Starting phenix.real_space_refine on Fri Mar 6 13:06:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pgh_71632/03_2026/9pgh_71632.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 97 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 18586 2.51 5 N 5378 2.21 5 O 5869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30040 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1763 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 218} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1818 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 227} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 10229 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 64, 'TRANS': 1284} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 12, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 24, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 226 Chain: "D" Number of atoms: 10070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10070 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1276} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 21, 'ASP:plan': 10, 'ASN:plan1': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 213 Chain: "E" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 508 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3667 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 12, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 164 Chain: "H" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1115 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "I" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 867 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} 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 14270 SG CYS D 71 104.080 114.127 87.785 1.00189.26 S ATOM 14284 SG CYS D 73 102.742 118.179 88.669 1.00189.02 S ATOM 14383 SG CYS D 86 105.320 115.406 90.439 1.00172.11 S ATOM 19986 SG CYS D 810 101.443 46.961 88.044 1.00159.60 S ATOM 20520 SG CYS D 884 99.015 49.659 88.020 1.00161.53 S ATOM 20568 SG CYS D 891 100.546 48.968 84.739 1.00158.87 S ATOM 20583 SG CYS D 894 98.224 46.598 85.701 1.00149.92 S Time building chain proxies: 6.44, per 1000 atoms: 0.21 Number of scatterers: 30040 At special positions: 0 Unit cell: (142.56, 157.68, 167.4, 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 107 16.00 P 97 15.00 Mg 1 11.99 O 5869 8.00 N 5378 7.00 C 18586 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 810 " Number of angles added : 6 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 49 sheets defined 41.5% alpha, 10.8% beta 30 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 4.000A pdb=" N LEU A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 3.525A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'B' and resid 37 through 52 removed outlier: 4.364A pdb=" N THR B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 211 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'C' and resid 28 through 37 removed outlier: 4.331A pdb=" N SER C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.858A pdb=" N VAL C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.792A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.562A pdb=" N THR C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.822A pdb=" N GLY C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.972A pdb=" N ILE C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 429 through 445 removed outlier: 4.248A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 463 through 490 removed outlier: 3.758A pdb=" N LEU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 490 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 Processing helix chain 'C' and resid 527 through 535 Processing helix chain 'C' and resid 548 through 552 removed outlier: 4.462A pdb=" N GLY C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.587A pdb=" N LYS C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.940A pdb=" N VAL C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.507A pdb=" N LEU C 674 " --> pdb=" O VAL C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 693 removed outlier: 4.015A pdb=" N MET C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 696 No H-bonds generated for 'chain 'C' and resid 694 through 696' Processing helix chain 'C' and resid 711 through 719 removed outlier: 4.156A pdb=" N ALA C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 902 through 913 Processing helix chain 'C' and resid 948 through 985 removed outlier: 3.636A pdb=" N GLU C 983 " --> pdb=" O GLY C 979 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 984 " --> pdb=" O ARG C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 removed outlier: 3.521A pdb=" N GLN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1016 removed outlier: 4.053A pdb=" N TRP C1016 " --> pdb=" O SER C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1055 removed outlier: 3.523A pdb=" N GLU C1028 " --> pdb=" O LYS C1024 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C1031 " --> pdb=" O GLY C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1121 Processing helix chain 'C' and resid 1127 through 1153 removed outlier: 3.592A pdb=" N PHE C1131 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP C1153 " --> pdb=" O LEU C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1170 Processing helix chain 'C' and resid 1179 through 1190 removed outlier: 3.754A pdb=" N GLU C1185 " --> pdb=" O GLU C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1217 Processing helix chain 'C' and resid 1275 through 1279 removed outlier: 3.584A pdb=" N GLN C1278 " --> pdb=" O GLY C1275 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1296 Processing helix chain 'C' and resid 1298 through 1306 Processing helix chain 'C' and resid 1314 through 1325 removed outlier: 3.687A pdb=" N TYR C1319 " --> pdb=" O ARG C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1334 through 1346 removed outlier: 3.534A pdb=" N ASN C1338 " --> pdb=" O PRO C1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 71 through 75 removed outlier: 4.158A pdb=" N GLY D 74 " --> pdb=" O CYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.762A pdb=" N LEU D 118 " --> pdb=" O HIS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.506A pdb=" N ALA D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.821A pdb=" N GLY D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 3.579A pdb=" N MET D 239 " --> pdb=" O PRO D 236 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 240 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 265 through 287 removed outlier: 4.106A pdb=" N ASP D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 379 through 390 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.724A pdb=" N ILE D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 removed outlier: 3.909A pdb=" N ILE D 436 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 506 through 516 removed outlier: 3.935A pdb=" N LEU D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 542 removed outlier: 3.619A pdb=" N ILE D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.721A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 Processing helix chain 'D' and resid 673 through 703 removed outlier: 3.527A pdb=" N GLU D 677 " --> pdb=" O ILE D 673 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 729 through 738 Processing helix chain 'D' and resid 764 through 800 removed outlier: 3.784A pdb=" N HIS D 773 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY D 774 " --> pdb=" O ASN D 770 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 836 Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.706A pdb=" N ALA D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 884 removed outlier: 3.619A pdb=" N CYS D 884 " --> pdb=" O VAL D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 896 removed outlier: 3.868A pdb=" N GLY D 896 " --> pdb=" O GLY D 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 892 through 896' Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1128 through 1138 Processing helix chain 'D' and resid 1212 through 1220 Processing helix chain 'D' and resid 1221 through 1241 removed outlier: 3.847A pdb=" N VAL D1236 " --> pdb=" O GLU D1232 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D1237 " --> pdb=" O ILE D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1245 through 1257 removed outlier: 4.284A pdb=" N ILE D1249 " --> pdb=" O ASN D1245 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D1257 " --> pdb=" O VAL D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1291 removed outlier: 