Starting phenix.real_space_refine on Thu Mar 21 13:50:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omf_20090/03_2024/6omf_20090.pdb" } resolution = 3.26 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= 0.097 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 91 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18704 2.51 5 N 5356 2.21 5 O 5984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30251 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10382 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2244 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 270} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "T" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 876 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1008 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14536 SG CYS D 70 76.782 56.932 39.310 1.00130.61 S ATOM 14550 SG CYS D 72 75.342 53.700 39.036 1.00135.78 S ATOM 14658 SG CYS D 85 75.580 55.675 35.979 1.00130.37 S ATOM 14682 SG CYS D 88 72.765 56.876 39.407 1.00132.90 S ATOM 20370 SG CYS D 814 113.580 111.847 46.036 1.00123.43 S ATOM 20935 SG CYS D 888 111.052 109.530 48.012 1.00119.80 S ATOM 20986 SG CYS D 895 114.938 108.672 48.811 1.00114.70 S ATOM 21007 SG CYS D 898 113.371 111.890 49.704 1.00114.60 S Time building chain proxies: 16.72, per 1000 atoms: 0.55 Number of scatterers: 30251 At special positions: 0 Unit cell: (176.8, 183.3, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 91 15.00 Mg 1 11.99 O 5984 8.00 N 5356 7.00 C 18704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 14.13 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 54 sheets defined 38.5% alpha, 14.9% beta 38 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 10.14 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.719A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.955A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.523A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.981A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.591A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.545A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.811A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.757A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.604A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.653A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.563A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 294' Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.251A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.752A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.540A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 703 through 711 removed outlier: 4.462A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.636A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 979 Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 996 through 1000 removed outlier: 3.692A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 removed outlier: 4.179A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.180A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.816A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.844A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 4.218A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.559A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.913A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.600A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.732A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.567A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.524A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.561A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.585A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.531A pdb=" N LEU D 412 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.596A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 531 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.529A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 612 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.831A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.852A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.597A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.858A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 776 through 804 removed outlier: 3.546A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 876 removed outlier: 4.184A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 872 " --> pdb=" O TRP D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.601A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.907A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.701A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1145 removed outlier: 3.689A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.567A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.883A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1295 removed outlier: 3.578A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.524A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.839A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.549A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 87 through 98 removed outlier: 3.563A pdb=" N ARG F 91 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 109 removed outlier: 4.028A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR F 109 " --> pdb=" O ILE F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 133 removed outlier: 3.543A pdb=" N GLY F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 161 removed outlier: 3.925A pdb=" N TYR F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP F 149 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 190 removed outlier: 4.421A pdb=" N HIS F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.719A pdb=" N ILE F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.670A pdb=" N ASP F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 279 removed outlier: 3.520A pdb=" N VAL F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.558A pdb=" N GLN F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 329 Processing helix chain 'J' and resid 10 through 20 removed outlier: 3.820A pdb=" N LYS J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY J 20 " --> pdb=" O PHE J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 114 Processing helix chain 'J' and resid 123 through 127 removed outlier: 3.968A pdb=" N ASP J 126 " --> pdb=" O ASP J 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.991A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.946A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.559A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.575A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.526A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.526A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.642A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 151 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET B 51 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'B' and resid 109 through 111 removed outlier: 7.070A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.426A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.144A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.347A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AC1, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.833A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 599 through 606 removed outlier: 5.267A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.623A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.664A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.804A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.947A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.947A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.870A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.804A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 5.921A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.510A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD9, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.165A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE3, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.545A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE5, first strand: chain 'D' and resid 553 through 556 removed outlier: 3.728A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE8, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AE9, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.501A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.366A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF4, first strand: chain 'D' and resid 1087 through 1088 removed outlier: 4.361A pdb=" N ILE D1080 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1046 through 1048 removed outlier: 3.696A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1189 through 1191 removed outlier: 6.529A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1266 through 1268 removed outlier: 6.808A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 34 through 41 removed outlier: 6.502A pdb=" N PHE J 34 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 60 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP J 36 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N MET J 58 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU J 38 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TRP J 56 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE J 53 " --> pdb=" O PHE J 76 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 34 through 41 removed outlier: 6.502A pdb=" N PHE J 34 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 60 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP J 36 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N MET J 58 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU J 38 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TRP J 56 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 59 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 70 " --> pdb=" O GLU J 59 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 14.32 Time building geometry restraints manager: 15.