Starting phenix.real_space_refine on Sat Feb 7 15:13:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.map" model { file = "/net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u62_63895/02_2026/9u62_63895.cif" } resolution = 2.7 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4798 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Ni 1 6.56 5 S 141 5.16 5 C 18714 2.51 5 N 5023 2.21 5 O 5634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29513 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7760 Classifications: {'peptide': 970} Link IDs: {'PTRANS': 40, 'TRANS': 929} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4012 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 479} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "P" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 11688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1474, 11688 Classifications: {'peptide': 1474} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1403} Chain breaks: 11 Chain: "C" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4922 Classifications: {'peptide': 632} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 594} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' NI': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.67, per 1000 atoms: 0.19 Number of scatterers: 29513 At special positions: 0 Unit cell: (209, 129.2, 204.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 1 28.00 S 141 16.00 O 5634 8.00 N 5023 7.00 C 18714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS D 693 " - pdb=" SG CYS D 720 " distance=2.03 Simple disulfide: pdb=" SG CYS D 694 " - pdb=" SG CYS D 727 " distance=2.03 Simple disulfide: pdb=" SG CYS D 707 " - pdb=" SG CYS D 728 " distance=2.03 Simple disulfide: pdb=" SG CYS D 816 " - pdb=" SG CYS C 559 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1158 " distance=2.03 Simple disulfide: pdb=" SG CYS D1358 " - pdb=" SG CYS D1489 " distance=2.03 Simple disulfide: pdb=" SG CYS D1389 " - pdb=" SG CYS D1458 " distance=2.03 Simple disulfide: pdb=" SG CYS D1518 " - pdb=" SG CYS D1590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 596 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 599 " - pdb=" SG CYS B 615 " distance=2.04 Simple disulfide: pdb=" SG CYS B 656 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS P 327 " - pdb=" SG CYS P 370 " distance=2.02 Simple disulfide: pdb=" SG CYS P 337 " - pdb=" SG CYS P 376 " distance=2.03 Simple disulfide: pdb=" SG CYS P 350 " - pdb=" SG CYS P 360 " distance=2.03 Simple disulfide: pdb=" SG CYS P 407 " - pdb=" SG CYS P 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 627 " - pdb=" SG CYS E 662 " distance=2.03 Simple disulfide: pdb=" SG CYS E 873 " - pdb=" SG CYS E1513 " distance=2.03 Simple disulfide: pdb=" SG CYS E1358 " - pdb=" SG CYS E1489 " distance=2.03 Simple disulfide: pdb=" SG CYS E1389 " - pdb=" SG CYS E1458 " distance=2.03 Simple disulfide: pdb=" SG CYS E1506 " - pdb=" SG CYS E1511 " distance=2.03 Simple disulfide: pdb=" SG CYS E1537 " - pdb=" SG CYS E1661 " distance=2.03 Simple disulfide: pdb=" SG CYS E1637 " - pdb=" SG CYS E1646 " distance=2.04 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 662 " distance=2.05 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN P 428 " " NAG B 801 " - " ASN B 378 " " NAG B 802 " - " ASN B 285 " " NAG C1701 " - " ASN C 85 " " NAG D1701 " - " ASN D 939 " " NAG E1701 " - " ASN E 939 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6968 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 51 sheets defined 20.9% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'D' and resid 675 through 684 removed outlier: 4.047A pdb=" N ASP D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS D 682 " --> pdb=" O LYS D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 686 No H-bonds generated for 'chain 'D' and resid 685 through 686' Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 691 through 699 removed outlier: 3.623A pdb=" N GLY D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 698 " --> pdb=" O CYS D 694 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 714 removed outlier: 3.643A pdb=" N PHE D 713 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 714 " --> pdb=" O THR D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 743 removed outlier: 3.630A pdb=" N ILE D 731 " --> pdb=" O CYS D 727 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 733 " --> pdb=" O ASN D 729 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 734 " --> pdb=" O TYR D 730 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 953 Processing helix chain 'D' and resid 987 through 996 removed outlier: 3.503A pdb=" N THR D 991 " --> pdb=" O VAL D 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 995 " --> pdb=" O THR D 991 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1004 removed outlier: 3.964A pdb=" N ILE D1004 " --> pdb=" O LYS D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1017 removed outlier: 3.584A pdb=" N MET D1015 " --> pdb=" O GLU D1012 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1016 " --> pdb=" O GLN D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1032 Processing helix chain 'D' and resid 1033 through 1038 Processing helix chain 'D' and resid 1041 through 1057 removed outlier: 3.855A pdb=" N ALA D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D1046 " --> pdb=" O ARG D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1060 No H-bonds generated for 'chain 'D' and resid 1058 through 1060' Processing helix chain 'D' and resid 1075 through 1089 Processing helix chain 'D' and resid 1096 through 1112 removed outlier: 3.610A pdb=" N LEU D1100 " --> pdb=" O ASP D1096 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN D1112 " --> pdb=" O ILE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1130 Processing helix chain 'D' and resid 1136 through 1152 removed outlier: 3.533A pdb=" N ASP D1140 " --> pdb=" O ASN D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1179 removed outlier: 6.283A pdb=" N THR D1170 " --> pdb=" O PRO D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1180 through 1183 removed outlier: 3.860A pdb=" N LEU D1183 " --> pdb=" O TYR D1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1180 through 1183' Processing helix chain 'D' and resid 1185 through 1199 removed outlier: 3.818A pdb=" N MET D1199 " --> pdb=" O ALA D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1213 removed outlier: 3.618A pdb=" N THR D1213 " --> pdb=" O LYS D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.617A