3.548A pdb=" N ARG D1291 " --> pdb=" O LYS D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1309 Processing helix chain 'D' and resid 1315 through 1322 removed outlier: 3.635A pdb=" N GLN D1322 " --> pdb=" O ALA D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1324 through 1335 removed outlier: 3.922A pdb=" N GLU D1330 " --> pdb=" O ARG D1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 1342 through 1350 removed outlier: 3.649A pdb=" N ASN D1346 " --> pdb=" O GLY D1342 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1377 Processing helix chain 'E' and resid 5 through 13 removed outlier: 4.035A pdb=" N CYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.603A pdb=" N LEU E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.850A pdb=" N LYS E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 126 removed outlier: 3.847A pdb=" N VAL F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 151 removed outlier: 3.637A pdb=" N ALA F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 167 removed outlier: 4.039A pdb=" N VAL F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 removed outlier: 3.588A pdb=" N THR F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 removed outlier: 3.528A pdb=" N ALA F 248 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 removed outlier: 3.541A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 297 removed outlier: 3.830A pdb=" N ARG F 282 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 333 removed outlier: 3.621A pdb=" N ILE F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 347 removed outlier: 4.495A pdb=" N GLY F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 356 Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.502A pdb=" N MET F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 362' Processing helix chain 'F' and resid 368 through 391 removed outlier: 3.887A pdb=" N GLN F 374 " --> pdb=" O GLU F 370 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 422 removed outlier: 3.561A pdb=" N ILE F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN F 402 " --> pdb=" O ARG F 398 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 431 removed outlier: 3.822A pdb=" N LYS F 431 " --> pdb=" O ILE F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 455 Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 465 through 485 removed outlier: 3.873A pdb=" N TYR F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP F 472 " --> pdb=" O THR F 468 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP F 473 " --> pdb=" O TYR F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 510 removed outlier: 3.575A pdb=" N GLU F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR F 498 " --> pdb=" O HIS F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 526 removed outlier: 3.920A pdb=" N GLU F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 removed outlier: 3.511A pdb=" N LEU F 537 " --> pdb=" O VAL F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 588 Processing helix chain 'F' and resid 591 through 602 Processing helix chain 'F' and resid 611 through 620 Processing helix chain 'F' and resid 625 through 638 Processing helix chain 'F' and resid 646 through 650 removed outlier: 3.565A pdb=" N PHE F 649 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 650 " --> pdb=" O ARG F 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 646 through 650' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 7.723A pdb=" N ARG A 143 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 64 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A 145 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 62 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 58 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 151 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 6.938A pdb=" N VAL A 113 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.971A pdb=" N VAL A 155 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 174 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 181 removed outlier: 7.030A pdb=" N GLU A 205 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.797A pdb=" N GLU B 18 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 28 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 200 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 197 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.832A pdb=" N GLU B 119 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR B 104 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 61 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 149 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 59 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY B 151 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA B 57 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 114 removed outlier: 7.032A pdb=" N GLY B 111 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR B 135 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 113 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 154 through 155 removed outlier: 3.865A pdb=" N VAL B 155 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.501A pdb=" N LYS C 13 " --> pdb=" O ALA C1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.799A pdb=" N ILE C 63 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR C 77 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.590A pdb=" N ILE C 133 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.619A pdb=" N SER C 153 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 164 removed outlier: 3.650A pdb=" N ASP C 191 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 233 through 237 Processing sheet with id=AB9, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AC1, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AC2, first strand: chain 'C' and resid 588 through 589 removed outlier: 3.558A pdb=" N ARG C 601 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU C 610 " --> pdb=" O ARG C 601 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 588 through 589 Processing sheet with id=AC4, first strand: chain 'C' and resid 624 through 625 Processing sheet with id=AC5, first strand: chain 'C' and resid 729 through 734 removed outlier: 6.981A pdb=" N VAL C 740 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE C 734 " --> pdb=" O ARG C 738 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG C 738 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 763 through 764 Processing sheet with id=AC7, first strand: chain 'C' and resid 774 through 775 Processing sheet with id=AC8, first strand: chain 'C' and resid 795 through 796 Processing sheet with id=AC9, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 6.692A pdb=" N ILE C 822 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE C1097 " --> pdb=" O ILE C 822 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 824 " --> pdb=" O ILE C1097 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR C1240 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 836 through 845 removed outlier: 6.731A pdb=" N MET C1067 " --> pdb=" O VAL C 939 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 939 " --> pdb=" O MET C1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS C1069 " --> pdb=" O VAL C 937 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL C 937 " --> pdb=" O LYS C1069 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C1071 " --> pdb=" O VAL C 935 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 855 through 856 removed outlier: 3.608A pdb=" N GLU C 855 " --> pdb=" O VAL C 893 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 893 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 888 through 890 removed outlier: 7.161A pdb=" N LEU C 924 " --> pdb=" O LEU C 889 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AD5, first strand: chain 'C' and resid 1258 through 1260 removed outlier: 8.072A pdb=" N ILE D 449 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 356 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU D 451 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 358 " --> pdb=" O LEU D 451 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1352 through 1353 Processing sheet with id=AD7, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AD8, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.635A pdb=" N LEU D 161 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 254 through 256 removed outlier: 3.738A pdb=" N ALA D 263 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE D 262 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.170A