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5073 1.27 - 1.40: 7169 1.40 - 1.53: 17919 1.53 - 1.67: 547 1.67 - 1.80: 196 Bond restraints: 30904 Sorted by residual: bond pdb=" CA GLN D 300 " pdb=" C GLN D 300 " ideal model delta sigma weight residual 1.523 1.371 0.152 1.34e-02 5.57e+03 1.29e+02 bond pdb=" CA ALA D 305 " pdb=" C ALA D 305 " ideal model delta sigma weight residual 1.521 1.432 0.088 9.90e-03 1.02e+04 7.97e+01 bond pdb=" C ALA D 302 " pdb=" O ALA D 302 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.19e-02 7.06e+03 7.47e+01 bond pdb=" CA ALA D 302 " pdb=" CB ALA D 302 " ideal model delta sigma weight residual 1.528 1.397 0.131 1.59e-02 3.96e+03 6.80e+01 bond pdb=" C ASP D 304 " pdb=" O ASP D 304 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.65e+01 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 95.02 - 103.23: 485 103.23 - 111.45: 13937 111.45 - 119.66: 13478 119.66 - 127.87: 13932 127.87 - 136.09: 309 Bond angle restraints: 42141 Sorted by residual: angle pdb=" N ALA D 305 " pdb=" CA ALA D 305 " pdb=" C ALA D 305 " ideal model delta sigma weight residual 112.93 102.82 10.11 1.33e+00 5.65e-01 5.78e+01 angle pdb=" N GLU D 301 " pdb=" CA GLU D 301 " pdb=" C GLU D 301 " ideal model delta sigma weight residual 113.88 105.30 8.58 1.23e+00 6.61e-01 4.87e+01 angle pdb=" C LEU D 903 " pdb=" N ALA D 904 " pdb=" CA ALA D 904 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.50e+01 angle pdb=" C GLN D 300 " pdb=" CA GLN D 300 " pdb=" CB GLN D 300 " ideal model delta sigma weight residual 110.42 97.69 12.73 1.99e+00 2.53e-01 4.09e+01 angle pdb=" N VAL D1240 " pdb=" CA VAL D1240 " pdb=" C VAL D1240 " ideal model delta sigma weight residual 111.90 106.91 4.99 8.10e-01 1.52e+00 3.79e+01 ... (remaining 42136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 17666 35.79 - 71.58: 1026 71.58 - 107.36: 45 107.36 - 143.15: 2 143.15 - 178.94: 4 Dihedral angle restraints: 18743 sinusoidal: 8351 harmonic: 10392 Sorted by residual: dihedral pdb=" CA GLN D1326 " pdb=" C GLN D1326 " pdb=" N GLU D1327 " pdb=" CA GLU D1327 " ideal model delta harmonic sigma weight residual -180.00 -136.00 -44.00 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA GLU A 7 " pdb=" C GLU A 7 " pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA ASP C 485 " pdb=" C ASP C 485 " pdb=" N THR C 486 " pdb=" CA THR C 486 " ideal model delta harmonic sigma weight residual -180.00 -145.60 -34.40 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 18740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4308 0.092 - 0.185: 466 0.185 - 0.277: 19 0.277 - 0.369: 2 0.369 - 0.462: 2 Chirality restraints: 4797 Sorted by residual: chirality pdb=" CA ASP D 304 " pdb=" N ASP D 304 " pdb=" C ASP D 304 " pdb=" CB ASP D 304 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA GLU D 301 " pdb=" N GLU D 301 " pdb=" C GLU D 301 " pdb=" CB GLU D 301 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4794 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 485 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C ASP C 485 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP C 485 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 486 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D1326 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN D1326 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN D1326 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU D1327 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 749 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO D 750 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " -0.041 5.00e-02 4.00e+02 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 173 2.42 - 3.04: 17570 3.04 - 3.66: 48373 3.66 - 4.28: 70542 4.28 - 4.90: 114774 Nonbonded interactions: 251432 Sorted by model distance: nonbonded pdb=" O ASP A 233 " pdb=" OE1 GLU A 235 " model vdw 1.800 3.040 nonbonded pdb=" O LEU D 299 " pdb=" N ALA D 302 " model vdw 1.853 2.520 nonbonded pdb=" NE2 GLN D 300 " pdb=" OD2 ASP D 304 " model vdw 1.854 2.520 nonbonded pdb=" O GLN D 300 " pdb=" NE2 GLN D 300 " model vdw 1.896 2.520 nonbonded pdb=" O LEU D 299 " pdb=" N GLU D 301 " model vdw 2.040 2.520 ... (remaining 251427 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 5 through 158 or resid 167 through 233)) selection = (chain 'B' and resid 5 through 233) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.530 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 95.240 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 0.152 30904 Z= 0.752 Angle : 1.035 15.679 42141 Z= 0.580 Chirality : 0.058 0.462 4797 Planarity : 0.007 0.075 5196 Dihedral : 19.649 178.938 12053 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.20 % Favored : 92.63 % Rotamer: Outliers : 12.34 % Allowed : 13.94 % Favored : 73.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.28 (0.11), residues: 3596 helix: -2.83 (0.10), residues: 1302 sheet: -3.09 (0.21), residues: 465 loop : -2.75 (0.12), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 807 HIS 0.018 0.002 HIS D 777 PHE 0.027 0.003 PHE D 57 TYR 0.026 0.003 TYR C1251 ARG 0.010 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 519 time to evaluate : 3.381 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: A 93 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7724 (tp40) REVERT: A 145 LYS cc_start: 0.8283 (tttt) cc_final: 0.7776 (tttp) REVERT: A 199 ASP cc_start: 0.7516 (m-30) cc_final: 0.7079 (m-30) REVERT: A 212 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5939 (t0) REVERT: A 215 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: A 223 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 10 LYS cc_start: 0.8373 (mttp) cc_final: 0.7986 (mppt) REVERT: B 25 LYS cc_start: 0.7423 (tttt) cc_final: 0.7119 (ttmm) REVERT: B 68 TYR cc_start: 0.8324 (p90) cc_final: 0.8026 (p90) REVERT: B 125 LYS cc_start: 0.7579 (tttt) cc_final: 0.7318 (ttpt) REVERT: B 145 LYS cc_start: 0.8037 (tttt) cc_final: 0.7607 (tttp) REVERT: B 147 GLN cc_start: 0.6350 (tt0) cc_final: 0.6105 (mt0) REVERT: B 200 LYS cc_start: 0.7856 (tttt) cc_final: 0.7186 (ttpp) REVERT: B 205 MET cc_start: 0.7568 (ttp) cc_final: 0.7019 (ttt) REVERT: C 36 GLN cc_start: 0.7529 (tt0) cc_final: 0.7203 (tt0) REVERT: C 60 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5885 (mt0) REVERT: C 62 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: C 118 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: C 130 MET cc_start: 0.8416 (ttm) cc_final: 0.8138 (ttp) REVERT: C 161 LYS cc_start: 0.8584 (mttt) cc_final: 0.8050 (pttm) REVERT: C 203 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7846 (mttt) REVERT: C 237 LEU cc_start: 0.6441 (mp) cc_final: 0.6232 (mp) REVERT: C 241 LEU cc_start: 0.8862 (tp) cc_final: 0.8009 (pp) REVERT: C 244 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8785 (pm20) REVERT: C 246 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7095 (tp) REVERT: C 295 LYS cc_start: 0.6415 (mmtt) cc_final: 0.6076 (mmmt) REVERT: C 297 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7672 (p) REVERT: C 315 MET cc_start: 0.8724 (ttm) cc_final: 0.8124 (ttm) REVERT: C 334 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: C 407 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7494 (ttp80) REVERT: C 412 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7584 (mm-30) REVERT: C 441 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 446 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: C 504 GLU cc_start: 0.8656 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 538 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6916 (pp) REVERT: C 546 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6873 (mp0) REVERT: C 568 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7567 (p0) REVERT: C 681 MET cc_start: 0.6567 (mtt) cc_final: 0.6107 (mtt) REVERT: C 737 ASN cc_start: 0.6328 (m-40) cc_final: 0.6036 (m110) REVERT: C 805 MET cc_start: 0.8476 (ptm) cc_final: 0.8250 (ptt) REVERT: C 814 ASP cc_start: 0.8232 (m-30) cc_final: 0.7987 (m-30) REVERT: C 1023 HIS cc_start: 0.7991 (t70) cc_final: 0.7489 (t70) REVERT: C 1073 LYS cc_start: 0.8425 (pttt) cc_final: 0.8113 (pttp) REVERT: C 1137 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: C 1142 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6634 (ttm110) REVERT: D 140 TYR cc_start: 0.8545 (m-80) cc_final: 0.7863 (m-10) REVERT: D 155 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: D 200 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7938 (tm-30) REVERT: D 322 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8031 (ptt90) REVERT: D 399 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7443 (mttp) REVERT: D 422 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8022 (mp) REVERT: D 425 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6566 (ttp-110) REVERT: D 458 ASN cc_start: 0.9184 (t0) cc_final: 0.8714 (t0) REVERT: D 466 MET cc_start: 0.8463 (mtp) cc_final: 0.8055 (mtm) REVERT: D 484 MET cc_start: 0.8658 (mtp) cc_final: 0.8365 (mtp) REVERT: D 508 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6767 (tp) REVERT: D 599 LYS cc_start: 0.7588 (mppt) cc_final: 0.7306 (mppt) REVERT: D 610 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7443 (mtm110) REVERT: D 612 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 665 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7817 (mm-40) REVERT: D 708 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7665 (p0) REVERT: D 731 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8099 (tpt-90) REVERT: D 798 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7106 (ttp-170) REVERT: D 918 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6847 (pt) REVERT: D 1025 MET cc_start: 0.7455 (tpt) cc_final: 0.7176 (tpt) REVERT: D 1149 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7671 (tpp-160) REVERT: D 1172 LYS cc_start: 0.6957 (mmtm) cc_final: 0.5673 (mmpt) REVERT: D 1174 ARG cc_start: 0.6729 (mtt-85) cc_final: 0.6423 (mtt-85) REVERT: D 1317 GLU cc_start: 0.5460 (tm-30) cc_final: 0.5195 (tm-30) REVERT: D 1345 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7951 (ttm-80) REVERT: E 55 GLU cc_start: 0.7163 (tt0) cc_final: 0.6661 (tt0) REVERT: E 62 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8019 (tp-100) REVERT: E 70 GLN cc_start: 0.8462 (tt0) cc_final: 0.8257 (tt0) REVERT: F 59 GLN cc_start: 0.6995 (mp10) cc_final: 0.6656 (mp10) REVERT: F 64 GLU cc_start: 0.8392 (tp30) cc_final: 0.8145 (tp30) REVERT: F 67 TYR cc_start: 0.7692 (m-80) cc_final: 0.7138 (m-10) REVERT: F 92 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7660 (ttt-90) REVERT: F 96 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7667 (mt-10) REVERT: F 216 ASN cc_start: 0.8090 (t0) cc_final: 0.7875 (t0) REVERT: F 224 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7273 (p) REVERT: F 240 ASP cc_start: 0.7843 (t0) cc_final: 0.7148 (t0) REVERT: F 243 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: F 256 LYS cc_start: 0.7907 (mttt) cc_final: 0.7658 (mmtm) REVERT: F 269 LYS cc_start: 0.8583 (tppt) cc_final: 0.8333 (tppt) REVERT: J 11 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8467 (ptp-170) REVERT: J 24 ARG cc_start: 0.7517 (mmt90) cc_final: 0.7267 (tpp80) REVERT: J 37 CYS cc_start: 0.7998 (t) cc_final: 0.7701 (t) REVERT: J 54 TRP cc_start: 0.8217 (m100) cc_final: 0.7913 (m100) REVERT: J 56 TRP cc_start: 0.6753 (p-90) cc_final: 0.5119 (p-90) REVERT: J 72 GLN cc_start: 0.7433 (mt0) cc_final: 0.7009 (mt0) REVERT: J 101 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7336 (mtt90) outliers start: 379 outliers final: 187 residues processed: 845 average time/residue: 0.4413 time to fit residues: 581.1174 Evaluate side-chains 575 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 362 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1142 ARG Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 798 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 267 ASN Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 84 ASN B 117 HIS B 186 ASN C 31 GLN C 46 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 258 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 513 GLN C 649 GLN C 856 ASN C1116 HIS C1220 GLN C1324 ASN D 206 ASN D 340 GLN D 365 GLN D 720 ASN D 771 GLN D 817 HIS D 954 ASN D1019 ASN D1126 GLN D1195 GLN D1235 ASN D1268 ASN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN F 160 ASN F 170 HIS ** F 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 GLN J 63 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30904 Z= 0.271 Angle : 0.649 10.961 42141 Z= 0.346 Chirality : 0.044 0.154 4797 Planarity : 0.005 0.055 5196 Dihedral : 18.970 172.780 5352 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 7.75 % Allowed : 18.43 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.91 (0.13), residues: 3596 helix: -1.16 (0.13), residues: 1327 sheet: -2.82 (0.22), residues: 424 loop : -2.30 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 997 HIS 0.010 0.001 HIS D 777 PHE 0.021 0.002 PHE D 437 TYR 0.020 0.001 TYR A 177 ARG 0.007 0.000 ARG D1372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 413 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7682 (tp40) REVERT: A 145 LYS cc_start: 0.8294 (tttt) cc_final: 0.7750 (tttm) REVERT: A 212 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.5995 (t0) REVERT: A 223 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7605 (mt) REVERT: B 125 LYS cc_start: 0.7582 (tttt) cc_final: 0.7095 (tppt) REVERT: B 145 LYS cc_start: 0.7644 (tttt) cc_final: 0.7171 (tttt) REVERT: B 200 LYS cc_start: 0.7794 (tttt) cc_final: 0.7293 (ttpp) REVERT: C 36 GLN cc_start: 0.7370 (tt0) cc_final: 0.7030 (tt0) REVERT: C 130 MET cc_start: 0.8584 (ttm) cc_final: 0.8263 (ttp) REVERT: C 241 LEU cc_start: 0.8981 (tp) cc_final: 0.8103 (pp) REVERT: C 246 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7115 (tp) REVERT: C 315 MET cc_start: 0.8729 (ttm) cc_final: 0.8318 (ttm) REVERT: C 334 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: C 369 MET cc_start: 0.8696 (ttp) cc_final: 0.8111 (tmm) REVERT: C 407 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7471 (ttp80) REVERT: C 424 ASP cc_start: 0.7534 (m-30) cc_final: 0.7307 (m-30) REVERT: C 441 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 446 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: C 456 VAL cc_start: 0.7667 (t) cc_final: 0.7421 (t) REVERT: C 510 GLN cc_start: 0.7985 (tp40) cc_final: 0.7713 (tp-100) REVERT: C 538 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7013 (pp) REVERT: C 546 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6955 (mp0) REVERT: C 641 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6365 (mm-30) REVERT: C 704 MET cc_start: 0.7841 (mmm) cc_final: 0.7003 (tpp) REVERT: C 737 ASN cc_start: 0.6188 (m-40) cc_final: 0.5897 (m110) REVERT: C 788 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 805 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8094 (ptp) REVERT: C 1023 HIS cc_start: 0.7732 (t70) cc_final: 0.7247 (t70) REVERT: C 1073 LYS cc_start: 0.8374 (pttt) cc_final: 0.8086 (pttp) REVERT: C 1085 MET cc_start: 0.8287 (mmt) cc_final: 0.7975 (mmt) REVERT: C 1157 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6718 (pp30) REVERT: C 1174 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7014 (mt-10) REVERT: C 1211 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6977 (mtp85) REVERT: C 1268 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6868 (mp10) REVERT: D 29 MET cc_start: 0.6587 (ttm) cc_final: 0.6273 (ttm) REVERT: D 39 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8431 (mtmm) REVERT: D 140 TYR cc_start: 0.8358 (m-80) cc_final: 0.7927 (m-10) REVERT: D 200 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7854 (tm-30) REVERT: D 322 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8314 (ptt90) REVERT: D 399 LYS cc_start: 0.7559 (mtpt) cc_final: 0.7246 (mttp) REVERT: D 422 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7614 (mp) REVERT: D 458 ASN cc_start: 0.8984 (t0) cc_final: 0.8655 (t0) REVERT: D 484 MET cc_start: 0.8801 (mtp) cc_final: 0.8437 (mtp) REVERT: D 610 ARG cc_start: 0.7685 (mmt-90) cc_final: 0.7254 (mtm110) REVERT: D 708 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7881 (p0) REVERT: D 765 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 905 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6579 (mpt180) REVERT: D 918 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6863 (pt) REVERT: D 1025 MET cc_start: 0.7022 (tpt) cc_final: 0.6775 (tpt) REVERT: D 1149 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7457 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7187 (mmtm) cc_final: 0.5936 (mmpt) REVERT: D 1345 ARG cc_start: 0.8301 (mtp85) cc_final: 0.8048 (ttm110) REVERT: D 1368 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.5476 (m-30) REVERT: E 3 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7163 (tpt170) REVERT: E 76 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 64 GLU cc_start: 0.8456 (tp30) cc_final: 0.8215 (tp30) REVERT: F 67 TYR cc_start: 0.7464 (m-80) cc_final: 0.7018 (m-10) REVERT: F 92 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7366 (ttt-90) REVERT: F 96 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7781 (mt-10) REVERT: F 216 ASN cc_start: 0.8171 (t0) cc_final: 0.7940 (t0) REVERT: F 240 ASP cc_start: 0.7804 (t0) cc_final: 0.6808 (t0) REVERT: F 256 LYS cc_start: 0.7926 (mttt) cc_final: 0.7692 (mttp) REVERT: F 269 LYS cc_start: 0.8579 (tppt) cc_final: 0.8217 (tppt) REVERT: J 11 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8531 (ptp-170) REVERT: J 24 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7364 (tpp80) REVERT: J 37 CYS cc_start: 0.8044 (t) cc_final: 0.7637 (t) REVERT: J 56 TRP cc_start: 0.6549 (p-90) cc_final: 0.5531 (p-90) REVERT: J 67 PHE cc_start: 0.7992 (m-80) cc_final: 0.7541 (m-80) REVERT: J 82 TRP cc_start: 0.6592 (m100) cc_final: 0.6259 (m100) REVERT: J 101 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7650 (mtt90) outliers start: 238 outliers final: 156 residues processed: 610 average time/residue: 0.4260 time to fit residues: 414.0676 Evaluate side-chains 518 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 347 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 267 ASN Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 226 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS B 137 ASN C 46 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 628 HIS C 684 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 954 ASN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30904 Z= 0.344 Angle : 0.651 9.225 42141 Z= 0.342 Chirality : 0.044 0.167 4797 Planarity : 0.005 0.057 5196 Dihedral : 18.371 172.019 5210 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.80 % Rotamer: Outliers : 7.00 % Allowed : 20.25 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3596 helix: -0.53 (0.14), residues: 1329 sheet: -2.56 (0.22), residues: 445 loop : -2.12 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 997 HIS 0.009 0.001 HIS D 777 PHE 0.021 0.002 PHE C 186 TYR 0.023 0.002 TYR A 177 ARG 0.008 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 371 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: A 25 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7320 (ttpt) REVERT: A 93 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7699 (tp40) REVERT: A 145 LYS cc_start: 0.8334 (tttt) cc_final: 0.7797 (tttp) REVERT: A 212 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6078 (t0) REVERT: B 71 LYS cc_start: 0.6305 (tppt) cc_final: 0.5892 (tppt) REVERT: B 125 LYS cc_start: 0.7653 (tttt) cc_final: 0.7185 (tppt) REVERT: B 145 LYS cc_start: 0.7756 (tttt) cc_final: 0.7279 (tttm) REVERT: B 200 LYS cc_start: 0.7838 (tttt) cc_final: 0.7170 (tttp) REVERT: C 36 GLN cc_start: 0.7388 (tt0) cc_final: 0.7035 (tt0) REVERT: C 124 MET cc_start: 0.8376 (ptm) cc_final: 0.7928 (ptm) REVERT: C 130 MET cc_start: 0.8654 (ttm) cc_final: 0.8327 (ttp) REVERT: C 161 LYS cc_start: 0.8642 (mttt) cc_final: 0.8122 (pttm) REVERT: C 241 LEU cc_start: 0.8947 (tp) cc_final: 0.8120 (pp) REVERT: C 244 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (pm20) REVERT: C 315 MET cc_start: 0.8746 (ttm) cc_final: 0.8330 (ttm) REVERT: C 407 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7207 (ttp-110) REVERT: C 424 ASP cc_start: 0.7533 (m-30) cc_final: 0.7203 (m-30) REVERT: C 441 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7767 (mm-30) REVERT: C 446 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: C 510 GLN cc_start: 0.7898 (tp40) cc_final: 0.7437 (tp-100) REVERT: C 513 GLN cc_start: 0.7491 (mt0) cc_final: 0.7235 (mt0) REVERT: C 538 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6998 (pp) REVERT: C 546 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 641 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6400 (mm-30) REVERT: C 704 MET cc_start: 0.7885 (mmm) cc_final: 0.7040 (tpp) REVERT: C 737 ASN cc_start: 0.6391 (m-40) cc_final: 0.6183 (m110) REVERT: C 805 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8075 (ptm) REVERT: C 1073 LYS cc_start: 0.8458 (pttt) cc_final: 0.8138 (pttp) REVERT: C 1085 MET cc_start: 0.8346 (mmt) cc_final: 0.8010 (mmt) REVERT: C 1088 ASP cc_start: 0.7781 (p0) cc_final: 0.7504 (p0) REVERT: C 1157 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6929 (pp30) REVERT: C 1174 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7068 (mt-10) REVERT: C 1268 GLN cc_start: 0.7573 (mm-40) cc_final: 0.6880 (mp10) REVERT: C 1290 MET cc_start: 0.8484 (ttm) cc_final: 0.7958 (ttm) REVERT: C 1315 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7980 (ttm) REVERT: D 29 MET cc_start: 0.6617 (ttm) cc_final: 0.6276 (ttm) REVERT: D 39 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8454 (mtmm) REVERT: D 200 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7914 (tm-30) REVERT: D 322 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8353 (ptt90) REVERT: D 375 GLU cc_start: 0.7735 (tp30) cc_final: 0.7526 (tp30) REVERT: D 395 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7715 (tptt) REVERT: D 422 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7494 (mp) REVERT: D 458 ASN cc_start: 0.9003 (t0) cc_final: 0.8710 (t0) REVERT: D 484 MET cc_start: 0.8893 (mtp) cc_final: 0.8547 (mtp) REVERT: D 610 ARG cc_start: 0.7700 (mmt-90) cc_final: 0.7236 (mtm110) REVERT: D 765 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 785 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7209 (t70) REVERT: D 918 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6754 (pt) REVERT: D 1025 MET cc_start: 0.7138 (tpt) cc_final: 0.6911 (tpt) REVERT: D 1146 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 1149 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7397 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7379 (mmtm) cc_final: 0.6171 (mmpt) REVERT: D 1174 ARG cc_start: 0.6561 (mtt-85) cc_final: 0.6240 (mtt-85) REVERT: D 1260 MET cc_start: 0.8550 (mtp) cc_final: 0.8283 (mtm) REVERT: D 1291 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 1345 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8276 (ttm-80) REVERT: D 1368 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.5606 (m-30) REVERT: E 3 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7271 (tpt170) REVERT: E 43 ASN cc_start: 0.8720 (m-40) cc_final: 0.8162 (t0) REVERT: F 64 GLU cc_start: 0.8407 (tp30) cc_final: 0.8099 (tp30) REVERT: F 67 TYR cc_start: 0.7450 (m-80) cc_final: 0.6972 (m-10) REVERT: F 92 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7230 (ttt-90) REVERT: F 96 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7578 (mt-10) REVERT: F 140 PHE cc_start: 0.6667 (m-80) cc_final: 0.6453 (m-80) REVERT: F 216 ASN cc_start: 0.8160 (t0) cc_final: 0.7951 (t0) REVERT: F 221 SER cc_start: 0.8909 (t) cc_final: 0.8576 (t) REVERT: F 240 ASP cc_start: 0.7779 (t0) cc_final: 0.6745 (t0) REVERT: F 269 LYS cc_start: 0.8590 (tppt) cc_final: 0.8284 (tppt) REVERT: J 11 ARG cc_start: 0.8794 (mtt180) cc_final: 0.8575 (ptp-170) REVERT: J 24 ARG cc_start: 0.7664 (mmt90) cc_final: 0.7334 (tpp80) REVERT: J 37 CYS cc_start: 0.8013 (t) cc_final: 0.7657 (t) REVERT: J 56 TRP cc_start: 0.6655 (p-90) cc_final: 0.5719 (p-90) REVERT: J 57 TRP cc_start: 0.7817 (p-90) cc_final: 0.7441 (p-90) REVERT: J 67 PHE cc_start: 0.8031 (m-80) cc_final: 0.7648 (m-80) REVERT: J 101 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7598 (mtt90) outliers start: 215 outliers final: 158 residues processed: 547 average time/residue: 0.4209 time to fit residues: 369.3826 Evaluate side-chains 514 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 341 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 104 HIS Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 223 optimal weight: 0.1980 chunk 334 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS D 954 ASN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30904 Z= 0.263 Angle : 0.603 10.783 42141 Z= 0.316 Chirality : 0.043 0.216 4797 Planarity : 0.004 0.053 5196 Dihedral : 17.973 172.496 5149 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 6.64 % Allowed : 22.24 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 3596 helix: -0.08 (0.14), residues: 1324 sheet: -2.43 (0.23), residues: 439 loop : -1.99 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 997 HIS 0.008 0.001 HIS D 777 PHE 0.023 0.001 PHE J 103 TYR 0.022 0.001 TYR A 177 ARG 0.004 0.000 ARG D1262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 368 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7773 (tp40) REVERT: A 145 LYS cc_start: 0.8521 (tttt) cc_final: 0.7943 (tttm) REVERT: A 212 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6040 (t0) REVERT: B 125 LYS cc_start: 0.7552 (tttt) cc_final: 0.7179 (tptm) REVERT: B 145 LYS cc_start: 0.7580 (tttt) cc_final: 0.6997 (tttm) REVERT: B 147 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.5911 (mt0) REVERT: B 200 LYS cc_start: 0.7721 (tttt) cc_final: 0.7080 (tttp) REVERT: C 36 GLN cc_start: 0.7329 (tt0) cc_final: 0.6970 (tt0) REVERT: C 130 MET cc_start: 0.8633 (ttm) cc_final: 0.8326 (ttp) REVERT: C 161 LYS cc_start: 0.8599 (mttt) cc_final: 0.8104 (pttm) REVERT: C 241 LEU cc_start: 0.8992 (tp) cc_final: 0.8098 (pp) REVERT: C 244 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8930 (pm20) REVERT: C 246 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7495 (tp) REVERT: C 315 MET cc_start: 0.8733 (ttm) cc_final: 0.8318 (ttm) REVERT: C 407 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7503 (ttp-110) REVERT: C 424 ASP cc_start: 0.7543 (m-30) cc_final: 0.7243 (m-30) REVERT: C 446 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: C 510 GLN cc_start: 0.7856 (tp40) cc_final: 0.7555 (tp-100) REVERT: C 538 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6937 (pp) REVERT: C 546 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7005 (mp0) REVERT: C 641 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6373 (mm-30) REVERT: C 699 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8352 (tp) REVERT: C 737 ASN cc_start: 0.6429 (m-40) cc_final: 0.6217 (m110) REVERT: C 788 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7326 (p) REVERT: C 1073 LYS cc_start: 0.8535 (pttt) cc_final: 0.8200 (pttp) REVERT: C 1085 MET cc_start: 0.8283 (mmt) cc_final: 0.8018 (mmt) REVERT: C 1088 ASP cc_start: 0.7734 (p0) cc_final: 0.7465 (p0) REVERT: C 1157 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: C 1174 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7096 (mt-10) REVERT: C 1268 GLN cc_start: 0.7558 (mm-40) cc_final: 0.6895 (mp10) REVERT: C 1290 MET cc_start: 0.8529 (ttm) cc_final: 0.8064 (ttm) REVERT: D 29 MET cc_start: 0.6490 (ttm) cc_final: 0.6170 (ttm) REVERT: D 39 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8440 (mtmm) REVERT: D 200 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7906 (tm-30) REVERT: D 322 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8367 (ptt90) REVERT: D 375 GLU cc_start: 0.7755 (tp30) cc_final: 0.7533 (tp30) REVERT: D 395 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7729 (tptt) REVERT: D 484 MET cc_start: 0.8858 (mtp) cc_final: 0.8564 (mtp) REVERT: D 610 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7199 (mtm110) REVERT: D 765 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7782 (mt-10) REVERT: D 785 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7248 (t70) REVERT: D 788 LEU cc_start: 0.8097 (mm) cc_final: 0.7790 (mp) REVERT: D 905 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6773 (mpt180) REVERT: D 918 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6762 (pt) REVERT: D 954 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6693 (t0) REVERT: D 992 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5561 (pttm) REVERT: D 1025 MET cc_start: 0.7135 (tpt) cc_final: 0.6802 (tpt) REVERT: D 1149 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7468 (tpp-160) REVERT: D 1172 LYS cc_start: 0.7575 (mmtm) cc_final: 0.6850 (mmtp) REVERT: D 1260 MET cc_start: 0.8589 (mtp) cc_final: 0.8351 (mtp) REVERT: D 1345 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8163 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6633 (m-70) REVERT: D 1368 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.5608 (m-30) REVERT: E 3 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7271 (tpt170) REVERT: E 43 ASN cc_start: 0.8765 (m-40) cc_final: 0.8118 (t0) REVERT: F 64 GLU cc_start: 0.8407 (tp30) cc_final: 0.8199 (tp30) REVERT: F 67 TYR cc_start: 0.7417 (m-80) cc_final: 0.6960 (m-10) REVERT: F 92 ARG cc_start: 0.7504 (ttm110) cc_final: 0.6985 (ttt-90) REVERT: F 96 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7482 (mt-10) REVERT: F 111 ASN cc_start: 0.7956 (t0) cc_final: 0.7544 (t0) REVERT: F 151 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.5552 (ttp80) REVERT: F 200 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8226 (tm-30) REVERT: F 221 SER cc_start: 0.8940 (t) cc_final: 0.8679 (t) REVERT: F 236 ASP cc_start: 0.7630 (t0) cc_final: 0.7397 (t0) REVERT: F 240 ASP cc_start: 0.7761 (t0) cc_final: 0.6732 (t0) REVERT: F 269 LYS cc_start: 0.8571 (tppt) cc_final: 0.8264 (tppt) REVERT: J 24 ARG cc_start: 0.7638 (mmt90) cc_final: 0.7256 (tpp80) REVERT: J 37 CYS cc_start: 0.7896 (t) cc_final: 0.7528 (t) REVERT: J 56 TRP cc_start: 0.6537 (p-90) cc_final: 0.5545 (p-90) REVERT: J 57 TRP cc_start: 0.7995 (p-90) cc_final: 0.7669 (p-90) REVERT: J 67 PHE cc_start: 0.8040 (m-80) cc_final: 0.7676 (m-80) REVERT: J 101 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7562 (mtt90) REVERT: J 114 MET cc_start: 0.5162 (ttt) cc_final: 0.4952 (ttt) outliers start: 204 outliers final: 150 residues processed: 535 average time/residue: 0.4100 time to fit residues: 351.7525 Evaluate side-chains 508 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 339 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 317 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 628 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30904 Z= 0.249 Angle : 0.591 10.157 42141 Z= 0.309 Chirality : 0.042 0.240 4797 Planarity : 0.004 0.051 5196 Dihedral : 17.766 174.025 5127 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 6.45 % Allowed : 22.50 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3596 helix: 0.14 (0.14), residues: 1322 sheet: -2.26 (0.23), residues: 437 loop : -1.91 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 997 HIS 0.007 0.001 HIS C1023 PHE 0.028 0.001 PHE A 8 TYR 0.022 0.001 TYR A 177 ARG 0.004 0.000 ARG D1304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 354 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7067 (mtm180) REVERT: A 25 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7145 (ttmm) REVERT: A 145 LYS cc_start: 0.8543 (tttt) cc_final: 0.8016 (tttm) REVERT: A 212 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6011 (t0) REVERT: B 125 LYS cc_start: 0.7564 (tttt) cc_final: 0.7182 (tptm) REVERT: B 145 LYS cc_start: 0.7758 (tttt) cc_final: 0.7289 (tttm) REVERT: B 200 LYS cc_start: 0.7709 (tttt) cc_final: 0.7343 (tttp) REVERT: C 36 GLN cc_start: 0.7302 (tt0) cc_final: 0.7010 (tt0) REVERT: C 130 MET cc_start: 0.8638 (ttm) cc_final: 0.8297 (ttp) REVERT: C 161 LYS cc_start: 0.8632 (mttt) cc_final: 0.8047 (pttm) REVERT: C 241 LEU cc_start: 0.8981 (tp) cc_final: 0.8204 (pp) REVERT: C 315 MET cc_start: 0.8753 (ttm) cc_final: 0.8345 (ttm) REVERT: C 407 ARG cc_start: 0.7730 (ttp80) cc_final: 0.6905 (ttp-170) REVERT: C 424 ASP cc_start: 0.7567 (m-30) cc_final: 0.7224 (m-30) REVERT: C 446 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: C 510 GLN cc_start: 0.7752 (tp40) cc_final: 0.7512 (tp-100) REVERT: C 538 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6892 (pp) REVERT: C 546 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7064 (mp0) REVERT: C 641 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: C 704 MET cc_start: 0.7815 (mmm) cc_final: 0.6966 (tpp) REVERT: C 805 MET cc_start: 0.8107 (ptm) cc_final: 0.7786 (ptp) REVERT: C 1073 LYS cc_start: 0.8572 (pttt) cc_final: 0.8201 (pttp) REVERT: C 1085 MET cc_start: 0.8367 (mmp) cc_final: 0.8055 (mmt) REVERT: C 1088 ASP cc_start: 0.7754 (p0) cc_final: 0.7483 (p0) REVERT: C 1157 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6823 (pp30) REVERT: C 1268 GLN cc_start: 0.7552 (mm-40) cc_final: 0.6882 (mp10) REVERT: C 1290 MET cc_start: 0.8541 (ttm) cc_final: 0.8026 (ttm) REVERT: D 29 MET cc_start: 0.6478 (ttm) cc_final: 0.6144 (ttm) REVERT: D 39 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8444 (mtmm) REVERT: D 200 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7902 (tm-30) REVERT: D 259 ARG cc_start: 0.7721 (ttt-90) cc_final: 0.7354 (ttp-110) REVERT: D 322 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8372 (ptt90) REVERT: D 363 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7087 (pt) REVERT: D 375 GLU cc_start: 0.7783 (tp30) cc_final: 0.7543 (tp30) REVERT: D 395 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7697 (tptt) REVERT: D 422 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7534 (mp) REVERT: D 484 MET cc_start: 0.8896 (mtp) cc_final: 0.8528 (mtp) REVERT: D 610 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.7216 (mtm110) REVERT: D 765 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 785 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7211 (t70) REVERT: D 918 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6760 (pt) REVERT: D 954 ASN cc_start: 0.7103 (t0) cc_final: 0.6845 (t0) REVERT: D 992 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5606 (pttm) REVERT: D 1025 MET cc_start: 0.7147 (tpt) cc_final: 0.6832 (tpt) REVERT: D 1149 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7586 (tpp-160) REVERT: D 1167 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6950 (ptmm) REVERT: D 1260 MET cc_start: 0.8545 (mtp) cc_final: 0.8334 (mtm) REVERT: D 1345 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8136 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6695 (m-70) REVERT: D 1368 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.5612 (m-30) REVERT: E 3 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7277 (tpt170) REVERT: E 43 ASN cc_start: 0.8779 (m-40) cc_final: 0.8223 (t0) REVERT: F 64 GLU cc_start: 0.8395 (tp30) cc_final: 0.8189 (tp30) REVERT: F 67 TYR cc_start: 0.7616 (m-80) cc_final: 0.7095 (m-10) REVERT: F 92 ARG cc_start: 0.7524 (ttm110) cc_final: 0.6978 (ttt-90) REVERT: F 96 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7634 (mt-10) REVERT: F 111 ASN cc_start: 0.7986 (t0) cc_final: 0.7575 (t0) REVERT: F 151 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5586 (ttp80) REVERT: F 200 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 221 SER cc_start: 0.8942 (t) cc_final: 0.8702 (t) REVERT: F 236 ASP cc_start: 0.7574 (t0) cc_final: 0.7314 (t0) REVERT: F 240 ASP cc_start: 0.7751 (t0) cc_final: 0.6715 (t0) REVERT: F 269 LYS cc_start: 0.8549 (tppt) cc_final: 0.8293 (tppt) REVERT: J 24 ARG cc_start: 0.7656 (mmt90) cc_final: 0.7248 (tpp80) REVERT: J 37 CYS cc_start: 0.7981 (t) cc_final: 0.7681 (t) REVERT: J 56 TRP cc_start: 0.6534 (p-90) cc_final: 0.4695 (p-90) REVERT: J 57 TRP cc_start: 0.7982 (p-90) cc_final: 0.7448 (p-90) REVERT: J 67 PHE cc_start: 0.8046 (m-80) cc_final: 0.7710 (m-80) REVERT: J 82 TRP cc_start: 0.6159 (m100) cc_final: 0.5756 (m100) REVERT: J 101 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7569 (mtt90) outliers start: 198 outliers final: 146 residues processed: 517 average time/residue: 0.4155 time to fit residues: 345.1746 Evaluate side-chains 504 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 342 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1135 THR Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 0.6980 chunk 318 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30904 Z= 0.196 Angle : 0.568 9.757 42141 Z= 0.297 Chirality : 0.041 0.262 4797 Planarity : 0.004 0.048 5196 Dihedral : 17.536 178.628 5111 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 5.86 % Allowed : 23.38 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3596 helix: 0.36 (0.15), residues: 1318 sheet: -2.03 (0.24), residues: 425 loop : -1.84 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 997 HIS 0.010 0.001 HIS J 104 PHE 0.022 0.001 PHE A 8 TYR 0.020 0.001 TYR A 177 ARG 0.004 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 365 time to evaluate : 3.078 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: A 25 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7078 (ttmm) REVERT: A 145 LYS cc_start: 0.8566 (tttt) cc_final: 0.8030 (tttm) REVERT: A 212 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6044 (t0) REVERT: B 10 LYS cc_start: 0.8525 (mttp) cc_final: 0.8195 (mtmm) REVERT: B 125 LYS cc_start: 0.7637 (tttt) cc_final: 0.7225 (tptm) REVERT: B 145 LYS cc_start: 0.7753 (tttt) cc_final: 0.7256 (tttm) REVERT: B 200 LYS cc_start: 0.7716 (tttt) cc_final: 0.7444 (tttm) REVERT: C 36 GLN cc_start: 0.7258 (tt0) cc_final: 0.6961 (tt0) REVERT: C 96 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7351 (pp) REVERT: C 130 MET cc_start: 0.8585 (ttm) cc_final: 0.8227 (ttp) REVERT: C 161 LYS cc_start: 0.8578 (mttt) cc_final: 0.8002 (pttm) REVERT: C 241 LEU cc_start: 0.8931 (tp) cc_final: 0.7963 (pp) REVERT: C 246 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7612 (tp) REVERT: C 315 MET cc_start: 0.8811 (ttm) cc_final: 0.8412 (ttm) REVERT: C 407 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7018 (ttp-170) REVERT: C 412 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 424 ASP cc_start: 0.7514 (m-30) cc_final: 0.7106 (m-30) REVERT: C 446 ASP cc_start: 0.8401 (m-30) cc_final: 0.8134 (m-30) REVERT: C 510 GLN cc_start: 0.7834 (tp40) cc_final: 0.7457 (tp-100) REVERT: C 513 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: C 546 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7049 (mp0) REVERT: C 636 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6991 (p) REVERT: C 641 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6553 (mm-30) REVERT: C 645 