pdb=" N VAL D1230 " --> pdb=" O GLN D1226 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1257 removed outlier: 4.047A pdb=" N VAL D1252 " --> pdb=" O PHE D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1283 removed outlier: 3.729A pdb=" N THR D1272 " --> pdb=" O SER D1268 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D1281 " --> pdb=" O GLN D1277 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D1283 " --> pdb=" O LEU D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1414 through 1424 removed outlier: 3.506A pdb=" N ALA D1422 " --> pdb=" O LEU D1418 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY D1424 " --> pdb=" O GLN D1420 " (cutoff:3.500A) Processing helix chain 'D' and resid 1509 through 1515 removed outlier: 3.581A pdb=" N CYS D1513 " --> pdb=" O GLU D1509 " (cutoff:3.500A) Processing helix chain 'D' and resid 1528 through 1536 Processing helix chain 'D' and resid 1589 through 1591 No H-bonds generated for 'chain 'D' and resid 1589 through 1591' Processing helix chain 'D' and resid 1607 through 1609 No H-bonds generated for 'chain 'D' and resid 1607 through 1609' Processing helix chain 'D' and resid 1645 through 1649 Processing helix chain 'B' and resid 282 through 302 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.623A pdb=" N SER B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER B 330 " --> pdb=" O ALA B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 331 through 341 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.756A pdb=" N ASP B 346 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS B 347 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 348' Processing helix chain 'B' and resid 354 through 366 removed outlier: 3.598A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 435 through 441 Processing helix chain 'B' and resid 460 through 467 removed outlier: 4.073A pdb=" N VAL B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 4.018A pdb=" N LYS B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 614 through 623 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.549A pdb=" N CYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 663 Processing helix chain 'B' and resid 748 through 756 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 303 through 311 removed outlier: 3.957A pdb=" N VAL E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 removed outlier: 3.890A pdb=" N ASP E 318 " --> pdb=" O ARG E 315 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 320 " --> pdb=" O GLU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.806A pdb=" N GLN E 436 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 487 removed outlier: 3.513A pdb=" N LYS E 486 " --> pdb=" O HIS E 483 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 487 " --> pdb=" O GLU E 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 483 through 487' Processing helix chain 'E' and resid 522 through 526 removed outlier: 3.583A pdb=" N PHE E 525 " --> pdb=" O THR E 522 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 526 " --> pdb=" O THR E 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 522 through 526' Processing helix chain 'E' and resid 601 through 606 removed outlier: 4.040A pdb=" N LEU E 605 " --> pdb=" O GLY E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 622 removed outlier: 3.534A pdb=" N ILE E 616 " --> pdb=" O THR E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 643 removed outlier: 3.516A pdb=" N VAL E 638 " --> pdb=" O ASP E 634 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 639 " --> pdb=" O TYR E 635 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 642 " --> pdb=" O VAL E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 757 through 761 Processing helix chain 'E' and resid 996 through 1001 removed outlier: 3.601A pdb=" N ARG E 999 " --> pdb=" O ASP E 996 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS E1001 " --> pdb=" O GLU E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1013 through 1032 removed outlier: 3.609A pdb=" N GLY E1017 " --> pdb=" O GLN E1013 " (cutoff:3.500A) Proline residue: E1020 - end of helix Processing helix chain 'E' and resid 1033 through 1038 Processing helix chain 'E' and resid 1041 through 1052 removed outlier: 3.730A pdb=" N GLU E1047 " --> pdb=" O GLN E1043 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1085 removed outlier: 3.770A pdb=" N ALA E1080 " --> pdb=" O THR E1076 " (cutoff:3.500A) Processing helix chain 'E' and resid 1130 through 1135 removed outlier: 3.793A pdb=" N LEU E1133 " --> pdb=" O ILE E1130 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN E1135 " --> pdb=" O GLY E1132 " (cutoff:3.500A) Processing helix chain 'E' and resid 1138 through 1154 removed outlier: 3.808A pdb=" N ALA E1142 " --> pdb=" O GLU E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1154 through 1159 removed outlier: 3.665A pdb=" N GLU E1159 " --> pdb=" O LYS E1155 " (cutoff:3.500A) Processing helix chain 'E' and resid 1170 through 1180 Processing helix chain 'E' and resid 1181 through 1183 No H-bonds generated for 'chain 'E' and resid 1181 through 1183' Processing helix chain 'E' and resid 1188 through 1200 removed outlier: 3.563A pdb=" N ALA E1195 " --> pdb=" O ILE E1191 " (cutoff:3.500A) Processing helix chain 'E' and resid 1204 through 1214 removed outlier: 3.983A pdb=" N ALA E1214 " --> pdb=" O PHE E1210 " (cutoff:3.500A) Processing helix chain 'E' and resid 1227 through 1243 Processing helix chain 'E' and resid 1248 through 1260 removed outlier: 3.860A pdb=" N VAL E1252 " --> pdb=" O PHE E1248 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E1260 " --> pdb=" O LEU E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1270 through 1284 removed outlier: 3.645A pdb=" N MET E1274 " --> pdb=" O GLN E1270 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1424 Processing helix chain 'E' and resid 1430 through 1435 Processing helix chain 'E' and resid 1639 through 1641 No H-bonds generated for 'chain 'E' and resid 1639 through 1641' Processing helix chain 'E' and resid 1642 through 1659 removed outlier: 3.505A pdb=" N CYS E1646 " --> pdb=" O ASN E1642 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY E1650 " --> pdb=" O CYS E1646 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA E1651 " --> pdb=" O GLN E1647 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR E1653 " --> pdb=" O LEU E1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 303 through 310 Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.625A pdb=" N ASP C 318 