pdb=" N CYS D 368 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE D 444 " --> pdb=" O CYS D 368 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU D 370 " --> pdb=" O ILE D 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 528 through 529 removed outlier: 3.797A pdb=" N ARG D 553 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 556 through 557 Processing sheet with id=AE4, first strand: chain 'D' and resid 805 through 807 Processing sheet with id=AE5, first strand: chain 'D' and resid 816 through 818 Processing sheet with id=AE6, first strand: chain 'D' and resid 822 through 823 Processing sheet with id=AE7, first strand: chain 'D' and resid 952 through 956 removed outlier: 4.303A pdb=" N GLU D 986 " --> pdb=" O VAL D 978 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AE9, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 4.121A pdb=" N ALA D1113 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1090 through 1091 removed outlier: 3.884A pdb=" N ALA D1069 " --> pdb=" O GLU D1031 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D1026 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D1104 " --> pdb=" O ILE D1028 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1039 through 1043 Processing sheet with id=AF3, first strand: chain 'D' and resid 1168 through 1169 Processing sheet with id=AF4, first strand: chain 'D' and resid 1275 through 1276 removed outlier: 6.846A pdb=" N VAL D1297 " --> pdb=" O LEU D1263 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9828 1.34 - 1.46: 4879 1.46 - 1.58: 15614 1.58 - 1.70: 192 1.70 - 1.82: 192 Bond restraints: 30705 Sorted by residual: bond pdb=" N PRO D 361 " pdb=" CD PRO D 361 " ideal model delta sigma weight residual 1.473 1.413 0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" CB PRO D 361 " pdb=" CG PRO D 361 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.59e+00 bond pdb=" CB PRO A 156 " pdb=" CG PRO A 156 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.49e+00 bond pdb=" CG1 ILE A 62 " pdb=" CD1 ILE A 62 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.48e+00 bond pdb=" CA ARG C 402 " pdb=" CB ARG C 402 " ideal model delta sigma weight residual 1.542 1.529 0.013 8.90e-03 1.26e+04 2.18e+00 ... (remaining 30700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 41833 3.60 - 7.21: 146 7.21 - 10.81: 11 10.81 - 14.42: 2 14.42 - 18.02: 1 Bond angle restraints: 41993 Sorted by residual: angle pdb=" CA PRO D 361 " pdb=" N PRO D 361 " pdb=" CD PRO D 361 " ideal model delta sigma weight residual 112.00 93.98 18.02 1.40e+00 5.10e-01 1.66e+02 angle pdb=" C ASP D 213 " pdb=" CA ASP D 213 " pdb=" CB ASP D 213 " ideal model delta sigma weight residual 116.34 109.84 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" CA ARG D 54 " pdb=" CB ARG D 54 " pdb=" CG ARG D 54 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CB PRO D 361 " pdb=" CG PRO D 361 " pdb=" CD PRO D 361 " ideal model delta sigma weight residual 106.10 94.53 11.57 3.20e+00 9.77e-02 1.31e+01 angle pdb=" N PRO D 361 " pdb=" CD PRO D 361 " pdb=" CG PRO D 361 " ideal model delta sigma weight residual 103.20 97.83 5.37 1.50e+00 4.44e-01 1.28e+01 ... (remaining 41988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 17867 35.06 - 70.11: 576 70.11 - 105.17: 35 105.17 - 140.23: 0 140.23 - 175.28: 5 Dihedral angle restraints: 18483 sinusoidal: 7861 harmonic: 10622 Sorted by residual: dihedral pdb=" CA ASP C1108 " pdb=" C ASP C1108 " pdb=" N GLY C1109 " pdb=" CA GLY C1109 " ideal model delta harmonic sigma weight residual -180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LYS C 504 " pdb=" C LYS C 504 " pdb=" N PRO C 505 " pdb=" CA PRO C 505 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU F 554 " pdb=" C GLU F 554 " pdb=" N ASP F 555 " pdb=" CA ASP F 555 " ideal model delta harmonic sigma weight residual 180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 18480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3698 0.046 - 0.092: 889 0.092 - 0.137: 257 0.137 - 0.183: 15 0.183 - 0.229: 5 Chirality restraints: 4864 Sorted by residual: chirality pdb=" CB THR C1110 " pdb=" CA THR C1110 " pdb=" OG1 THR C1110 " pdb=" CG2 THR C1110 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 4861 not shown) Planarity restraints: 5172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 238 " 0.030 2.00e-02 2.50e+03 3.52e-02 3.10e+01 pdb=" CG TRP D 238 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP D 238 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP D 238 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 238 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 238 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 238 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 238 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 238 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP D 238 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 34 " -0.034 2.00e-02 2.50e+03 3.06e-02 2.35e+01 pdb=" CG TRP D 34 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP D 34 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP D 34 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 34 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 34 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 34 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 360 " 0.060 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO D 361 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " 0.046 5.00e-02 4.00e+02 ... (remaining 5169 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 420 2.65 - 3.21: 28190 3.21 - 3.78: 44313 3.78 - 4.34: 56991 4.34 - 4.90: 93188 Nonbonded interactions: 223102 Sorted by model distance: nonbonded pdb=" O LYS D 30 " pdb=" OG SER D 33 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D2001 " model vdw 2.109 2.170 nonbonded pdb=" OD1 ASP C 524 " pdb=" OG SER C 530 " model vdw 2.123 3.040 nonbonded pdb=" NH2 ARG D 204 " pdb=" OE2 GLU D 227 " model vdw 2.170 3.120 nonbonded pdb=" OG1 THR B 104 " pdb=" OE2 GLU B 119 " model vdw 2.196 3.040 ... (remaining 223097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 74 or (resid 75 and (name N or name CA \ or name C or name O or name CB )) or resid 76 through 159 or (resid 160 and (na \ me N or name CA or name C or name O or name CB )) or resid 161 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 233 or (resid 234 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'B' and (resid 2 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 192 or (resid 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 217 or (resid 2 \ 18 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 219 through 232 or (r \ esid 233 through 234 and (name N or name CA or name C or name O or name CB )))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.004 0.147 30712 Z= 0.153 Angle : 0.666 18.024 41999 Z= 0.342 Chirality : 0.043 0.229 4864 Planarity : 0.005 0.081 5172 Dihedral : 16.393 175.284 11633 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.07 % Allowed : 0.49 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3696 helix: 0.99 (0.15), residues: 1369 sheet: -0.48 (0.28), residues: 357 loop : -1.89 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 727 TYR 0.019 0.001 TYR B 184 PHE 0.028 0.001 PHE D1321 TRP 0.094 0.003 TRP D 238 HIS 0.006 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00359 (30705) covalent geometry : angle 0.65837 (41993) hydrogen bonds : bond 0.16743 ( 1240) hydrogen bonds : angle 5.89812 ( 3448) metal coordination : bond 0.01058 ( 7) metal coordination : angle 8.34277 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 624 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7888 (tptt) cc_final: 0.7502 (tppt) REVERT: A 16 GLN cc_start: 0.7564 (tp40) cc_final: 0.7303 (pt0) REVERT: A 26 LYS cc_start: 0.7400 (mtpp) cc_final: 0.6925 (mtmm) REVERT: A 36 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.6900 (mmm160) REVERT: A 65 ASP cc_start: 0.7717 (p0) cc_final: 0.7271 (m-30) REVERT: A 68 VAL cc_start: 0.8454 (m) cc_final: 0.7971 (p) REVERT: A 75 GLU cc_start: 0.7677 (tp30) cc_final: 0.6999 (mt-10) REVERT: A 86 LEU cc_start: 0.7514 (tp) cc_final: 0.6949 (mp) REVERT: A 106 ARG cc_start: 0.8323 (ttm110) cc_final: 0.8022 (ttm110) REVERT: A 119 GLU cc_start: 0.6539 (tp30) cc_final: 0.6157 (mm-30) REVERT: A 123 ASP cc_start: 0.7775 (t0) cc_final: 0.6971 (t0) REVERT: A 125 GLU cc_start: 0.7172 (pp20) cc_final: 0.6860 (pm20) REVERT: A 199 LYS cc_start: 0.6853 (ptmt) cc_final: 0.6384 (ptmm) REVERT: B 14 LYS cc_start: 