 4 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.6126 (t) REVERT: C 16 PRO cc_start: 0.6615 (Cg_exo) cc_final: 0.6387 (Cg_endo) REVERT: D 95 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6166 (mtmt) REVERT: E 14 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.7880 (m) REVERT: E 30 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.5979 (p) REVERT: E 158 THR cc_start: 0.1484 (OUTLIER) cc_final: 0.1005 (m) REVERT: F 36 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5660 (m) outliers start: 513 outliers final: 100 residues processed: 977 average time/residue: 0.4482 time to fit residues: 647.3069 Evaluate side-chains 419 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 294 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1226 HIS B1349 GLN ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 178 GLN D 114 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN F 74 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27011 Z= 0.246 Angle : 0.739 8.604 36751 Z= 0.379 Chirality : 0.045 0.227 4155 Planarity : 0.007 0.108 4862 Dihedral : 5.664 57.754 3876 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 0.33 % Allowed : 4.85 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.13), residues: 3521 helix: -1.94 (0.15), residues: 1004 sheet: -2.00 (0.19), residues: 599 loop : -2.27 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 569 HIS 0.012 0.001 HIS A 856 PHE 0.031 0.002 PHE C 173 TYR 0.053 0.002 TYR D 51 ARG 0.015 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 388 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.4636 (m-80) cc_final: 0.4279 (m-80) REVERT: A 278 GLU cc_start: 0.5871 (tt0) cc_final: 0.5093 (tt0) REVERT: B 694 MET cc_start: -0.1641 (mmm) cc_final: -0.4901 (ttt) REVERT: C 16 PRO cc_start: 0.6622 (Cg_exo) cc_final: 0.6267 (Cg_endo) REVERT: C 85 LEU cc_start: 0.6100 (tp) cc_final: 0.4562 (tp) outliers start: 9 outliers final: 0 residues processed: 397 average time/residue: 0.3972 time to fit residues: 249.2111 Evaluate side-chains 242 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 256 optimal weight: 30.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 556 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN A1349 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1257 ASN ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 182 GLN F 188 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 27011 Z= 0.535 Angle : 0.946 13.132 36751 Z= 0.488 Chirality : 0.048 0.237 4155 Planarity : 0.008 0.077 4862 Dihedral : 6.124 54.731 3876 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 31.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 0.40 % Allowed : 6.40 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.04 % 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: -2.71 (0.13), residues: 3521 helix: -1.50 (0.15), residues: 1024 sheet: -1.63 (0.20), residues: 581 loop : -2.02 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 38 HIS 0.027 0.003 HIS A 405 PHE 0.028 0.003 PHE B 785 TYR 0.063 0.004 TYR C 183 ARG 0.014 0.001 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8224 (mt) cc_final: 0.8014 (mt) REVERT: A 572 MET cc_start: -0.1314 (tpp) cc_final: -0.1555 (tpp) REVERT: A 631 MET cc_start: -0.5330 (ptm) cc_final: -0.5590 (ptm) REVERT: B 694 MET cc_start: -0.1192 (mmm) cc_final: -0.4796 (ttt) REVERT: C 4 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.7120 (p) REVERT: F 54 LEU cc_start: 0.7903 (tp) cc_final: 0.7696 (tp) outliers start: 11 outliers final: 4 residues processed: 284 average time/residue: 0.3764 time to fit residues: 171.0070 Evaluate side-chains 187 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.9980 chunk 240 optimal weight: 0.4980 chunk 166 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 321 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A 904 GLN A1061 ASN A1064 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1257 ASN ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27011 Z= 0.195 Angle : 0.648 7.914 36751 Z= 0.330 Chirality : 0.044 0.168 4155 Planarity : 0.005 0.070 4862 Dihedral : 5.367 50.572 3876 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -2.18 (0.14), residues: 3521 helix: -0.85 (0.16), residues: 1000 sheet: -1.48 (0.20), residues: 612 loop : -1.75 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 74 HIS 0.007 0.001 HIS A 856 PHE 0.025 0.002 PHE A 583 TYR 0.028 0.002 TYR E 183 ARG 0.007 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 MET cc_start: 0.6046 (mtt) cc_final: 0.5449 (mtt) REVERT: B 392 VAL cc_start: 0.7918 (t) cc_final: 0.7626 (t) REVERT: B 694 MET cc_start: -0.1381 (mmm) cc_final: -0.4852 (ttt) REVERT: B 1322 MET cc_start: 0.5029 (mmt) cc_final: 0.4799 (mmt) REVERT: F 127 ASP cc_start: 0.4470 (p0) cc_final: 0.4158 (p0) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 0.3680 time to fit residues: 176.7414 Evaluate side-chains 194 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 253 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 235 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 305 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27011 Z= 0.236 Angle : 0.631 9.292 36751 Z= 0.322 Chirality : 0.043 0.191 4155 Planarity : 0.005 0.066 4862 Dihedral : 5.133 43.016 3876 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.87 (0.14), residues: 3521 helix: -0.43 (0.16), residues: 994 sheet: -1.46 (0.20), residues: 606 loop : -1.59 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 909 HIS 0.005 0.001 HIS A 856 PHE 0.020 0.002 PHE A 583 TYR 0.022 0.002 TYR E 183 ARG 0.022 0.000 ARG B 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ILE cc_start: 0.8209 (mt) cc_final: 0.7747 (mt) REVERT: B 320 ILE cc_start: 0.8954 (pt) cc_final: 0.8609 (pt) REVERT: B 694 MET cc_start: -0.1040 (mmm) cc_final: -0.4742 (ttt) REVERT: B 1322 MET cc_start: 0.5054 (mmt) cc_final: 0.4792 (mmt) REVERT: E 39 VAL cc_start: 0.8250 (t) cc_final: 0.7996 (m) REVERT: F 110 MET cc_start: 0.6952 (tmm) cc_final: 0.6604 (tmm) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.3639 time to fit residues: 158.6107 Evaluate side-chains 185 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 40.0000 chunk 306 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 282 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 27011 Z= 0.282 Angle : 0.661 9.783 36751 Z= 0.336 Chirality : 0.043 0.169 4155 Planarity : 0.005 0.071 4862 Dihedral : 5.152 45.119 3876 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.71 (0.14), residues: 3521 helix: -0.24 (0.16), residues: 1006 sheet: -1.36 (0.21), residues: 608 loop : -1.54 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.006 0.001 HIS A 451 PHE 0.024 0.002 PHE F 92 TYR 0.034 0.002 TYR E 98 ARG 0.008 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 ILE cc_start: 0.8928 (pt) cc_final: 0.8605 (pt) REVERT: B 694 MET cc_start: -0.0973 (mmm) cc_final: -0.4703 (ttt) REVERT: B 1322 MET cc_start: 0.5165 (mmt) cc_final: 0.4787 (mmt) REVERT: C 85 LEU cc_start: 0.5838 (tp) cc_final: 0.4776 (tp) REVERT: F 96 ILE cc_start: 0.8595 (mm) cc_final: 0.8394 (mp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3669 time to fit residues: 149.4981 Evaluate side-chains 173 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 192 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 339 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1349 GLN B 340 HIS ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN C 178 GLN E 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27011 Z= 0.184 Angle : 0.612 11.767 36751 Z= 0.307 Chirality : 0.042 0.168 4155 Planarity : 0.005 0.067 4862 Dihedral : 4.913 43.178 3876 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.56 (0.14), residues: 3521 helix: -0.11 (0.16), residues: 1031 sheet: -1.29 (0.21), residues: 622 loop : -1.46 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1366 HIS 0.004 0.001 HIS A1334 PHE 0.021 0.002 PHE F 92 TYR 0.027 0.001 TYR E 183 ARG 0.016 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 SER cc_start: 0.8860 (m) cc_final: 0.8239 (t) REVERT: A 511 LEU cc_start: 0.8014 (pp) cc_final: 0.7673 (tp) REVERT: B 320 ILE cc_start: 0.8886 (pt) cc_final: 0.8540 (pt) REVERT: B 395 MET cc_start: 0.6259 (tpp) cc_final: 0.5899 (ttt) REVERT: B 694 MET cc_start: -0.1284 (mmm) cc_final: -0.4768 (ttt) REVERT: B 1322 MET cc_start: 0.5154 (mmt) cc_final: 0.4802 (mmt) REVERT: D 110 MET cc_start: 0.7571 (tpp) cc_final: 0.7320 (tpp) REVERT: F 96 ILE cc_start: 0.8722 (mm) cc_final: 0.8372 (mp) REVERT: F 207 ASP cc_start: 0.4988 (p0) cc_final: 0.4597 (p0) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.3698 time to fit residues: 164.0499 Evaluate side-chains 174 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 30.0000 chunk 231 optimal weight: 0.0670 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 chunk 266 optimal weight: 10.0000 overall best weight: 1.