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 319 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 320 " --> pdb=" O GLU C 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 320' Processing helix chain 'C' and resid 448 through 452 removed outlier: 4.004A pdb=" N ASN C 451 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 452 " --> pdb=" O VAL C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 452' Processing helix chain 'C' and resid 483 through 487 removed outlier: 3.610A pdb=" N ILE C 487 " --> pdb=" O GLU C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.821A pdb=" N ILE C 526 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.609A pdb=" N LEU C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.579A pdb=" N VAL C 619 " --> pdb=" O LYS C 615 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 620 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.595A pdb=" N ALA C 642 " --> pdb=" O VAL C 638 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 750 through 752 removed outlier: 3.555A pdb=" N ASN D 750 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 579 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 553 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 581 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 550 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 537 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 775 through 777 Processing sheet with id=AA3, first strand: chain 'D' and resid 775 through 777 Processing sheet with id=AA4, first strand: chain 'D' and resid 787 through 794 Processing sheet with id=AA5, first strand: chain 'D' and resid 829 through 834 Processing sheet with id=AA6, first strand: chain 'D' and resid 829 through 834 removed outlier: 4.348A pdb=" N ASN D1468 " --> pdb=" O GLU D 846 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 839 through 840 removed outlier: 6.538A pdb=" N VAL D 839 " --> pdb=" O VAL D 932 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS D 882 " --> pdb=" O LEU D 866 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 936 through 947 removed outlier: 6.732A pdb=" N VAL D1344 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D 944 " --> pdb=" O LEU D1342 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D1342 " --> pdb=" O VAL D 944 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR D 946 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY D1340 " --> pdb=" O THR D 946 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 957 through 962 removed outlier: 4.055A pdb=" N THR D1331 " --> pdb=" O GLN D1299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1361 through 1369 Processing sheet with id=AB2, first strand: chain 'D' and resid 1431 through 1434 removed outlier: 3.770A pdb=" N LYS D1431 " --> pdb=" O TYR D1447 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D1476 " --> pdb=" O SER D1406 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU D1487 " --> pdb=" O ALA D1481 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1611 through 1613 removed outlier: 3.557A pdb=" N SER D1619 " --> pdb=" O TRP D1612 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU D1618 " --> pdb=" O GLN D1581 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR D1583 " --> pdb=" O LEU D1618 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU D1560 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D1552 " --> pdb=" O GLU D1560 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE D1562 " --> pdb=" O VAL D1550 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS D1546 " --> pdb=" O GLU D1566 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR D1568 " --> pdb=" O VAL D1544 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D1544 " --> pdb=" O THR D1568 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS D1570 " --> pdb=" O ASP D1542 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP D1542 " --> pdb=" O LYS D1570 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR D1543 " --> pdb=" O GLY D1606 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D1606 " --> pdb=" O TYR D1543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 261 through 262 removed outlier: 6.222A pdb=" N ILE B 261 " --> pdb=" O ASP B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 319 through 322 removed outlier: 6.626A pdb=" N LEU B 311 " --> pdb=" O TRP B 321 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET B 269 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 310 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 271 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 312 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 273 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER B 268 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL B 383 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 270 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 385 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 272 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N MET B 387 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 274 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP B 424 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS B 382 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR B 426 " --> pdb=" O HIS B 382 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 384 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE B 428 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 386 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 627 through 636 Processing sheet with id=AB7, first strand: chain 'B' and resid 680 through 684 removed outlier: 6.110A pdb=" N ILE B 743 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 717 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 703 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 317 through 318 removed outlier: 3.807A pdb=" N GLU P 317 " --> pdb=" O ARG P 351 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG P 351 " --> pdb=" O GLU P 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'P' and resid 342 through 347 removed outlier: 19.330A pdb=" N GLN P 365 " --> pdb=" O GLU P 426 " (cutoff:3.500A) removed outlier: 14.898A pdb=" N ASN P 428 " --> pdb=" O GLN P 365 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N ILE P 367 " --> pdb=" O ASN P 428 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N THR P 430 " --> pdb=" O ILE P 367 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS P 369 " --> pdb=" O THR P 430 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TRP P 432 " --> pdb=" O HIS