0.7747 (pttm) cc_final: 0.7426 (ptpp) REVERT: B 26 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7584 (ptpp) REVERT: B 35 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6812 (mm-30) REVERT: B 78 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7660 (mtt-85) REVERT: B 90 GLN cc_start: 0.7260 (tp-100) cc_final: 0.6789 (mt0) REVERT: B 101 LYS cc_start: 0.7144 (mmtp) cc_final: 0.6804 (mmtp) REVERT: B 144 MET cc_start: 0.6480 (mmp) cc_final: 0.6209 (mmt) REVERT: B 150 ASN cc_start: 0.8384 (t0) cc_final: 0.8140 (t0) REVERT: B 198 ASP cc_start: 0.7105 (m-30) cc_final: 0.6902 (m-30) REVERT: B 199 LYS cc_start: 0.7248 (ptpt) cc_final: 0.6932 (ttpp) REVERT: B 201 ILE cc_start: 0.7477 (pt) cc_final: 0.7174 (mp) REVERT: B 205 GLU cc_start: 0.6089 (tt0) cc_final: 0.5882 (tt0) REVERT: C 29 GLU cc_start: 0.7062 (tp30) cc_final: 0.6179 (tt0) REVERT: C 36 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6323 (tp30) REVERT: C 87 GLU cc_start: 0.8510 (tp30) cc_final: 0.8051 (mm-30) REVERT: C 130 MET cc_start: 0.6671 (mtm) cc_final: 0.6239 (mpp) REVERT: C 155 MET cc_start: 0.7670 (ttp) cc_final: 0.7371 (ttt) REVERT: C 206 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7330 (ptm160) REVERT: C 372 PHE cc_start: 0.6410 (m-80) cc_final: 0.5789 (m-80) REVERT: C 392 MET cc_start: 0.5986 (tmm) cc_final: 0.5630 (tmm) REVERT: C 415 MET cc_start: 0.8197 (ttm) cc_final: 0.7806 (ptp) REVERT: C 449 GLU cc_start: 0.7785 (pt0) cc_final: 0.7430 (pm20) REVERT: C 454 ASP cc_start: 0.7067 (m-30) cc_final: 0.6815 (t0) REVERT: C 504 LYS cc_start: 0.7549 (pttt) cc_final: 0.7336 (pptt) REVERT: C 518 GLN cc_start: 0.8205 (tp40) cc_final: 0.7469 (tm-30) REVERT: C 522 PHE cc_start: 0.7912 (m-80) cc_final: 0.7354 (m-80) REVERT: C 549 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7311 (mp0) REVERT: C 557 ASP cc_start: 0.7693 (t0) cc_final: 0.7323 (m-30) REVERT: C 603 LYS cc_start: 0.6741 (mmmm) cc_final: 0.6067 (mmtt) REVERT: C 617 MET cc_start: 0.7202 (ptt) cc_final: 0.6954 (pmm) REVERT: C 618 GLU cc_start: 0.7432 (tt0) cc_final: 0.7015 (tt0) REVERT: C 621 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7389 (pttt) REVERT: C 622 HIS cc_start: 0.7035 (m-70) cc_final: 0.6518 (m170) REVERT: C 630 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6692 (mtmt) REVERT: C 648 GLU cc_start: 0.7119 (pt0) cc_final: 0.6761 (pm20) REVERT: C 684 ASN cc_start: 0.7770 (t0) cc_final: 0.7429 (m-40) REVERT: C 688 MET cc_start: 0.6716 (mtm) cc_final: 0.6340 (mtt) REVERT: C 735 ASP cc_start: 0.7280 (t0) cc_final: 0.6892 (t0) REVERT: C 748 ASP cc_start: 0.6233 (t0) cc_final: 0.6026 (m-30) REVERT: C 778 LYS cc_start: 0.7647 (mttt) cc_final: 0.6932 (mmtm) REVERT: C 782 ARG cc_start: 0.8201 (ptp-110) cc_final: 0.7990 (mtp-110) REVERT: C 843 GLU cc_start: 0.8209 (tt0) cc_final: 0.7877 (tt0) REVERT: C 851 LEU cc_start: 0.7981 (mp) cc_final: 0.7680 (tt) REVERT: C 855 GLU cc_start: 0.7942 (pt0) cc_final: 0.7457 (pt0) REVERT: C 866 GLU cc_start: 0.7697 (pp20) cc_final: 0.7122 (mp0) REVERT: C 905 GLU cc_start: 0.5904 (tp30) cc_final: 0.5622 (tt0) REVERT: C 936 ASP cc_start: 0.6817 (m-30) cc_final: 0.6539 (t0) REVERT: C 943 HIS cc_start: 0.7105 (t70) cc_final: 0.6862 (t-90) REVERT: C 958 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 962 LEU cc_start: 0.7628 (mp) cc_final: 0.7426 (mp) REVERT: C 975 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7545 (mtm180) REVERT: C 1192 LYS cc_start: 0.8237 (tptt) cc_final: 0.7981 (ttpt) REVERT: C 1324 ARG cc_start: 0.6466 (ttm-80) cc_final: 0.5933 (mtt-85) REVERT: C 1326 ASP cc_start: 0.6677 (t0) cc_final: 0.6346 (t0) REVERT: C 1327 ASP cc_start: 0.7363 (m-30) cc_final: 0.6915 (p0) REVERT: C 1354 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6819 (mt-10) REVERT: D 59 CYS cc_start: 0.8057 (t) cc_final: 0.7788 (t) REVERT: D 67 LYS cc_start: 0.7032 (tptm) cc_final: 0.6385 (tppt) REVERT: D 88 LYS cc_start: 0.7789 (tptm) cc_final: 0.7588 (ttmt) REVERT: D 94 THR cc_start: 0.7900 (m) cc_final: 0.7562 (p) REVERT: D 147 VAL cc_start: 0.8231 (m) cc_final: 0.7899 (p) REVERT: D 189 ASN cc_start: 0.7032 (t0) cc_final: 0.6644 (m-40) REVERT: D 198 LYS cc_start: 0.7950 (tptp) cc_final: 0.7591 (tmmt) REVERT: D 202 ARG cc_start: 0.7571 (tmm-80) cc_final: 0.7309 (mtp-110) REVERT: D 214 MET cc_start: 0.6897 (mmp) cc_final: 0.6367 (tmm) REVERT: D 221 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7055 (pttt) REVERT: D 331 ASP cc_start: 0.7003 (t70) cc_final: 0.6719 (m-30) REVERT: D 350 ASP cc_start: 0.7726 (p0) cc_final: 0.7459 (p0) REVERT: D 364 LYS cc_start: 0.6730 (mttm) cc_final: 0.6272 (mmmt) REVERT: D 377 GLU cc_start: 0.8247 (tp30) cc_final: 0.7975 (tp30) REVERT: D 401 ARG cc_start: 0.6410 (ttm-80) cc_final: 0.6062 (mtp180) REVERT: D 402 MET cc_start: 0.6854 (ttm) cc_final: 0.6100 (mtp) REVERT: D 431 LEU cc_start: 0.8459 (mm) cc_final: 0.8238 (mt) REVERT: D 486 MET cc_start: 0.7835 (mtm) cc_final: 0.7620 (mtp) REVERT: D 566 LYS cc_start: 0.8282 (ptmm) cc_final: 0.7608 (pttp) REVERT: D 577 ILE cc_start: 0.7076 (tt) cc_final: 0.6871 (mt) REVERT: D 610 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6852 (tpp-160) REVERT: D 630 LYS cc_start: 0.5578 (mtpt) cc_final: 0.4815 (mmtp) REVERT: D 642 ASP cc_start: 0.8492 (m-30) cc_final: 0.8221 (p0) REVERT: D 679 TYR cc_start: 0.6521 (t80) cc_final: 0.6281 (t80) REVERT: D 684 ASP cc_start: 0.6901 (t0) cc_final: 0.6421 (m-30) REVERT: D 691 ASP cc_start: 0.6896 (m-30) cc_final: 0.6310 (t0) REVERT: D 743 MET cc_start: 0.6266 (mmm) cc_final: 0.5999 (mmm) REVERT: D 806 VAL cc_start: 0.8334 (p) cc_final: 0.8070 (m) REVERT: D 826 ASP cc_start: 0.6736 (t0) cc_final: 0.6516 (p0) REVERT: D 828 LEU cc_start: 0.8256 (mm) cc_final: 0.8016 (mm) REVERT: D 840 THR cc_start: 0.7229 (p) cc_final: 0.6974 (p) REVERT: D 866 ASP cc_start: 0.8323 (m-30) cc_final: 0.8074 (m-30) REVERT: D 909 GLU cc_start: 0.8212 (tt0) cc_final: 0.7432 (tm-30) REVERT: D 1231 ASP cc_start: 0.6729 (t70) cc_final: 0.6210 (m-30) REVERT: D 1235 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6697 (tt0) REVERT: D 1270 LEU cc_start: 0.6732 (tp) cc_final: 0.6473 (tp) REVERT: D 1271 ILE cc_start: 0.8179 (tt) cc_final: 0.7379 (tt) REVERT: D 1274 ASP cc_start: 0.6550 (m-30) cc_final: 0.6280 (p0) REVERT: D 1301 VAL cc_start: 0.8889 (p) cc_final: 0.8511 (m) REVERT: D 1326 ARG cc_start: 0.7128 (ptp-170) cc_final: 0.6662 (mtp-110) REVERT: E 28 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6495 (tpp80) REVERT: E 39 ASP cc_start: 0.7653 (p0) cc_final: 0.6690 (p0) REVERT: E 42 ASN cc_start: 0.8189 (m110) cc_final: 0.7547 (t0) REVERT: E 52 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6305 (mt-10) REVERT: F 408 GLU cc_start: 0.8038 (tp30) cc_final: 0.7563 (tm-30) REVERT: F 508 GLN cc_start: 0.7289 (tt0) cc_final: 0.6601 (tm-30) REVERT: F 610 HIS cc_start: 0.7742 (m90) cc_final: 0.7437 (m90) REVERT: F 629 ILE cc_start: 0.7301 (mm) cc_final: 0.7099 (mt) outliers start: 2 outliers final: 1 residues processed: 626 average time/residue: 0.2045 time to fit residues: 196.0981 Evaluate side-chains 397 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 398 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 16 GLN C 525 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 723 HIS D 735 GLN ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN F 448 ASN F 494 HIS F 576 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146044 restraints weight = 40903.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144619 restraints weight = 90834.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138526 restraints weight = 94183.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135965 restraints weight = 88981.