PHE cc_start: 0.7765 (m-80) cc_final: 0.6498 (m-80) REVERT: C 704 MET cc_start: 0.7754 (mmm) cc_final: 0.6897 (tpp) REVERT: C 805 MET cc_start: 0.8003 (ptm) cc_final: 0.7711 (ptp) REVERT: C 834 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: C 1073 LYS cc_start: 0.8617 (pttt) cc_final: 0.8233 (pttp) REVERT: C 1085 MET cc_start: 0.8316 (mmp) cc_final: 0.8020 (mmt) REVERT: C 1157 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6709 (pp30) REVERT: C 1290 MET cc_start: 0.8533 (ttm) cc_final: 0.7997 (ttm) REVERT: C 1296 ASP cc_start: 0.8701 (t0) cc_final: 0.8327 (t0) REVERT: D 29 MET cc_start: 0.6328 (ttm) cc_final: 0.6009 (ttm) REVERT: D 39 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8452 (mtmm) REVERT: D 130 MET cc_start: 0.8366 (ttt) cc_final: 0.8153 (ptm) REVERT: D 200 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7910 (tm-30) REVERT: D 322 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8378 (ptt90) REVERT: D 363 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7108 (pt) REVERT: D 375 GLU cc_start: 0.7782 (tp30) cc_final: 0.7539 (tp30) REVERT: D 395 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7658 (tptt) REVERT: D 441 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7562 (mm) REVERT: D 484 MET cc_start: 0.8894 (mtp) cc_final: 0.8595 (mtp) REVERT: D 525 MET cc_start: 0.8403 (ptp) cc_final: 0.8166 (ptm) REVERT: D 610 ARG cc_start: 0.7690 (mmt-90) cc_final: 0.7476 (ttp80) REVERT: D 765 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7894 (mt-10) REVERT: D 785 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7043 (t70) REVERT: D 788 LEU cc_start: 0.8103 (mm) cc_final: 0.7815 (mp) REVERT: D 905 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6889 (mpt180) REVERT: D 918 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6836 (pt) REVERT: D 983 LYS cc_start: 0.8111 (mmmm) cc_final: 0.7663 (mmmm) REVERT: D 992 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5601 (pttm) REVERT: D 1025 MET cc_start: 0.7164 (tpt) cc_final: 0.6942 (tpt) REVERT: D 1111 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7259 (t0) REVERT: D 1149 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7526 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6498 (ptmm) REVERT: D 1345 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8125 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6628 (m-70) REVERT: D 1368 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.5850 (m-30) REVERT: E 3 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7214 (tpt170) REVERT: E 43 ASN cc_start: 0.8826 (m-40) cc_final: 0.8252 (t0) REVERT: F 64 GLU cc_start: 0.8407 (tp30) cc_final: 0.8192 (tp30) REVERT: F 67 TYR cc_start: 0.7622 (m-80) cc_final: 0.7025 (m-10) REVERT: F 78 TYR cc_start: 0.8517 (m-10) cc_final: 0.8294 (m-80) REVERT: F 90 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.8089 (p) REVERT: F 92 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7051 (tmm-80) REVERT: F 96 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7622 (mt-10) REVERT: F 111 ASN cc_start: 0.7935 (t0) cc_final: 0.7561 (t0) REVERT: F 151 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.5577 (ttp80) REVERT: F 200 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8127 (tm-30) REVERT: F 221 SER cc_start: 0.8941 (t) cc_final: 0.8660 (t) REVERT: F 236 ASP cc_start: 0.7567 (t0) cc_final: 0.7250 (t0) REVERT: F 240 ASP cc_start: 0.7743 (t0) cc_final: 0.6681 (t0) REVERT: F 269 LYS cc_start: 0.8571 (tppt) cc_final: 0.8325 (tppt) REVERT: J 24 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7215 (tpp80) REVERT: J 37 CYS cc_start: 0.7972 (t) cc_final: 0.7647 (t) REVERT: J 51 ARG cc_start: 0.7332 (mtm180) cc_final: 0.7108 (mtt180) REVERT: J 56 TRP cc_start: 0.6418 (p-90) cc_final: 0.4640 (p-90) REVERT: J 57 TRP cc_start: 0.8015 (p-90) cc_final: 0.7424 (p-90) REVERT: J 67 PHE cc_start: 0.8038 (m-80) cc_final: 0.7750 (m-80) REVERT: J 82 TRP cc_start: 0.6112 (m100) cc_final: 0.5697 (m100) REVERT: J 101 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7582 (mtt90) outliers start: 180 outliers final: 125 residues processed: 511 average time/residue: 0.4337 time to fit residues: 354.0892 Evaluate side-chains 495 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 348 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN D1326 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30904 Z= 0.215 Angle : 0.568 9.418 42141 Z= 0.297 Chirality : 0.042 0.280 4797 Planarity : 0.004 0.047 5196 Dihedral : 17.346 177.603 5079 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 5.83 % Allowed : 23.87 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3596 helix: 0.43 (0.14), residues: 1331 sheet: -2.02 (0.24), residues: 428 loop : -1.78 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP C 997 HIS 0.006 0.001 HIS D 777 PHE 0.022 0.001 PHE J 103 TYR 0.020 0.001 TYR A 177 ARG 0.004 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 356 time to evaluate : 3.304 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: A 12 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7218 (mtm180) REVERT: A 25 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7109 (ttmm) REVERT: A 145 LYS cc_start: 0.8594 (tttt) cc_final: 0.8041 (tttm) REVERT: A 212 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6080 (t0) REVERT: B 10 LYS cc_start: 0.8532 (mttp) cc_final: 0.8204 (mtmm) REVERT: B 125 LYS cc_start: 0.7585 (tttt) cc_final: 0.7200 (tptm) REVERT: B 145 LYS cc_start: 0.7764 (tttt) cc_final: 0.7264 (tttm) REVERT: B 200 LYS cc_start: 0.7701 (tttt) cc_final: 0.6838 (tttm) REVERT: C 36 GLN cc_start: 0.7252 (tt0) cc_final: 0.6950 (tt0) REVERT: C 96 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7456 (pp) REVERT: C 130 MET cc_start: 0.8618 (ttm) cc_final: 0.8267 (ttp) REVERT: C 161 LYS cc_start: 0.8542 (mttt) cc_final: 0.7985 (pttm) REVERT: C 241 LEU cc_start: 0.8939 (tp) cc_final: 0.7982 (pp) REVERT: C 246 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7627 (tp) REVERT: C 315 MET cc_start: 0.8825 (ttm) cc_final: 0.8440 (ttm) REVERT: C 407 ARG cc_start: 0.7751 (ttp80) cc_final: 0.6928 (ttp-170) REVERT: C 412 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 424 ASP cc_start: 0.7481 (m-30) cc_final: 0.7121 (m-30) REVERT: C 446 ASP cc_start: 0.8409 (m-30) cc_final: 0.8146 (m-30) REVERT: C 510 GLN cc_start: 0.7852 (tp40) cc_final: 0.7538 (tp-100) REVERT: C 546 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7038 (mp0) REVERT: C 641 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6709 (mm-30) REVERT: C 704 MET cc_start: 0.7756 (mmm) cc_final: 0.6908 (tpp) REVERT: C 805 MET cc_start: 0.8048 (ptm) cc_final: 0.7742 (ptp) REVERT: C 1073 LYS cc_start: 0.8609 (pttt) cc_final: 0.8225 (pttp) REVERT: C 1085 MET cc_start: 0.8321 (mmp) cc_final: 0.8039 (mmt) REVERT: C 1157 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6756 (pp30) REVERT: C 1290 MET cc_start: 0.8507 (ttm) cc_final: 0.7913 (ttm) REVERT: C 1296 ASP cc_start: 0.8691 (t0) cc_final: 0.8319 (t0) REVERT: D 29 MET cc_start: 0.6427 (ttm) cc_final: 0.6100 (ttm) REVERT: D 39 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8463 (mtmm) REVERT: D 200 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7911 (tm-30) REVERT: D 322 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8392 (ptt90) REVERT: D 375 GLU cc_start: 0.7790 (tp30) cc_final: 0.7549 (tp30) REVERT: D 395 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7644 (tptt) REVERT: D 441 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7565 (mm) REVERT: D 484 MET cc_start: 0.8908 (mtp) cc_final: 0.8600 (mtp) REVERT: D 525 MET cc_start: 0.8412 (ptp) cc_final: 0.8167 (ptm) REVERT: D 610 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7482 (ttp80) REVERT: D 765 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 905 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6914 (mpt180) REVERT: D 918 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6857 (pt) REVERT: D 983 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7665 (mmmm) REVERT: D 992 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5565 (pttm) REVERT: D 1025 MET cc_start: 0.7083 (tpt) cc_final: 0.6866 (tpt) REVERT: D 1111 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7265 (t0) REVERT: D 1149 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7563 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6460 (ptmm) REVERT: D 1345 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8061 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6627 (m-70) REVERT: D 1368 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.5854 (m-30) REVERT: E 3 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7123 (tpt170) REVERT: E 43 ASN cc_start: 0.8825 (m-40) cc_final: 0.8298 (t0) REVERT: F 64 GLU cc_start: 0.8398 (tp30) cc_final: 0.8185 (tp30) REVERT: F 67 TYR cc_start: 0.7612 (m-80) cc_final: 0.6996 (m-10) REVERT: F 90 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (p) REVERT: F 92 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7075 (tmm-80) REVERT: F 96 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7613 (mt-10) REVERT: F 111 ASN cc_start: 0.7919 (t0) cc_final: 0.7545 (t0) REVERT: F 200 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8143 (tm-30) REVERT: F 221 SER cc_start: 0.8965 (t) cc_final: 0.8686 (t) REVERT: F 236 ASP cc_start: 0.7549 (t0) cc_final: 0.7194 (t0) REVERT: F 240 ASP cc_start: 0.7700 (t0) cc_final: 0.6622 (t0) REVERT: F 269 LYS cc_start: 0.8559 (tppt) cc_final: 0.8353 (tptt) REVERT: J 24 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7241 (tpp80) REVERT: J 37 CYS cc_start: 0.7948 (t) cc_final: 0.7635 (t) REVERT: J 56 TRP cc_start: 0.6420 (p-90) cc_final: 0.4670 (p-90) REVERT: J 57 TRP cc_start: 0.7958 (p-90) cc_final: 0.7433 (p-90) REVERT: J 67 PHE cc_start: 0.8006 (m-80) cc_final: 0.7725 (m-80) REVERT: J 82 TRP