P 369 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR P 371 " --> pdb=" O TRP P 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 382 through 385 removed outlier: 4.248A pdb=" N TRP P 385 " --> pdb=" O GLN P 404 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN P 404 " --> pdb=" O TRP P 385 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG P 403 " --> pdb=" O GLU P 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 83 through 89 removed outlier: 8.709A pdb=" N THR E 41 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET E 25 " --> pdb=" O HIS E 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 30 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.533A pdb=" N LEU E 34 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP E 61 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL E 68 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 134 Processing sheet with id=AC5, first strand: chain 'E' and resid 138 through 139 removed outlier: 6.494A pdb=" N VAL E 163 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 179 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL E 165 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN E 177 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE E 167 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 232 through 238 Processing sheet with id=AC7, first strand: chain 'E' and resid 243 through 244 removed outlier: 5.814A pdb=" N LEU E 324 " --> pdb=" O GLY E 345 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE E 273 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER E 287 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N ILE E 275 " --> pdb=" O PRO E 285 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N ASP E 277 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N SER E 283 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 354 through 356 Processing sheet with id=AC9, first strand: chain 'E' and resid 363 through 364 Processing sheet with id=AD1, first strand: chain 'E' and resid 455 through 460 removed outlier: 3.757A pdb=" N GLU E 469 " --> pdb=" O ILE E 521 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 499 through 507 removed outlier: 5.114A pdb=" N LEU E 500 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN E 496 " --> pdb=" O LEU E 500 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR E 489 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR E 536 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 563 through 567 Processing sheet with id=AD4, first strand: chain 'E' and resid 770 through 771 Processing sheet with id=AD5, first strand: chain 'E' and resid 775 through 777 Processing sheet with id=AD6, first strand: chain 'E' and resid 829 through 834 removed outlier: 3.524A pdb=" N PHE E 830 " --> pdb=" O TYR E 852 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 834 " --> pdb=" O ARG E 848 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG E 848 " --> pdb=" O ARG E 834 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 838 through 840 removed outlier: 6.273A pdb=" N VAL E 839 " --> pdb=" O VAL E 932 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS E 882 " --> pdb=" O LEU E 866 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 936 through 946 removed outlier: 6.465A pdb=" N VAL E1344 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL E 944 " --> pdb=" O LEU E1342 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU E1342 " --> pdb=" O VAL E 944 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR E 946 " --> pdb=" O GLY E1340 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY E1340 " --> pdb=" O THR E 946 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 958 through 962 removed outlier: 3.567A pdb=" N PHE E1330 " --> pdb=" O ILE E 962 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR E1333 " --> pdb=" O VAL E1296 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 1361 through 1369 Processing sheet with id=AE2, first strand: chain 'E' and resid 1427 through 1428 removed outlier: 3.742A pdb=" N ALA E1476 " --> pdb=" O SER E1406 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 1504 through 1507 Processing sheet with id=AE4, first strand: chain 'E' and resid 1568 through 1569 removed outlier: 6.954A pdb=" N ILE E1562 " --> pdb=" O VAL E1550 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL E1552 " --> pdb=" O GLU E1560 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU E1560 " --> pdb=" O VAL E1552 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N GLN E1581 " --> pdb=" O LEU E1618 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N TYR E1620 " --> pdb=" O GLN E1581 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR E1583 " --> pdb=" O TYR E1620 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 1568 through 1569 removed outlier: 4.262A pdb=" N HIS E1601 " --> pdb=" O TRP E1631 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 89 Processing sheet with id=AE7, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.541A pdb=" N PHE C 105 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 70 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP C 61 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL C 68 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 129 through 134 Processing sheet with id=AE9, first strand: chain 'C' and resid 138 through 139 removed outlier: 6.616A pdb=" N VAL C 163 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C 179 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL C 165 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN C 177 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 167 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 233 through 238 Processing sheet with id=AF2, first strand: chain 'C' and resid 243 through 244 removed outlier: 3.775A pdb=" N GLY C 345 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 324 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N GLY C 267 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N ARG C 290 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ALA C 269 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N LEU C 288 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL C 271 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU C 286 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE C 273 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AF4, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AF5, first strand: chain 'C' and resid 455 through 459 Processing sheet with id=AF6, first strand: chain 'C' and resid 499 through 507 removed outlier: 5.226A pdb=" N LEU C 500 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 496 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 502 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR C 489 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR C 536 " --> pdb=" O TYR C 489 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5016 1.31 - 1.44: 7585 1.44 - 1.58: 17275 1.58 - 1.71: 4 1.71 - 1.84: 219 Bond restraints: 30099 Sorted by residual: bond pdb=" C THR E 628 " pdb=" N PRO E 629 " ideal model delta sigma weight residual 1.331 1.377 -0.045 7.90e-03 1.60e+04 3.29e+01 bond pdb=" CA LYS E 633 " pdb=" C LYS E 633 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.37e-02 5.33e+03 2.98e+01 bond pdb=" CA THR C 628 " pdb=" C THR C 628 " ideal model delta sigma weight residual 1.519 1.470 0.049 1.01e-02 9.80e+03 2.32e+01 bond pdb=" C GLY C 632 " pdb=" O GLY C 632 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.06e-02 8.90e+03 2.08e+01 bond pdb=" C THR E 628 " pdb=" O THR E 628 " ideal model delta sigma weight residual 1.238 1.180 0.058 1.28e-02 6.10e+03 2.06e+01 ... (remaining 30094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 40163 2.72 - 5.43: 495 5.43 - 8.15: 79 8.15 - 10.87: 22 10.87 - 13.58: 5 Bond angle restraints: 40764 Sorted by residual: angle pdb=" N ASP E 277 " pdb=" CA ASP E 277 " pdb=" C ASP E 277 " ideal model delta sigma weight residual 110.55 98.48 12.07 1.35e+00 5.49e-01 7.99e+01 angle pdb=" C PHE E1248 " pdb=" N VAL E1249 " pdb=" CA VAL E1249 " ideal model delta sigma weight residual 120.24 125.20 -4.96 6.30e-01 2.52e+00 6.20e+01 angle pdb=" N TRP E1077 " pdb=" CA TRP E1077 " pdb=" C TRP E1077 " ideal model delta sigma weight residual 111.33 119.84 -8.51 1.21e+00 6.83e-01 4.94e+01 angle pdb=" C PHE C 525 " pdb=" N ILE C 526 " pdb=" CA ILE C 526 " ideal model delta sigma weight residual 120.33 125.06 -4.73 8.00e-01 1.56e+00 3.49e+01 angle pdb=" CA LYS D1337 " pdb=" CB LYS D1337 " pdb=" CG LYS D1337 " ideal model delta sigma weight residual 114.10 125.77 -11.67 2.00e+00 2.50e-01 3.40e+01 ... (remaining 40759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.32: 15965 18.32 - 36.64: 1895 36.64 - 54.96: 484 54.96 - 73.29: 112 73.29 - 91.61: 37 Dihedral angle restraints: 18493 sinusoidal: 7702 harmonic: 10791 Sorted by residual: dihedral pdb=" CB CYS E 873 " pdb=" SG CYS E 873 " pdb=" SG CYS E1513 " pdb=" CB CYS E1513 " ideal model delta sinusoidal sigma weight residual 93.00 172.40 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS P 327 " pdb=" SG CYS P 327 " pdb=" SG CYS P 370 " pdb=" CB CYS P 370 " ideal model delta sinusoidal sigma weight residual 93.00 169.70 -76.70 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS D1101 " pdb=" SG CYS D1101 " pdb=" SG CYS D1158 " pdb=" CB CYS D1158 " ideal model delta sinusoidal sigma weight residual 93.00 153.01 -60.01 1 1.00e+01 1.00e-02 4.80e+01 ... (remaining 18490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4468 0.123 - 0.247: 136 0.247 - 0.370: 4 0.370 - 0.494: 3 0.494 - 0.617: 2 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CA SER E 631 " pdb=" N SER E 631 " pdb=" C SER E 631 " pdb=" CB SER E 631 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA SER C 631 " pdb=" N SER C 631 " pdb=" C SER C 631 " pdb=" CB SER C 631 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CB VAL B 686 " pdb=" CA VAL B 686 " pdb=" CG1 VAL B 686 " pdb=" CG2 VAL B 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 4610 not shown) Planarity restraints: 5249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D1538 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO D1539 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO D1539 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D1539 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 311 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C VAL C 311 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL C 311 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN C 312 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 169 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO C 170 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " 0.040 5.00e-02 4.00e+02 ... (remaining 5246 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 206 2.63 - 3.20: 21610 3.20 - 3.76: 41839 3.76 - 4.33: 60151 4.33 - 4.90: 101694 Nonbonded interactions: 225500 Sorted by model distance: nonbonded pdb=" OG SER B 280 " pdb="NI NI B 803 " model vdw 2.059 2.180 nonbonded pdb=" OG1 THR B 353 " pdb="NI NI B 803 " model vdw 2.094 2.180 nonbonded pdb=" O LYS E1209 " pdb=" OG1 THR E1213 " model vdw 2.259 3.040 nonbonded pdb=" O VAL D 971 " pdb=" OG1 THR D 974 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP E 135 " pdb=" OH TYR E 139 " model vdw 2.304 3.040 ... (remaining 225495 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 0.089 30131 Z= 0.227 Angle : 0.791 13.583 40835 Z= 0.436 Chirality : 0.055 0.617 4613 Planarity : 0.007 0.088 5243 Dihedral : 17.072 91.606 11450 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.62 % Allowed : 23.16 % Favored : 74.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.10 % 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: -0.95 (0.13), residues: 3668 helix: -2.00 (0.16), residues: 614 sheet: 1.11 (0.14), residues: 1260 loop : -1.44 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 926 TYR 0.032 0.002 TYR E 209 PHE 0.019 0.002 PHE E1652 TRP 0.031 0.002 TRP E1605 HIS 0.013 0.001 HIS D1312 Details of bonding type rmsd covalent geometry : bond 0.00433 (30099) covalent geometry : angle 0.78555 (40764) SS BOND : bond 0.00459 ( 25) SS BOND : angle 1.38235 ( 50) hydrogen bonds : bond 0.14772 ( 1083) hydrogen bonds : angle 6.58972 ( 3033) link_BETA1-4 : bond 0.01668 ( 1) link_BETA1-4 : angle 3.13028 ( 3) link_NAG-ASN : bond 0.00898 ( 6) link_NAG-ASN : angle 3.77478 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 462 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6897 (tppt) REVERT: D 863 ARG cc_start: 0.6859 (ttm110) cc_final: 0.6658 (ttt90) REVERT: D 879 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7662 (mmtm) REVERT: D 909 GLU cc_start: 0.7433 (tp30) cc_final: 0.7158 (tp30) REVERT: D 936 ILE cc_start: 0.7755 (tt) cc_final: 0.7473 (pp) REVERT: D 959 LYS cc_start: 0.7197 (tttt) cc_final: 0.6830 (tmtm) REVERT: D 968 SER cc_start: 0.8143 (m) cc_final: 0.7935 (t) REVERT: D 1032 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6598 (mm-30) REVERT: D 1097 