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135957 restraints weight = 88108.670| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30712 Z= 0.138 Angle : 0.606 13.608 41999 Z= 0.312 Chirality : 0.043 0.206 4864 Planarity : 0.005 0.058 5172 Dihedral : 14.830 176.449 5061 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.26 % Allowed : 9.63 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3696 helix: 1.04 (0.15), residues: 1405 sheet: -0.42 (0.27), residues: 383 loop : -1.95 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 550 TYR 0.018 0.001 TYR C 74 PHE 0.019 0.001 PHE C1047 TRP 0.039 0.001 TRP D 34 HIS 0.011 0.001 HIS F 494 Details of bonding type rmsd covalent geometry : bond 0.00323 (30705) covalent geometry : angle 0.59920 (41993) hydrogen bonds : bond 0.04011 ( 1240) hydrogen bonds : angle 4.43459 ( 3448) metal coordination : bond 0.00867 ( 7) metal coordination : angle 7.83015 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 411 time to evaluate : 0.857 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 86 LEU cc_start: 0.9103 (tp) cc_final: 0.8612 (mp) REVERT: A 123 ASP cc_start: 0.7276 (t0) cc_final: 0.7039 (t0) REVERT: B 199 LYS cc_start: 0.9242 (ptpt) cc_final: 0.8857 (ptmt) REVERT: C 372 PHE cc_start: 0.7407 (m-80) cc_final: 0.7043 (m-80) REVERT: C 505 PRO cc_start: 0.8099 (Cg_endo) cc_final: 0.7655 (Cg_exo) REVERT: C 976 ASN cc_start: 0.8237 (t0) cc_final: 0.7912 (t0) REVERT: C 1036 PHE cc_start: 0.8182 (t80) cc_final: 0.7644 (t80) REVERT: C 1246 MET cc_start: 0.8654 (mmm) cc_final: 0.8417 (mmm) REVERT: C 1324 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6937 (mtt-85) REVERT: D 59 CYS cc_start: 0.8092 (t) cc_final: 0.7753 (t) REVERT: D 402 MET cc_start: 0.8174 (ttm) cc_final: 0.7923 (mtp) REVERT: D 539 MET cc_start: 0.8795 (mtp) cc_final: 0.8573 (mtp) REVERT: D 696 GLU cc_start: 0.7261 (tp30) cc_final: 0.6955 (tp30) REVERT: D 720 MET cc_start: 0.8875 (ttm) cc_final: 0.8571 (ttp) REVERT: D 781 ASP cc_start: 0.7333 (t0) cc_final: 0.7132 (t0) REVERT: D 1270 LEU cc_start: 0.6300 (tp) cc_final: 0.5839 (tp) REVERT: E 11 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7250 (pp20) REVERT: E 65 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: F 481 SER cc_start: 0.9169 (t) cc_final: 0.8960 (p) REVERT: F 544 ILE cc_start: 0.9246 (tp) cc_final: 0.9045 (tt) REVERT: F 629 ILE cc_start: 0.8047 (mm) cc_final: 0.7738 (mt) outliers start: 36 outliers final: 19 residues processed: 436 average time/residue: 0.1779 time to fit residues: 124.1254 Evaluate side-chains 329 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 309 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 398 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 179 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 349 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 203 optimal weight: 0.0020 chunk 127 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 610 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129597 restraints weight = 40462.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127569 restraints weight = 73280.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128349 restraints weight = 73958.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127856 restraints weight = 48954.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128192 restraints weight = 46654.325| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30712 Z= 0.197 Angle : 0.650 15.686 41999 Z= 0.332 Chirality : 0.045 0.170 4864 Planarity : 0.005 0.062 5172 Dihedral : 14.909 176.592 5061 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.30 % Allowed : 14.52 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3696 helix: 0.88 (0.14), residues: 1405 sheet: -0.58 (0.28), residues: 369 loop : -1.98 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 206 TYR 0.022 0.002 TYR C 201 PHE 0.018 0.002 PHE C 677 TRP 0.031 0.001 TRP D 34 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00475 (30705) covalent geometry : angle 0.64003 (41993) hydrogen bonds : bond 0.04287 ( 1240) hydrogen bonds : angle 4.36526 ( 3448) metal coordination : bond 0.01044 ( 7) metal coordination : angle 9.67105 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 330 time to evaluate : 1.049 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 123 ASP cc_start: 0.7473 (t0) cc_final: 0.7191 (t0) REVERT: A 199 LYS cc_start: 0.8778 (ptmm) cc_final: 0.8550 (ptmm) REVERT: B 199 LYS cc_start: 0.9231 (ptpt) cc_final: 0.8812 (ptmt) REVERT: C 372 PHE cc_start: 0.7628 (m-80) cc_final: 0.7246 (m-80) REVERT: C 851 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7921 (tt) REVERT: C 976 ASN cc_start: 0.8324 (t0) cc_final: 0.7879 (t0) REVERT: C 1036 PHE cc_start: 0.8449 (t80) cc_final: 0.7847 (t80) REVERT: C 1324 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7399 (mtt-85) REVERT: D 59 CYS cc_start: 0.8502 (t) cc_final: 0.8159 (t) REVERT: D 118 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8670 (tp) REVERT: D 720 MET cc_start: 0.8982 (ttm) cc_final: 0.8716 (ttp) REVERT: D 781 ASP cc_start: 0.7583 (t0) cc_final: 0.7376 (t0) REVERT: D 794 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: D 842 GLU cc_start: 0.6987 (pp20) cc_final: 0.6736 (pp20) REVERT: E 11 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7334 (pp20) REVERT: E 59 ASP cc_start: 0.6762 (t0) cc_final: 0.6395 (t0) REVERT: F 476 GLN cc_start: 0.7760 (pp30) cc_final: 0.7466 (pp30) REVERT: F 481 SER cc_start: 0.9223 (t) cc_final: 0.8964 (p) REVERT: F 629 ILE cc_start: 0.8099 (mm) cc_final: 0.7824 (mt) outliers start: 66 outliers final: 40 residues processed: 374 average time/residue: 0.1815 time to fit residues: 108.7762 Evaluate side-chains 340 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 794 ARG Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 398 ARG Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 265 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 299 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 236 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 283 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 525 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 GLN C1212 HIS D 409 GLN ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128501 restraints weight = 40306.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126814 restraints weight = 72231.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127176 restraints weight = 72961.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126717 restraints weight = 47526.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126942 restraints weight = 42589.260| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30712 Z= 0.167 Angle : 0.596 12.563 41999 Z= 0.306 Chirality : 0.043 0.164 4864 Planarity : 0.004 0.053 5172 Dihedral : 14.863 175.196 5061 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.00 % Allowed : 16.57 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3696 helix: 0.95 (0.14), residues: 1406 sheet: -0.47 (0.28), residues: 366 loop : -2.00 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 727 TYR 0.015 0.001 TYR C 201 PHE 0.015 0.002 PHE C 61 TRP 0.020 0.001 TRP D 34 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00397 (30705) covalent geometry : angle 0.58772 (41993) hydrogen bonds : bond 0.03675 ( 1240) hydrogen bonds : angle 4.24291 ( 3448) metal coordination : bond 0.00810 ( 7) metal coordination : angle 8.10029 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 314 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 123 ASP cc_start: 0.7372 (t0) cc_final: 0.7054 (t0) REVERT: A 186 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8850 (t) REVERT: A 199 LYS cc_start: 0.8704 (ptmm) cc_final: 0.8460 (ptmm) REVERT: B 199 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8836 (ptmt) REVERT: C 372 PHE cc_start: 0.7682 (m-80) cc_final: 0.7326 (m-80) REVERT: C 392 MET cc_start: 0.8015 (tmm) cc_final: 0.7722 (tmm) REVERT: C 679 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: C 851 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7972 (tt) REVERT: C 976 ASN cc_start: 0.8375 (t0) cc_final: 0.7956 (t0) REVERT: C 1036 PHE cc_start: 0.8502 (t80) cc_final: 0.7861 (t80) REVERT: C 1065 MET cc_start: 0.8295 (ptp) cc_final: 0.8065 (ptp) REVERT: C 1106 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8729 (tp) REVERT: C 1324 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7464 (mtt-85) REVERT: D 59 CYS cc_start: 0.8479 (t) cc_final: 0.8162 (t) REVERT: D 118 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8714 (tp) REVERT: D 229 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7513 (t80) REVERT: D 332 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.5806 (ptp) REVERT: D 539 MET cc_start: 0.9001 (mtp) cc_final: 0.8717 (mtp) REVERT: D 698 MET cc_start: 0.8438 (tpp) cc_final: 0.8102 (tpt) REVERT: D 720 MET cc_start: 0.8986 (ttm) cc_final: 0.8697 (ttp) REVERT: D 794 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7519 (ttt90) REVERT: D 863 ASN cc_start: 0.7722 (m-40) cc_final: 0.7503 (m-40) REVERT: D 1150 MET cc_start: 0.7831 (pmm) cc_final: 0.7568 (pmm) REVERT: E 11 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7273 (pp20) REVERT: E 59 ASP cc_start: 0.6953 (t0) cc_final: 0.6497 (t0) REVERT: F 426 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6476 (m) REVERT: F 476 GLN cc_start: 0.7985 (pp30) cc_final: 0.7631 (pp30) REVERT: F 481 SER cc_start: 0.9176 (t) cc_final: 0.8905 (p) REVERT: F 629 ILE cc_start: 0.8198 (mm) cc_final: 0.7939 (mt) outliers start: 86 outliers final: 51 residues processed: 378 average time/residue: 0.1665 time to fit residues: 102.8031 Evaluate side-chains 355 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 794 ARG Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 398 ARG Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 536 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 188 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 278 optimal weight: 0.0370 chunk 244 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 25 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.163542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128665 restraints weight = 40457.