cc_start: 0.6423 (m100) cc_final: 0.5927 (m100) REVERT: J 101 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7542 (mtp85) outliers start: 179 outliers final: 146 residues processed: 500 average time/residue: 0.4278 time to fit residues: 340.6249 Evaluate side-chains 503 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 341 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 277 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30904 Z= 0.249 Angle : 0.581 9.014 42141 Z= 0.303 Chirality : 0.042 0.312 4797 Planarity : 0.004 0.048 5196 Dihedral : 17.259 175.242 5072 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 6.02 % Allowed : 23.64 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3596 helix: 0.43 (0.14), residues: 1330 sheet: -1.94 (0.25), residues: 426 loop : -1.76 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP C 997 HIS 0.005 0.001 HIS D 430 PHE 0.020 0.001 PHE A 8 TYR 0.021 0.001 TYR A 177 ARG 0.005 0.000 ARG C 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 350 time to evaluate : 3.256 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: A 12 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7208 (mtm180) REVERT: A 25 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7159 (ttmm) REVERT: A 145 LYS cc_start: 0.8578 (tttt) cc_final: 0.8026 (tttm) REVERT: A 212 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6085 (t0) REVERT: B 10 LYS cc_start: 0.8550 (mttp) cc_final: 0.8218 (mtmm) REVERT: B 125 LYS cc_start: 0.7608 (tttt) cc_final: 0.7228 (tptm) REVERT: B 145 LYS cc_start: 0.7764 (tttt) cc_final: 0.7082 (tttm) REVERT: B 147 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.5811 (mt0) REVERT: B 200 LYS cc_start: 0.7621 (tttt) cc_final: 0.6758 (tttm) REVERT: C 36 GLN cc_start: 0.7254 (tt0) cc_final: 0.6949 (tt0) REVERT: C 130 MET cc_start: 0.8618 (ttm) cc_final: 0.8292 (ttp) REVERT: C 161 LYS cc_start: 0.8538 (mttt) cc_final: 0.7987 (pttm) REVERT: C 241 LEU cc_start: 0.8940 (tp) cc_final: 0.7981 (pp) REVERT: C 246 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 315 MET cc_start: 0.8836 (ttm) cc_final: 0.8448 (ttm) REVERT: C 412 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 424 ASP cc_start: 0.7490 (m-30) cc_final: 0.7110 (m-30) REVERT: C 446 ASP cc_start: 0.8426 (m-30) cc_final: 0.8164 (m-30) REVERT: C 510 GLN cc_start: 0.7856 (tp40) cc_final: 0.7582 (tp-100) REVERT: C 542 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7191 (ptp-170) REVERT: C 546 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7054 (mp0) REVERT: C 641 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: C 645 PHE cc_start: 0.7616 (m-80) cc_final: 0.7172 (m-80) REVERT: C 805 MET cc_start: 0.8090 (ptm) cc_final: 0.7781 (ptp) REVERT: C 1034 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8584 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8617 (pttt) cc_final: 0.8243 (pttp) REVERT: C 1085 MET cc_start: 0.8343 (mmp) cc_final: 0.8067 (mmt) REVERT: C 1157 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6810 (pp30) REVERT: C 1290 MET cc_start: 0.8464 (ttm) cc_final: 0.7916 (ttm) REVERT: D 29 MET cc_start: 0.6470 (ttm) cc_final: 0.6130 (ttm) REVERT: D 39 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8478 (mtmm) REVERT: D 200 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7906 (tm-30) REVERT: D 322 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8359 (ptt90) REVERT: D 375 GLU cc_start: 0.7853 (tp30) cc_final: 0.7604 (tp30) REVERT: D 395 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7657 (tptt) REVERT: D 484 MET cc_start: 0.8917 (mtp) cc_final: 0.8594 (mtp) REVERT: D 525 MET cc_start: 0.8361 (ptp) cc_final: 0.8105 (ptm) REVERT: D 765 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 788 LEU cc_start: 0.8073 (mm) cc_final: 0.7792 (mp) REVERT: D 905 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6960 (mpt180) REVERT: D 918 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6874 (pt) REVERT: D 983 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7745 (mmmm) REVERT: D 984 LEU cc_start: 0.6031 (tp) cc_final: 0.5330 (tp) REVERT: D 992 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5397 (pttm) REVERT: D 1025 MET cc_start: 0.6913 (tpt) cc_final: 0.6704 (tpt) REVERT: D 1111 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7289 (t0) REVERT: D 1149 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7636 (tpp-160) REVERT: D 1345 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: D 1366 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6627 (m-70) REVERT: D 1368 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.5733 (m-30) REVERT: E 3 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7128 (tpt170) REVERT: E 43 ASN cc_start: 0.8826 (m-40) cc_final: 0.8269 (t0) REVERT: F 64 GLU cc_start: 0.8409 (tp30) cc_final: 0.8195 (tp30) REVERT: F 67 TYR cc_start: 0.7606 (m-80) cc_final: 0.6985 (m-10) REVERT: F 90 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.8066 (p) REVERT: F 92 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7034 (tmm-80) REVERT: F 96 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7608 (mt-10) REVERT: F 111 ASN cc_start: 0.7849 (t0) cc_final: 0.7520 (t0) REVERT: F 140 PHE cc_start: 0.6689 (m-80) cc_final: 0.6473 (m-80) REVERT: F 200 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8146 (tm-30) REVERT: F 221 SER cc_start: 0.8975 (t) cc_final: 0.8664 (t) REVERT: F 236 ASP cc_start: 0.7523 (t0) cc_final: 0.7128 (t0) REVERT: F 240 ASP cc_start: 0.7632 (t0) cc_final: 0.6542 (t0) REVERT: J 37 CYS cc_start: 0.7836 (t) cc_final: 0.7550 (t) REVERT: J 56 TRP cc_start: 0.6392 (p-90) cc_final: 0.4689 (p-90) REVERT: J 57 TRP cc_start: 0.7959 (p-90) cc_final: 0.7451 (p-90) REVERT: J 67 PHE cc_start: 0.7995 (m-80) cc_final: 0.7731 (m-80) REVERT: J 82 TRP cc_start: 0.6401 (m100) cc_final: 0.5889 (m100) REVERT: J 95 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7579 (tpp80) REVERT: J 101 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7511 (mtp85) REVERT: J 123 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5195 (p0) outliers start: 185 outliers final: 154 residues processed: 502 average time/residue: 0.4330 time to fit residues: 347.3547 Evaluate side-chains 509 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 340 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 308 optimal weight: 0.6980 chunk 328 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 258 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN F 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30904 Z= 0.177 Angle : 0.557 11.249 42141 Z= 0.291 Chirality : 0.041 0.322 4797 Planarity : 0.004 0.045 5196 Dihedral : 17.072 174.043 5067 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.41 % Allowed : 24.26 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3596 helix: 0.63 (0.15), residues: 1331 sheet: -1.80 (0.25), residues: 420 loop : -1.69 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP C 997 HIS 0.006 0.001 HIS D 450 PHE 0.021 0.001 PHE A 8 TYR 0.019 0.001 TYR A 177 ARG 0.006 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 360 time to evaluate : 3.551 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: A 145 LYS cc_start: 0.8584 (tttt) cc_final: 0.8014 (tttm) REVERT: A 212 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6122 (t0) REVERT: B 10 LYS cc_start: 0.8553 (mttp) cc_final: 0.8224 (mtmm) REVERT: B 51 MET cc_start: 0.7263 (ttt) cc_final: 0.6860 (ttt) REVERT: B 125 LYS cc_start: 0.7572 (tttt) cc_final: 0.7227 (tptm) REVERT: B 145 LYS cc_start: 0.7689 (tttt) cc_final: 0.7190 (tttm) REVERT: B 200 LYS cc_start: 0.7641 (tttt) cc_final: 0.7366 (tttm) REVERT: C 36 GLN cc_start: 0.7220 (tt0) cc_final: 0.6895 (tt0) REVERT: C 130 MET cc_start: 0.8485 (ttm) cc_final: 0.8181 (ttp) REVERT: C 161 LYS cc_start: 0.8494 (mttt) cc_final: 0.7960 (pttm) REVERT: C 246 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7999 (mp) REVERT: C 315 MET cc_start: 0.8862 (ttm) cc_final: 0.8482 (ttm) REVERT: C 424 ASP cc_start: 0.7425 (m-30) cc_final: 0.7215 (m-30) REVERT: C 446 ASP cc_start: 0.8217 (m-30) cc_final: 0.8016 (m-30) REVERT: C 510 GLN cc_start: 0.7806 (tp40) cc_final: 0.7527 (tp40) REVERT: C 546 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6989 (mp0) REVERT: C 641 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: C 645 PHE cc_start: 0.7352 (m-80) cc_final: 0.7049 (m-80) REVERT: C 704 MET cc_start: 0.7724 (mmm) cc_final: 0.6863 (tpp) REVERT: C 741 MET cc_start: 0.8317 (ttp) cc_final: 0.8046 (ttm) REVERT: C 805 MET cc_start: 0.7975 (ptm) cc_final: 0.7723 (ptp) REVERT: C 1034 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8534 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8542 (pttt) cc_final: 0.8134 (pttp) REVERT: C 1085 MET cc_start: 0.8262 (mmp) cc_final: 0.8014 (mmt) REVERT: C 1157 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6623 (pp30) REVERT: C 1223 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7255 (mmm-85) REVERT: C 1256 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7955 (mm-40) REVERT: C 1290 MET cc_start: 0.8552 (ttm) cc_final: 0.7991 (ttm) REVERT: C 1296 ASP cc_start: 0.8658 (t0) cc_final: 0.8291 (t0) REVERT: D 29 MET cc_start: 0.6256 (ttm) cc_final: 0.6023 (ttm) REVERT: D 39 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8477 (mtmm) REVERT: D 200 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7899 (tm-30) REVERT: D 375 GLU cc_start: 0.7772 (tp30) cc_final: 0.7543 (tp30) REVERT: D 395 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (tptp) REVERT: D 441 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7702 (mm) REVERT: D 484 MET cc_start: 0.8900 (mtp) cc_final: 0.8565 (mtp) REVERT: D 525 MET cc_start: 0.8375 (ptp) cc_final: 0.8020 (ptm) REVERT: D 765 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7920 (mt-10) REVERT: D 785 