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7899 (m) REVERT: D 1105 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7147 (ttmm) REVERT: D 1159 GLU cc_start: 0.7034 (pt0) cc_final: 0.6822 (pt0) REVERT: D 1277 GLN cc_start: 0.7566 (tt0) cc_final: 0.7355 (tm-30) REVERT: D 1311 ILE cc_start: 0.7137 (mt) cc_final: 0.6931 (mt) REVERT: D 1325 LYS cc_start: 0.7070 (ttpt) cc_final: 0.6401 (tptt) REVERT: D 1396 GLN cc_start: 0.7216 (pt0) cc_final: 0.6692 (mt0) REVERT: D 1455 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: D 1456 ASP cc_start: 0.8126 (m-30) cc_final: 0.7465 (m-30) REVERT: D 1560 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5830 (mp0) REVERT: D 1595 LYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5768 (mttt) REVERT: B 454 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7653 (mmmm) REVERT: B 587 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7676 (tttm) REVERT: B 616 GLN cc_start: 0.6978 (tp40) cc_final: 0.6459 (tp-100) REVERT: B 619 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7351 (tttp) REVERT: B 639 LYS cc_start: 0.7607 (ptmm) cc_final: 0.7256 (tmtt) REVERT: B 754 GLU cc_start: 0.7336 (tp30) cc_final: 0.7015 (tt0) REVERT: P 368 ARG cc_start: 0.4733 (ttm170) cc_final: 0.4191 (ttp80) REVERT: P 403 ARG cc_start: 0.1435 (OUTLIER) cc_final: 0.1216 (ttp-110) REVERT: E 35 ARG cc_start: 0.6737 (mtm180) cc_final: 0.6497 (mtt90) REVERT: E 104 LYS cc_start: 0.7100 (mptt) cc_final: 0.6871 (tppt) REVERT: E 126 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6291 (mt0) REVERT: E 171 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6710 (mm-30) REVERT: E 305 LYS cc_start: 0.7194 (tttp) cc_final: 0.6529 (mptt) REVERT: E 447 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8020 (t) REVERT: E 453 ASN cc_start: 0.7600 (m-40) cc_final: 0.7346 (m110) REVERT: E 571 GLU cc_start: 0.5770 (tt0) cc_final: 0.5336 (mm-30) REVERT: E 659 GLU cc_start: 0.7414 (mp0) cc_final: 0.7137 (mm-30) REVERT: E 660 LEU cc_start: 0.8333 (mt) cc_final: 0.7913 (mm) REVERT: E 977 GLU cc_start: 0.6356 (tt0) cc_final: 0.6016 (tt0) REVERT: E 1181 MET cc_start: 0.4021 (mpm) cc_final: 0.3595 (mmt) REVERT: E 1385 ILE cc_start: 0.7814 (mt) cc_final: 0.7509 (mm) REVERT: E 1396 GLN cc_start: 0.7687 (pt0) cc_final: 0.7483 (pt0) REVERT: E 1426 ASP cc_start: 0.6962 (m-30) cc_final: 0.6523 (t0) REVERT: E 1431 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7033 (tttm) REVERT: E 1563 MET cc_start: 0.7688 (mmt) cc_final: 0.7351 (mmt) REVERT: E 1656 MET cc_start: 0.7873 (mmm) cc_final: 0.7557 (mmm) REVERT: C 104 LYS cc_start: 0.6826 (tttt) cc_final: 0.6226 (mtpt) REVERT: C 201 MET cc_start: 0.8631 (mmt) cc_final: 0.8011 (mmt) REVERT: C 205 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8105 (mppt) REVERT: C 240 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6868 (mm-30) REVERT: C 249 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7871 (mtmm) REVERT: C 299 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7470 (tp30) REVERT: C 342 GLU cc_start: 0.7993 (tt0) cc_final: 0.7674 (tt0) REVERT: C 371 ASP cc_start: 0.7536 (m-30) cc_final: 0.7287 (m-30) REVERT: C 466 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7880 (mtm110) REVERT: C 480 ASP cc_start: 0.7453 (m-30) cc_final: 0.7082 (m-30) REVERT: C 509 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 513 ASP cc_start: 0.8104 (m-30) cc_final: 0.7829 (m-30) REVERT: C 615 LYS cc_start: 0.8348 (mttm) cc_final: 0.8123 (mtmt) REVERT: C 648 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8228 (t) outliers start: 86 outliers final: 38 residues processed: 533 average time/residue: 0.6831 time to fit residues: 424.7560 Evaluate side-chains 362 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 722 LYS Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1595 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 619 LYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 408 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1188 THR Chi-restraints excluded: chain E residue 1488 SER Chi-restraints excluded: chain E residue 1528 THR Chi-restraints excluded: chain E residue 1609 SER Chi-restraints excluded: chain E residue 1626 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 648 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 738 HIS D 760 ASN D1119 GLN D1327 ASN D1503 ASN D1645 GLN B 435 ASN B 436 GLN B 493 GLN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN B 744 ASN E 103 ASN E 109 GLN E 276 GLN E1014 ASN E1229 ASN C 82 HIS C 126 GLN C 212 ASN C 472 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117614 restraints weight = 33263.854| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.40 r_work: 0.3071 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30131 Z= 0.129 Angle : 0.566 12.372 40835 Z= 0.298 Chirality : 0.046 0.370 4613 Planarity : 0.005 0.067 5243 Dihedral : 5.835 57.274 4221 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.27 % Allowed : 22.13 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -0.24 (0.13), residues: 3668 helix: -0.47 (0.20), residues: 629 sheet: 1.31 (0.15), residues: 1254 loop : -1.15 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 353 TYR 0.021 0.002 TYR E 209 PHE 0.016 0.002 PHE E 112 TRP 0.018 0.001 TRP E1605 HIS 0.006 0.001 HIS D1312 Details of bonding type rmsd covalent geometry : bond 0.00301 (30099) covalent geometry : angle 0.56253 (40764) SS BOND : bond 0.01020 ( 25) SS BOND : angle 0.80209 ( 50) hydrogen bonds : bond 0.03754 ( 1083) hydrogen bonds : angle 5.08141 ( 3033) link_BETA1-4 : bond 0.00408 ( 1) link_BETA1-4 : angle 1.46271 ( 3) link_NAG-ASN : bond 0.00571 ( 6) link_NAG-ASN : angle 2.72901 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 334 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 680 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6247 (mpp) REVERT: D 716 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7942 (mp) REVERT: D 722 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7411 (tppt) REVERT: D 879 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7929 (mmtm) REVERT: D 909 GLU cc_start: 0.7829 (tp30) cc_final: 0.7594 (tp30) REVERT: D 959 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7105 (tmtm) REVERT: D 1030 GLU cc_start: 0.7280 (tm-30) cc_final: 0.7066 (tt0) REVERT: D 1061 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: D 1105 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7846 (ttmm) REVERT: D 1110 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: D 1159 GLU cc_start: 0.7330 (pt0) cc_final: 