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126947 restraints weight = 77683.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126577 restraints weight = 71331.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122766 restraints weight = 50261.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123033 restraints weight = 50670.391| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30712 Z= 0.132 Angle : 0.572 10.942 41999 Z= 0.293 Chirality : 0.042 0.157 4864 Planarity : 0.004 0.095 5172 Dihedral : 14.804 176.206 5061 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.69 % Allowed : 17.83 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3696 helix: 1.06 (0.14), residues: 1400 sheet: -0.51 (0.28), residues: 374 loop : -1.94 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 727 TYR 0.013 0.001 TYR C 201 PHE 0.013 0.001 PHE C 61 TRP 0.015 0.001 TRP D 34 HIS 0.005 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00313 (30705) covalent geometry : angle 0.56535 (41993) hydrogen bonds : bond 0.03410 ( 1240) hydrogen bonds : angle 4.13070 ( 3448) metal coordination : bond 0.00647 ( 7) metal coordination : angle 7.16453 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 123 ASP cc_start: 0.7248 (t0) cc_final: 0.7016 (t0) REVERT: A 138 ASP cc_start: 0.7526 (p0) cc_final: 0.7130 (p0) REVERT: A 186 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8837 (t) REVERT: A 199 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8406 (ptmm) REVERT: B 199 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8813 (ptmt) REVERT: C 372 PHE cc_start: 0.7727 (m-80) cc_final: 0.7250 (m-80) REVERT: C 392 MET cc_start: 0.8096 (tmm) cc_final: 0.7785 (tmm) REVERT: C 679 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: C 851 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 976 ASN cc_start: 0.8458 (t0) cc_final: 0.7967 (t0) REVERT: C 1036 PHE cc_start: 0.8455 (t80) cc_final: 0.7805 (t80) REVERT: C 1065 MET cc_start: 0.8435 (ptp) cc_final: 0.8216 (ptp) REVERT: C 1324 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7530 (mtt-85) REVERT: D 59 CYS cc_start: 0.8416 (t) cc_final: 0.8049 (t) REVERT: D 118 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8691 (tp) REVERT: D 206 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7663 (tp30) REVERT: D 229 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7701 (t80) REVERT: D 332 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6058 (ppp) REVERT: D 698 MET cc_start: 0.8460 (tpp) cc_final: 0.8183 (tpt) REVERT: D 720 MET cc_start: 0.9007 (ttm) cc_final: 0.8709 (ttp) REVERT: D 794 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7655 (ttt90) REVERT: D 863 ASN cc_start: 0.7811 (m-40) cc_final: 0.7593 (m-40) REVERT: E 11 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7278 (pp20) REVERT: E 59 ASP cc_start: 0.6875 (t0) cc_final: 0.6194 (t0) REVERT: F 476 GLN cc_start: 0.8136 (pp30) cc_final: 0.7788 (pp30) REVERT: F 481 SER cc_start: 0.9186 (t) cc_final: 0.8916 (p) outliers start: 77 outliers final: 53 residues processed: 372 average time/residue: 0.1742 time to fit residues: 104.5382 Evaluate side-chains 355 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 901 MET Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1070 VAL Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 794 ARG Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 398 ARG Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 612 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 108 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 132 optimal weight: 0.1980 chunk 309 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS C 608 GLN ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 974 ASN D 730 GLN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.161786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127053 restraints weight = 40383.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125490 restraints weight = 73105.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123934 restraints weight = 71223.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120093 restraints weight = 52026.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120361 restraints weight = 51020.382| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30712 Z= 0.171 Angle : 0.604 12.352 41999 Z= 0.307 Chirality : 0.043 0.156 4864 Planarity : 0.004 0.100 5172 Dihedral : 14.805 177.466 5061 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.07 % Allowed : 18.56 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3696 helix: 1.02 (0.14), residues: 1399 sheet: -0.55 (0.28), residues: 376 loop : -1.96 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 727 TYR 0.016 0.001 TYR C 129 PHE 0.014 0.001 PHE C 61 TRP 0.014 0.001 TRP D 34 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00416 (30705) covalent geometry : angle 0.59580 (41993) hydrogen bonds : bond 0.03670 ( 1240) hydrogen bonds : angle 4.16081 ( 3448) metal coordination : bond 0.00755 ( 7) metal coordination : angle 8.11895 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 301 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 86 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8926 (mp) REVERT: A 123 ASP cc_start: 0.7250 (t0) cc_final: 0.7005 (t0) REVERT: A 138 ASP cc_start: 0.7703 (p0) cc_final: 0.7338 (p0) REVERT: A 186 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8848 (t) REVERT: B 199 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8698 (ptmt) REVERT: C 372 PHE cc_start: 0.7738 (m-80) cc_final: 0.7236 (m-80) REVERT: C 392 MET cc_start: 0.8124 (tmm) cc_final: 0.7822 (tmm) REVERT: C 631 VAL cc_start: 0.8645 (t) cc_final: 0.8354 (m) REVERT: C 908 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8743 (mp) REVERT: C 976 ASN cc_start: 0.8408 (t0) cc_final: 0.7995 (t0) REVERT: C 1036 PHE cc_start: 0.8499 (t80) cc_final: 0.7819 (t80) REVERT: C 1124 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7947 (ptp-170) REVERT: C 1324 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7631 (mtt-85) REVERT: D 35 SER cc_start: 0.8916 (t) cc_final: 0.8543 (p) REVERT: D 59 CYS cc_start: 0.8512 (t) cc_final: 0.8168 (t) REVERT: D 118 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8729 (tp) REVERT: D 207 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8090 (tt) REVERT: D 229 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7889 (t80) REVERT: D 332 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6100 (ppp) REVERT: D 392 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7997 (mt) REVERT: D 698 MET cc_start: 0.8488 (tpp) cc_final: 0.8232 (tpt) REVERT: D 720 MET cc_start: 0.8984 (ttm) cc_final: 0.8705 (ttp) REVERT: D 794 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7723 (ttt90) REVERT: D 863 ASN cc_start: 0.7914 (m-40) cc_final: 0.7700 (m-40) REVERT: E 11 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7246 (pp20) REVERT: E 59 ASP cc_start: 0.6902 (t0) cc_final: 0.6193 (t0) REVERT: F 426 VAL cc_start: 0.7169 (OUTLIER) cc_final: 0.6512 (m) REVERT: F 476 GLN cc_start: 0.8169 (pp30) cc_final: 0.7830 (pp30) REVERT: F 481 SER cc_start: 0.9179 (t) cc_final: 0.8876 (p) outliers start: 88 outliers final: 64 residues processed: 367 average time/residue: 0.1738 time to fit residues: 103.5331 Evaluate side-chains 367 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 901 MET Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1070 VAL Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1124 ARG Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 794 ARG Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1268 THR Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 355 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 218 optimal weight: 0.2980 chunk 225 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 96 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.163312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128785 restraints weight = 40234.