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27011 Z= 0.253 Angle : 0.635 8.034 36751 Z= 0.322 Chirality : 0.042 0.162 4155 Planarity : 0.005 0.066 4862 Dihedral : 4.978 44.132 3876 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.53 (0.14), residues: 3521 helix: -0.07 (0.16), residues: 1043 sheet: -1.31 (0.21), residues: 636 loop : -1.44 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1366 HIS 0.004 0.001 HIS B 340 PHE 0.018 0.002 PHE D 120 TYR 0.022 0.002 TYR E 183 ARG 0.016 0.000 ARG A1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.6825 (tpp) cc_final: 0.6427 (tpp) REVERT: A 207 SER cc_start: 0.8902 (m) cc_final: 0.8261 (t) REVERT: A 511 LEU cc_start: 0.7972 (pp) cc_final: 0.7726 (tp) REVERT: B 126 MET cc_start: 0.7429 (mmt) cc_final: 0.7179 (tpp) REVERT: B 320 ILE cc_start: 0.8916 (pt) cc_final: 0.8562 (pt) REVERT: B 395 MET cc_start: 0.6349 (tpp) cc_final: 0.5973 (ttt) REVERT: B 694 MET cc_start: -0.1301 (mmm) cc_final: -0.4781 (ttt) REVERT: B 1322 MET cc_start: 0.5234 (mmt) cc_final: 0.4731 (mmt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3579 time to fit residues: 144.5197 Evaluate side-chains 181 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 296 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.8161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 27011 Z= 0.413 Angle : 0.777 15.033 36751 Z= 0.397 Chirality : 0.046 0.307 4155 Planarity : 0.006 0.068 4862 Dihedral : 5.493 43.705 3876 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.76 (0.14), residues: 3521 helix: -0.38 (0.16), residues: 1049 sheet: -1.30 (0.21), residues: 606 loop : -1.56 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 55 HIS 0.010 0.002 HIS B 451 PHE 0.024 0.002 PHE E 72 TYR 0.029 0.003 TYR C 109 ARG 0.008 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 MET cc_start: 0.6685 (tpp) cc_final: 0.6266 (ttt) REVERT: B 641 MET cc_start: 0.6518 (mmp) cc_final: 0.6177 (mmm) REVERT: B 694 MET cc_start: -0.1069 (mmm) cc_final: -0.4717 (ttt) REVERT: B 1237 ASP cc_start: 0.6201 (p0) cc_final: 0.5721 (m-30) REVERT: B 1322 MET cc_start: 0.5110 (mmt) cc_final: 0.4606 (mmt) REVERT: C 29 PHE cc_start: 0.7756 (p90) cc_final: 0.7483 (p90) REVERT: F 185 VAL cc_start: 0.8498 (t) cc_final: 0.7900 (t) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3679 time to fit residues: 131.1289 Evaluate side-chains 156 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27011 Z= 0.258 Angle : 0.666 16.168 36751 Z= 0.335 Chirality : 0.043 0.170 4155 Planarity : 0.005 0.119 4862 Dihedral : 5.204 45.180 3876 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.62 (0.14), residues: 3521 helix: -0.15 (0.16), residues: 1043 sheet: -1.28 (0.21), residues: 595 loop : -1.53 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 55 HIS 0.005 0.001 HIS A 856 PHE 0.017 0.002 PHE A 583 TYR 0.027 0.002 TYR B 12 ARG 0.007 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 SER cc_start: 0.8763 (m) cc_final: 0.8212 (t) REVERT: A 1058 ARG cc_start: 0.4779 (tpt-90) cc_final: 0.4193 (ttp80) REVERT: B 694 MET cc_start: -0.0901 (mmm) cc_final: -0.4666 (ttt) REVERT: B 1322 MET cc_start: 0.5042 (mmt) cc_final: 0.4568 (mmt) REVERT: C 29 PHE cc_start: 0.7510 (p90) cc_final: 0.7287 (p90) REVERT: F 58 LEU cc_start: 0.7490 (tp) cc_final: 0.7077 (tt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3622 time to fit residues: 135.8929 Evaluate side-chains 167 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 chunk 297 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 257 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 279 optimal weight: 4.9990 chunk 117 optimal weight: 0.0770 chunk 287 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.130971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084978 restraints weight = 101327.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.085691 restraints weight = 60514.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086718 restraints weight = 43957.118| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.8362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27011 Z= 0.185 Angle : 0.635 11.611 36751 Z= 0.316 Chirality : 0.043 0.175 4155 Planarity : 0.005 0.076 4862 Dihedral : 4.962 42.824 3876 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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 (0.14), residues: 3521 helix: 0.10 (0.16), residues: 1037 sheet: -1.18 (0.21), residues: 621 loop : -1.48 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 55 HIS 0.010 0.001 HIS A 499 PHE 0.019 0.002 PHE F 92 TYR 0.030 0.001 TYR D 51 ARG 0.005 0.000 ARG A 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.65 seconds wall clock time: 99 minutes 41.21 seconds (5981.21 seconds total)