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6908 (t70) REVERT: D 788 LEU cc_start: 0.8081 (mm) cc_final: 0.7796 (mp) REVERT: D 905 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6867 (mpt180) REVERT: D 907 HIS cc_start: 0.7884 (p90) cc_final: 0.7485 (p-80) REVERT: D 918 ILE cc_start: 0.7198 (pt) cc_final: 0.6893 (pt) REVERT: D 983 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7786 (mmmm) REVERT: D 984 LEU cc_start: 0.5996 (tp) cc_final: 0.5374 (tp) REVERT: D 992 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5459 (pttm) REVERT: D 1025 MET cc_start: 0.6918 (tpt) cc_final: 0.6707 (tpt) REVERT: D 1149 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7395 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6325 (ptmm) REVERT: D 1366 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6767 (m-70) REVERT: D 1368 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.5894 (m-30) REVERT: E 3 ARG cc_start: 0.7669 (tpp-160) cc_final: 0.7130 (tpt170) REVERT: E 43 ASN cc_start: 0.8829 (m-40) cc_final: 0.8397 (t0) REVERT: F 78 TYR cc_start: 0.8452 (m-80) cc_final: 0.8115 (m-10) REVERT: F 90 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8123 (p) REVERT: F 92 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7095 (tmm-80) REVERT: F 96 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7416 (mt-10) REVERT: F 111 ASN cc_start: 0.7866 (t0) cc_final: 0.7555 (t0) REVERT: F 140 PHE cc_start: 0.6583 (m-80) cc_final: 0.6353 (m-80) REVERT: F 200 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8170 (tm-30) REVERT: F 221 SER cc_start: 0.9020 (t) cc_final: 0.8687 (t) REVERT: F 240 ASP cc_start: 0.7606 (t0) cc_final: 0.6561 (t0) REVERT: F 270 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: J 37 CYS cc_start: 0.7770 (t) cc_final: 0.7547 (t) REVERT: J 56 TRP cc_start: 0.6379 (p-90) cc_final: 0.4729 (p-90) REVERT: J 57 TRP cc_start: 0.7957 (p-90) cc_final: 0.7411 (p-90) REVERT: J 75 LEU cc_start: 0.7599 (pt) cc_final: 0.6829 (mt) REVERT: J 82 TRP cc_start: 0.6261 (m100) cc_final: 0.5826 (m100) REVERT: J 101 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7550 (mtp85) REVERT: J 123 ASP cc_start: 0.5768 (OUTLIER) cc_final: 0.5282 (p0) outliers start: 166 outliers final: 131 residues processed: 496 average time/residue: 0.4276 time to fit residues: 340.9916 Evaluate side-chains 489 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 342 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1223 ARG Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 270 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.5980 chunk 347 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 364 optimal weight: 8.9990 chunk 335 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 628 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30904 Z= 0.178 Angle : 0.571 12.010 42141 Z= 0.298 Chirality : 0.042 0.359 4797 Planarity : 0.004 0.044 5196 Dihedral : 17.031 174.077 5058 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.85 % Allowed : 25.11 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3596 helix: 0.70 (0.15), residues: 1328 sheet: -1.71 (0.25), residues: 415 loop : -1.66 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 997 HIS 0.006 0.001 HIS D 450 PHE 0.020 0.001 PHE A 8 TYR 0.019 0.001 TYR A 177 ARG 0.007 0.000 ARG D 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 348 time to evaluate : 3.765 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: A 12 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7201 (mtm180) REVERT: A 25 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7127 (ttmm) REVERT: A 145 LYS cc_start: 0.8612 (tttt) cc_final: 0.8063 (tttm) REVERT: A 212 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6174 (t0) REVERT: B 10 LYS cc_start: 0.8548 (mttp) cc_final: 0.8221 (mtmm) REVERT: B 51 MET cc_start: 0.7267 (ttt) cc_final: 0.6859 (ttt) REVERT: B 125 LYS cc_start: 0.7510 (tttt) cc_final: 0.7126 (tptm) REVERT: B 145 LYS cc_start: 0.7694 (tttt) cc_final: 0.7008 (tttm) REVERT: B 147 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.5829 (mt0) REVERT: B 200 LYS cc_start: 0.7637 (tttt) cc_final: 0.7079 (tttp) REVERT: C 36 GLN cc_start: 0.7175 (tt0) cc_final: 0.6881 (tt0) REVERT: C 130 MET cc_start: 0.8490 (ttm) cc_final: 0.8178 (ttp) REVERT: C 161 LYS cc_start: 0.8464 (mttt) cc_final: 0.7953 (pttm) REVERT: C 246 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7613 (tp) REVERT: C 315 MET cc_start: 0.8871 (ttm) cc_final: 0.8481 (ttm) REVERT: C 424 ASP cc_start: 0.7374 (m-30) cc_final: 0.7168 (m-30) REVERT: C 446 ASP cc_start: 0.8307 (m-30) cc_final: 0.8039 (m-30) REVERT: C 510 GLN cc_start: 0.7841 (tp40) cc_final: 0.7571 (tp40) REVERT: C 542 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7416 (ptp-170) REVERT: C 546 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6975 (mp0) REVERT: C 573 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7715 (t0) REVERT: C 641 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: C 645 PHE cc_start: 0.7292 (m-80) cc_final: 0.7047 (m-80) REVERT: C 704 MET cc_start: 0.7716 (mmm) cc_final: 0.6868 (tpp) REVERT: C 711 ASP cc_start: 0.7668 (m-30) cc_final: 0.7344 (m-30) REVERT: C 741 MET cc_start: 0.8301 (ttp) cc_final: 0.8033 (ttm) REVERT: C 805 MET cc_start: 0.7992 (ptm) cc_final: 0.7726 (ptp) REVERT: C 1034 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8533 (mmm-85) REVERT: C 1073 LYS cc_start: 0.8483 (pttt) cc_final: 0.8065 (pttp) REVERT: C 1085 MET cc_start: 0.8261 (mmp) cc_final: 0.8018 (mmt) REVERT: C 1157 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6597 (pp30) REVERT: C 1256 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7945 (mm-40) REVERT: C 1290 MET cc_start: 0.8523 (ttm) cc_final: 0.7932 (ttm) REVERT: C 1296 ASP cc_start: 0.8649 (t0) cc_final: 0.8288 (t0) REVERT: D 29 MET cc_start: 0.6247 (ttm) cc_final: 0.6011 (ttm) REVERT: D 39 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8501 (mtmm) REVERT: D 200 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7894 (tm-30) REVERT: D 375 GLU cc_start: 0.7783 (tp30) cc_final: 0.7545 (tp30) REVERT: D 395 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7744 (tptp) REVERT: D 441 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7653 (mm) REVERT: D 484 MET cc_start: 0.8894 (mtp) cc_final: 0.8574 (mtp) REVERT: D 525 MET cc_start: 0.8384 (ptp) cc_final: 0.8028 (ptm) REVERT: D 765 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 788 LEU cc_start: 0.8018 (mm) cc_final: 0.7753 (mp) REVERT: D 905 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6881 (mpt180) REVERT: D 907 HIS cc_start: 0.7884 (p90) cc_final: 0.7482 (p-80) REVERT: D 918 ILE cc_start: 0.7190 (pt) cc_final: 0.6897 (pt) REVERT: D 983 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7777 (mmmm) REVERT: D 984 LEU cc_start: 0.5973 (tp) cc_final: 0.5345 (tp) REVERT: D 992 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5459 (pttm) REVERT: D 1025 MET cc_start: 0.6919 (tpt) cc_final: 0.6705 (tpt) REVERT: D 1149 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7520 (tpp-160) REVERT: D 1167 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6318 (ptmm) REVERT: D 1366 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6769 (m-70) REVERT: D 1368 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.5812 (m-30) REVERT: E 3 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.7126 (tpt170) REVERT: E 43 ASN cc_start: 0.8811 (m-40) cc_final: 0.8404 (t0) REVERT: F 59 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: F 78 TYR cc_start: 0.8308 (m-80) cc_final: 0.8102 (m-10) REVERT: F 90 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8149 (p) REVERT: F 92 ARG cc_start: 0.7520 (ttm110) cc_final: 0.7030 (tmm-80) REVERT: F 96 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7451 (mt-10) REVERT: F 111 ASN cc_start: 0.7856 (t0) cc_final: 0.7549 (t0) REVERT: F 140 PHE cc_start: 0.6579 (m-80) cc_final: 0.6350 (m-80) REVERT: F 200 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 240 ASP cc_start: 0.7596 (t0) cc_final: 0.6548 (t0) REVERT: J 37 CYS cc_start: 0.7793 (t) cc_final: 0.7568 (t) REVERT: J 56 TRP cc_start: 0.6402 (p-90) cc_final: 0.4701 (p-90) REVERT: J 57 TRP cc_start: 0.8033 (p-90) cc_final: 0.7468 (p-90) REVERT: J 82 TRP cc_start: 0.6331 (m100) cc_final: 0.5819 (m100) REVERT: J 101 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7544 (mtp85) REVERT: J 123 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5276 (p0) outliers start: 149 outliers final: 129 residues processed: 469 average time/residue: 0.4249 time to fit residues: 317.8947 Evaluate side-chains 491 residues out of total 3089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 345 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1212 ASP Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 267 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 290 optimal weight: 0.0770 chunk 121 optimal weight: 0.0170 chunk 298 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.151427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100067 restraints weight = 43681.238| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.02 r_work: 0.3206 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 30904 Z= 0.202 Angle : 0.786 59.189 42141 Z= 0.451 Chirality : 0.042 0.339 4797 Planarity : 0.004 0.066 5196 Dihedral : 17.034 174.074 5057 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.05 % Allowed : 24.85 % Favored : 70.11 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3596 helix: 0.70 (0.15), residues: 1328 sheet: -1.70 (0.25), residues: 415 loop : -1.66 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 997 HIS 0.024 0.001 HIS D 777 PHE 0.019 0.001 PHE A 8 TYR 0.032 0.001 TYR F 67 ARG 0.005 0.000 ARG C 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7783.90 seconds wall clock time: 140 minutes 18.38 seconds (8418.38 seconds total)