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127138 restraints weight = 73455.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124399 restraints weight = 71790.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121663 restraints weight = 58955.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121545 restraints weight = 53851.935| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30712 Z= 0.125 Angle : 0.571 10.288 41999 Z= 0.291 Chirality : 0.041 0.159 4864 Planarity : 0.004 0.098 5172 Dihedral : 14.749 178.069 5057 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.93 % Allowed : 19.02 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3696 helix: 1.12 (0.15), residues: 1400 sheet: -0.54 (0.28), residues: 376 loop : -1.93 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 727 TYR 0.014 0.001 TYR C 129 PHE 0.013 0.001 PHE D 178 TRP 0.013 0.001 TRP D 34 HIS 0.005 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00295 (30705) covalent geometry : angle 0.56501 (41993) hydrogen bonds : bond 0.03269 ( 1240) hydrogen bonds : angle 4.07343 ( 3448) metal coordination : bond 0.00651 ( 7) metal coordination : angle 6.84015 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 299 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7536 (t80) REVERT: A 86 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8960 (mp) REVERT: A 123 ASP cc_start: 0.7238 (t0) cc_final: 0.6982 (t0) REVERT: A 138 ASP cc_start: 0.7622 (p0) cc_final: 0.7302 (p0) REVERT: A 186 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 136 MET cc_start: 0.8293 (tpp) cc_final: 0.8022 (ttm) REVERT: C 221 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5859 (ppp) REVERT: C 372 PHE cc_start: 0.7752 (m-80) cc_final: 0.7259 (m-80) REVERT: C 392 MET cc_start: 0.8121 (tmm) cc_final: 0.7893 (tmm) REVERT: C 631 VAL cc_start: 0.8578 (t) cc_final: 0.8306 (m) REVERT: C 908 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 976 ASN cc_start: 0.8506 (t0) cc_final: 0.8070 (t0) REVERT: C 1036 PHE cc_start: 0.8443 (t80) cc_final: 0.7776 (t80) REVERT: C 1324 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7628 (mtt-85) REVERT: D 35 SER cc_start: 0.8920 (t) cc_final: 0.8580 (p) REVERT: D 59 CYS cc_start: 0.8463 (t) cc_final: 0.8112 (t) REVERT: D 118 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8711 (tp) REVERT: D 207 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 229 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7940 (t80) REVERT: D 332 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6085 (ppp) REVERT: D 392 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7985 (mt) REVERT: D 698 MET cc_start: 0.8459 (tpp) cc_final: 0.8145 (tpt) REVERT: D 720 MET cc_start: 0.9006 (ttm) cc_final: 0.8731 (ttp) REVERT: D 730 GLN cc_start: 0.8004 (tp40) cc_final: 0.7756 (tp-100) REVERT: D 863 ASN cc_start: 0.7890 (m-40) cc_final: 0.7674 (m-40) REVERT: E 11 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7228 (pp20) REVERT: E 59 ASP cc_start: 0.6793 (t0) cc_final: 0.6461 (t0) REVERT: F 426 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6442 (m) REVERT: F 476 GLN cc_start: 0.8145 (pp30) cc_final: 0.7794 (pp30) REVERT: F 481 SER cc_start: 0.9162 (t) cc_final: 0.8864 (p) outliers start: 84 outliers final: 54 residues processed: 361 average time/residue: 0.1673 time to fit residues: 98.8289 Evaluate side-chains 355 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1070 VAL Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1268 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 612 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 323 optimal weight: 9.9990 chunk 99 optimal weight: 0.2980 chunk 288 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127517 restraints weight = 40511.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126204 restraints weight = 72351.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124044 restraints weight = 71464.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120987 restraints weight = 50430.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120757 restraints weight = 52218.482| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30712 Z= 0.155 Angle : 0.599 12.550 41999 Z= 0.303 Chirality : 0.042 0.221 4864 Planarity : 0.004 0.080 5172 Dihedral : 14.753 179.247 5057 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.11 % Allowed : 19.40 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3696 helix: 1.07 (0.14), residues: 1401 sheet: -0.60 (0.28), residues: 383 loop : -1.93 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 727 TYR 0.014 0.001 TYR C 129 PHE 0.013 0.001 PHE C 61 TRP 0.014 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00374 (30705) covalent geometry : angle 0.59151 (41993) hydrogen bonds : bond 0.03518 ( 1240) hydrogen bonds : angle 4.09256 ( 3448) metal coordination : bond 0.00717 ( 7) metal coordination : angle 7.66962 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 292 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 86 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8950 (mp) REVERT: A 123 ASP cc_start: 0.7312 (t0) cc_final: 0.7041 (t0) REVERT: A 138 ASP cc_start: 0.7553 (p0) cc_final: 0.7274 (p0) REVERT: A 186 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8864 (t) REVERT: C 221 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5916 (ppp) REVERT: C 372 PHE cc_start: 0.7743 (m-80) cc_final: 0.7232 (m-80) REVERT: C 392 MET cc_start: 0.8179 (tmm) cc_final: 0.7926 (tmm) REVERT: C 631 VAL cc_start: 0.8655 (t) cc_final: 0.8379 (m) REVERT: C 908 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8724 (mp) REVERT: C 976 ASN cc_start: 0.8523 (t0) cc_final: 0.8111 (t0) REVERT: C 1036 PHE cc_start: 0.8474 (t80) cc_final: 0.7795 (t80) REVERT: C 1124 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7990 (ptt180) REVERT: C 1324 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7643 (mtt-85) REVERT: D 35 SER cc_start: 0.9010 (t) cc_final: 0.8665 (p) REVERT: D 59 CYS cc_start: 0.8512 (t) cc_final: 0.8154 (t) REVERT: D 118 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8720 (tp) REVERT: D 207 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8148 (tt) REVERT: D 229 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8003 (t80) REVERT: D 332 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6208 (ppp) REVERT: D 698 MET cc_start: 0.8509 (tpp) cc_final: 0.8161 (tpt) REVERT: D 720 MET cc_start: 0.9031 (ttm) cc_final: 0.8755 (ttp) REVERT: D 730 GLN cc_start: 0.8115 (tp40) cc_final: 0.7888 (tp-100) REVERT: D 863 ASN cc_start: 0.7909 (m-40) cc_final: 0.7688 (m-40) REVERT: D 891 CYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7921 (p) REVERT: E 11 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7230 (pp20) REVERT: E 59 ASP cc_start: 0.6888 (t0) cc_final: 0.6577 (t0) REVERT: F 426 VAL cc_start: 0.7279 (OUTLIER) cc_final: 0.6577 (m) REVERT: F 476 GLN cc_start: 0.8206 (pp30) cc_final: 0.7859 (pp30) REVERT: F 481 SER cc_start: 0.9167 (t) cc_final: 0.8862 (p) outliers start: 89 outliers final: 61 residues processed: 358 average time/residue: 0.1685 time to fit residues: 98.1708 Evaluate side-chains 359 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 286 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1070 VAL Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1124 ARG Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 891 CYS Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1268 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 320 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 356 optimal weight: 0.4980 chunk 344 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 96 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.163669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129425 restraints weight = 40465.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127268 restraints weight = 76348.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123198 restraints weight = 52013.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122638 restraints weight = 58552.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122817 restraints weight = 52751.675| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30712 Z= 0.121 Angle : 0.576 12.485 41999 Z= 0.291 Chirality : 0.041 0.207 4864 Planarity : 0.004 0.106 5172 Dihedral : 14.686 179.910 5057 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.69 % Allowed : 20.13 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3696 helix: 1.24 (0.15), residues: 1388 sheet: -0.60 (0.27), residues: 390 loop : -1.88 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 727 TYR 0.016 0.001 TYR D 144 PHE 0.039 0.001 PHE C1047 TRP 0.014 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00287 (30705) covalent geometry : angle 0.57084 (41993) hydrogen bonds : bond 0.03147 ( 1240) hydrogen bonds : angle 4.02373 ( 3448) metal coordination : bond 0.00655 ( 7) metal coordination : angle 6.57761 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 305 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7512 (t80) REVERT: A 86 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 123 ASP cc_start: 0.7234 (t0) cc_final: 0.7016 (t0) REVERT: A 138 ASP cc_start: 0.7492 (p0) cc_final: 0.7218 (p0) REVERT: A 186 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8827 (t) REVERT: C 136 MET cc_start: 0.8316 (tpp) cc_final: 0.8022 (ttm) REVERT: C 221 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5850 (ppp) REVERT: C 372 PHE cc_start: 0.7739 (m-80) cc_final: 0.7284 (m-80) REVERT: C 392 MET cc_start: 0.8105 (tmm) cc_final: 0.7855 (tmm) REVERT: C 631 VAL cc_start: 0.8597 (t) cc_final: 0.8334 (m) REVERT: C 908 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 976 ASN cc_start: 0.8520 (t0) cc_final: 0.8090 (t0) REVERT: C 1036 PHE cc_start: 0.8446 (t80) cc_final: 0.7777 (t80) REVERT: C 1324 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7644 (mtt-85) REVERT: D 35 SER cc_start: 0.9040 (t) cc_final: 0.8678 (p) REVERT: D 59 CYS cc_start: 0.8467 (t) cc_final: 0.8113 (t) REVERT: D 118 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8699 (tp) REVERT: D 207 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (tt) REVERT: D 229 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7973 (t80) REVERT: D 332 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6207 (ppp) REVERT: D 481 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 698 MET cc_start: 0.8499 (tpp) cc_final: 0.8144 (tpt) REVERT: D 720 MET cc_start: 0.9033 (ttm) cc_final: 0.8751 (ttp) REVERT: D 730 GLN cc_start: 0.8097 (tp40) cc_final: 0.7832 (tp-100) REVERT: D 863 ASN cc_start: 0.7891 (m-40) cc_final: 0.7664 (m-40) REVERT: D 891 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7811 (p) REVERT: E 11 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7222 (pp20) REVERT: F 426 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.6592 (m) REVERT: F 476 GLN cc_start: 0.8136 (pp30) cc_final: 0.7794 (pp30) REVERT: F 481 SER cc_start: 0.9147 (t) cc_final: 0.8849 (p) outliers start: 77 outliers final: 58 residues processed: 360 average time/residue: 0.1693 time to fit residues: 99.4138 Evaluate side-chains 363 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 294 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain C residue 1344 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 891 CYS Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1268 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 181 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 306 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127046 restraints weight = 40130.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125454 restraints weight = 77145.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124059 restraints weight = 72229.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120628 restraints weight = 56173.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120909 restraints weight = 53882.061| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30712 Z= 0.161 Angle : 0.605 12.583 41999 Z= 0.305 Chirality : 0.043 0.206 4864 Planarity : 0.004 0.103 5172 Dihedral : 14.679 179.112 5057 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.65 % Allowed : 20.34 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3696 helix: 1.17 (0.15), residues: 1389 sheet: -0.59 (0.27), residues: 393 loop : -1.89 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG C 550 TYR 0.027 0.001 TYR C 129 PHE 0.013 0.001 PHE C 61 TRP 0.014 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00391 (30705) covalent geometry : angle 0.59813 (41993) hydrogen bonds : bond 0.03478 ( 1240) hydrogen bonds : angle 4.05830 ( 3448) metal coordination : bond 0.00704 ( 7) metal coordination : angle 7.53763 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 288 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 86 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8994 (mp) REVERT: A 123 ASP cc_start: 0.7267 (t0) cc_final: 0.7024 (t0) REVERT: A 138 ASP cc_start: 0.7554 (p0) cc_final: 0.7329 (p0) REVERT: C 221 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5911 (ppp) REVERT: C 372 PHE cc_start: 0.7762 (m-80) cc_final: 0.7265 (m-80) REVERT: C 392 MET cc_start: 0.8168 (tmm) cc_final: 0.7944 (tmm) REVERT: C 631 VAL cc_start: 0.8665 (t) cc_final: 0.8390 (m) REVERT: C 727 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8111 (ttp-110) REVERT: C 908 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 976 ASN cc_start: 0.8587 (t0) cc_final: 0.8171 (t0) REVERT: C 1036 PHE cc_start: 0.8498 (t80) cc_final: 0.7814 (t80) REVERT: C 1324 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7708 (mtt-85) REVERT: D 35 SER cc_start: 0.8970 (t) cc_final: 0.8658 (p) REVERT: D 59 CYS cc_start: 0.8490 (t) cc_final: 0.8149 (t) REVERT: D 118 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8711 (tp) REVERT: D 207 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8237 (tt) REVERT: D 229 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8020 (t80) REVERT: D 332 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6381 (ppp) REVERT: D 654 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8740 (t) REVERT: D 698 MET cc_start: 0.8502 (tpp) cc_final: 0.8136 (tpt) REVERT: D 720 MET cc_start: 0.9019 (ttm) cc_final: 0.8746 (ttp) REVERT: D 730 GLN cc_start: 0.8131 (tp40) cc_final: 0.7871 (tp-100) REVERT: D 863 ASN cc_start: 0.7928 (m-40) cc_final: 0.7702 (m-40) REVERT: D 891 CYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7923 (p) REVERT: E 11 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7227 (pp20) REVERT: E 59 ASP cc_start: 0.6853 (t0) cc_final: 0.6524 (t0) REVERT: F 426 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6727 (m) REVERT: F 476 GLN cc_start: 0.8173 (pp30) cc_final: 0.7844 (pp30) REVERT: F 481 SER cc_start: 0.9158 (t) cc_final: 0.8861 (p) outliers start: 76 outliers final: 58 residues processed: 345 average time/residue: 0.1742 time to fit residues: 98.3659 Evaluate side-chains 355 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1341 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 891 CYS Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1268 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 39 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 303 optimal weight: 0.0070 chunk 306 optimal weight: 0.0040 chunk 171 optimal weight: 2.9990 chunk 338 optimal weight: 0.4980 chunk 189 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 ASN D 158 HIS D 276 ASN D1248 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.165454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131558 restraints weight = 40552.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130639 restraints weight = 73590.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126941 restraints weight = 71960.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124144 restraints weight = 62115.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124402 restraints weight = 57348.756| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30712 Z= 0.105 Angle : 0.569 12.579 41999 Z= 0.287 Chirality : 0.041 0.204 4864 Planarity : 0.004 0.119 5172 Dihedral : 14.599 178.490 5057 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.16 % Allowed : 20.94 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3696 helix: 1.33 (0.15), residues: 1388 sheet: -0.56 (0.28), residues: 389 loop : -1.84 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 550 TYR 0.026 0.001 TYR C 129 PHE 0.012 0.001 PHE D 178 TRP 0.015 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00238 (30705) covalent geometry : angle 0.56461 (41993) hydrogen bonds : bond 0.02895 ( 1240) hydrogen bonds : angle 3.94781 ( 3448) metal coordination : bond 0.00630 ( 7) metal coordination : angle 5.70075 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.92 seconds wall clock time: 76 minutes 5.41 seconds (4565.41 seconds total)