0.6878 (tp30) REVERT: D 1212 THR cc_start: 0.7991 (m) cc_final: 0.7648 (t) REVERT: D 1310 ARG cc_start: 0.7070 (mmm160) cc_final: 0.6630 (tmt170) REVERT: D 1356 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8290 (mm) REVERT: D 1384 MET cc_start: 0.9090 (mtp) cc_final: 0.8848 (mtp) REVERT: D 1396 GLN cc_start: 0.8120 (pt0) cc_final: 0.7575 (mt0) REVERT: D 1509 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5501 (tp30) REVERT: D 1560 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: B 328 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7088 (t70) REVERT: B 387 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7608 (mmm) REVERT: B 410 TYR cc_start: 0.7505 (t80) cc_final: 0.6998 (t80) REVERT: B 422 TYR cc_start: 0.7121 (m-80) cc_final: 0.6454 (m-80) REVERT: B 454 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7824 (mmmm) REVERT: B 587 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8043 (tttm) REVERT: B 616 GLN cc_start: 0.7368 (tp40) cc_final: 0.6830 (tp-100) REVERT: B 639 LYS cc_start: 0.7890 (ptmm) cc_final: 0.7453 (tmtt) REVERT: B 672 ILE cc_start: 0.6007 (OUTLIER) cc_final: 0.5323 (pp) REVERT: B 754 GLU cc_start: 0.7542 (tp30) cc_final: 0.7159 (tt0) REVERT: P 403 ARG cc_start: 0.1694 (OUTLIER) cc_final: 0.1416 (ttp-110) REVERT: E 35 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6873 (mtt90) REVERT: E 171 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7701 (mm-30) REVERT: E 275 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8449 (mm) REVERT: E 305 LYS cc_start: 0.7867 (tttp) cc_final: 0.7182 (mptt) REVERT: E 453 ASN cc_start: 0.8081 (m-40) cc_final: 0.7806 (m-40) REVERT: E 478 ARG cc_start: 0.8467 (tpm170) cc_final: 0.7818 (tpt170) REVERT: E 571 GLU cc_start: 0.5897 (tt0) cc_final: 0.5436 (tp30) REVERT: E 659 GLU cc_start: 0.7934 (mp0) cc_final: 0.7518 (mm-30) REVERT: E 977 GLU cc_start: 0.6261 (tt0) cc_final: 0.5888 (tt0) REVERT: E 1015 MET cc_start: 0.3975 (pmm) cc_final: 0.3264 (mmp) REVERT: E 1181 MET cc_start: 0.4236 (mpm) cc_final: 0.3683 (tpp) REVERT: E 1241 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4254 (tm) REVERT: E 1385 ILE cc_start: 0.8159 (mt) cc_final: 0.7906 (mm) REVERT: E 1396 GLN cc_start: 0.8059 (pt0) cc_final: 0.7841 (pt0) REVERT: E 1426 ASP cc_start: 0.7335 (m-30) cc_final: 0.7106 (t70) REVERT: E 1431 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8076 (tttm) REVERT: E 1455 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6061 (pp20) REVERT: E 1535 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6274 (pttm) REVERT: E 1563 MET cc_start: 0.7411 (mmt) cc_final: 0.7075 (mmt) REVERT: E 1598 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: E 1603 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6627 (tp) REVERT: E 1629 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: C 104 LYS cc_start: 0.7045 (tttt) cc_final: 0.6485 (mtpt) REVERT: C 179 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9121 (m) REVERT: C 240 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: C 249 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8282 (mtmm) REVERT: C 258 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8172 (mtp180) REVERT: C 299 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8319 (tp30) REVERT: C 373 MET cc_start: 0.9468 (mtt) cc_final: 0.9139 (mtp) REVERT: C 427 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: C 513 ASP cc_start: 0.8873 (m-30) cc_final: 0.8529 (m-30) REVERT: C 618 ASP cc_start: 0.8787 (m-30) cc_final: 0.8523 (m-30) outliers start: 140 outliers final: 36 residues processed: 433 average time/residue: 0.6778 time to fit residues: 342.7475 Evaluate side-chains 358 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 722 LYS Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1343 SER Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain D residue 1509 GLU Chi-restraints excluded: chain D residue 1560 GLU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 434 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1367 ILE Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 199 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 138 optimal weight: 0.0570 chunk 265 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 701 ASN D 760 ASN D1098 GLN D1119 GLN D1327 ASN D1556 ASN B 392 HIS B 727 ASN E1033 GLN E1289 HIS E1647 GLN C 126 GLN C 212 ASN C 313 ASN C 414 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107583 restraints weight = 32852.131| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.40 r_work: 0.2950 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30131 Z= 0.189 Angle : 0.649 10.740 40835 Z= 0.342 Chirality : 0.050 0.368 4613 Planarity : 0.005 0.067 5243 Dihedral : 5.762 56.758 4180 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.51 % Allowed : 21.40 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.15 (0.13), residues: 3668 helix: 0.01 (0.21), residues: 643 sheet: 1.26 (0.14), residues: 1237 loop : -1.15 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 353 TYR 0.025 0.002 TYR D1262 PHE 0.023 0.002 PHE C 112 TRP 0.019 0.002 TRP E1605 HIS 0.008 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00466 (30099) covalent geometry : angle 0.64552 (40764) SS BOND : bond 0.00416 ( 25) SS BOND : angle 1.02584 ( 50) hydrogen bonds : bond 0.04751 ( 1083) hydrogen bonds : angle 5.17190 ( 3033) link_BETA1-4 : bond 0.00723 ( 1) link_BETA1-4 : angle 1.62517 ( 3) link_NAG-ASN : bond 0.00680 ( 6) link_NAG-ASN : angle 2.73660 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 314 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 709 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: D 716 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 722 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7389 (ttmt) REVERT: D 789 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8422 (ttmt) REVERT: D 858 GLN cc_start: 0.8248 (mt0) cc_final: 0.7751 (tt0) REVERT: D 909 GLU cc_start: 0.8004 (tp30) cc_final: 0.7507 (tt0) REVERT: D 1030 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7241 (tt0) REVERT: D 1061 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: D 1105 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8102 (ttmm) REVERT: D 1110 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: D 1159 GLU cc_start: 0.7474 (pt0) cc_final: 0.7081 (tp30) REVERT: D 1174 ASP cc_start: 0.7818 (m-30) cc_final: 0.7500 (m-30) REVERT: D 1295 ASP cc_start: 0.7352 (p0) cc_final: 0.7067 (p0) REVERT: D 1299 GLN cc_start: 0.7249 (tp40) cc_final: 0.6947 (tp40) REVERT: D 1310 ARG cc_start: 0.7079 (mmm160) cc_final: 0.6523 (tmt170) REVERT: D 1313 TRP cc_start: 0.7591 (t-100) cc_final: 0.7301 (t-100) REVERT: D 1314 GLU cc_start: 0.7466 (mp0) cc_final: 0.7098 (mm-30) REVERT: D 1396 GLN cc_start: 0.8178 (pt0) cc_final: 0.7696 (mt0) REVERT: D 1441 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7614 (mmp-170) REVERT: D 1600 LYS cc_start: 0.6728 (mptp) cc_final: 0.6141 (mtpt) REVERT: B 387 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7682 (mmm) REVERT: B 410 TYR cc_start: 0.7571 (t80) cc_final: 0.7077 (m-80) REVERT: B 422 TYR cc_start: 0.7231 (m-80) cc_final: 0.6742 (m-80) REVERT: B 587 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: B 616 GLN cc_start: 0.7403 (tp40) cc_final: 0.6934 (tp-100) REVERT: B 658 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7071 (mtm110) REVERT: B 754 GLU cc_start: 0.7780 (tp30) cc_final: 0.7509 (tt0) REVERT: P 403 ARG cc_start: 0.1656 (OUTLIER) cc_final: 0.1380 (ttp-110) REVERT: E 35 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7234 (mtt90) REVERT: E 125 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6580 (mt) REVERT: E 171 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 177 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: E 211 GLU cc_start: 0.8115 (tt0) cc_final: 0.7858 (tp30) REVERT: E 240 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: E 305 LYS cc_start: 0.8041 (tttp) cc_final: 0.7228 (mptt) REVERT: E 453 ASN cc_start: 0.8144 (m-40) cc_final: 0.7884 (m-40) REVERT: E 464 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7192 (tp30) REVERT: E 478 ARG cc_start: 0.8463 (tpm170) cc_final: 0.7855 (tpt-90) REVERT: E 571 GLU cc_start: 0.5931 (tt0) cc_final: 0.5543 (tp30) REVERT: E 659 GLU cc_start: 0.7683 (mp0) cc_final: 0.7409 (mm-30) REVERT: E 977 GLU cc_start: 0.6532 (tt0) cc_final: 0.6063 (tt0) REVERT: E 1015 MET cc_start: 0.4939 (pmm) cc_final: 0.4153 (mmp) REVERT: E 1018 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1144 (tmt) REVERT: E 1241 LEU cc_start: 0.4568 (OUTLIER) cc_final: 0.4194 (tm) REVERT: E 1396 GLN cc_start: 0.8159 (pt0) cc_final: 0.7876 (pt0) REVERT: E 1431 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8101 (tttm) REVERT: E 1455 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6352 (pp20) REVERT: E 1567 GLN cc_start: 0.6144 (tt0) cc_final: 0.5919 (tm-30) REVERT: E 1598 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: E 1603 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6831 (tp) REVERT: E 1629 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: C 104 LYS cc_start: 0.7292 (tttt) cc_final: 0.6589 (mtpt) REVERT: C 240 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: C 249 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8312 (mtmm) REVERT: C 258 ARG cc_start: 0.8618 (ttm170) cc_final: 0.8297 (mtp180) REVERT: C 299 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: C 313 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.6065 (p0) REVERT: C 373 MET cc_start: 0.9476 (mtt) cc_final: 0.9246 (mtt) REVERT: C 427 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8315 (mmtt) REVERT: C 513 ASP cc_start: 0.8901 (m-30) cc_final: 0.8649 (m-30) outliers start: 148 outliers final: 53 residues processed: 422 average time/residue: 0.6943 time to fit residues: 340.4160 Evaluate side-chains 377 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 301 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 722 LYS Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1343 SER Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 658 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1018 MET Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1367 ILE Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 11 optimal weight: 0.0020 chunk 47 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 208 optimal weight: 0.0870 chunk 279 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 overall best weight: 1.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN ** D1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN B 270 ASN B 360 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN E 50 GLN E 93 ASN E1309 HIS E1601 HIS C 126 GLN C 313 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110197 restraints weight = 32575.499| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.38 r_work: 0.2974 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30131 Z= 0.127 Angle : 0.547 9.173 40835 Z= 0.290 Chirality : 0.046 0.361 4613 Planarity : 0.005 0.059 5243 Dihedral : 5.345 56.501 4176 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.60 % Allowed : 22.58 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.02 (0.13), residues: 3668 helix: 0.42 (0.21), residues: 637 sheet: 1.28 (0.14), residues: 1241 loop : -1.09 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 573 TYR 0.019 0.001 TYR D1543 PHE 0.016 0.001 PHE C 112 TRP 0.019 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00310 (30099) covalent geometry : angle 0.54394 (40764) SS BOND : bond 0.00540 ( 25) SS BOND : angle 0.75945 ( 50) hydrogen bonds : bond 0.03657 ( 1083) hydrogen bonds : angle 4.90339 ( 3033) link_BETA1-4 : bond 0.00654 ( 1) link_BETA1-4 : angle 1.23998 ( 3) link_NAG-ASN : bond 0.00614 ( 6) link_NAG-ASN : angle 2.58247 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 301 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 680 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6202 (mpp) REVERT: D 716 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8099 (mp) REVERT: D 722 LYS cc_start: 0.7822 (tptt) cc_final: 0.7358 (ttmt) REVERT: D 789 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8420 (ttmt) REVERT: D 858 GLN cc_start: 0.8229 (mt0) cc_final: 0.7750 (tt0) REVERT: D 909 GLU cc_start: 0.8022 (tp30) cc_final: 0.7540 (tt0) REVERT: D 959 LYS cc_start: 0.7936 (tttt) cc_final: 0.7530 (tmtm) REVERT: D 1030 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7148 (tt0) REVERT: D 1105 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8068 (ttmm) REVERT: D 1110 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: D 1129 MET cc_start: 0.8879 (mmp) cc_final: 0.8352 (mmt) REVERT: D 1159 GLU cc_start: 0.7544 (pt0) cc_final: 0.7115 (tp30) REVERT: D 1174 ASP cc_start: 0.7793 (m-30) cc_final: 0.7448 (m-30) REVERT: D 1295 ASP cc_start: 0.7261 (p0) cc_final: 0.7020 (p0) REVERT: D 1299 GLN cc_start: 0.7207 (tp40) cc_final: 0.6942 (tp40) REVERT: D 1313 TRP cc_start: 0.7553 (t-100) cc_final: 0.7240 (t-100) REVERT: D 1314 GLU cc_start: 0.7609 (mp0) cc_final: 0.7313 (mm-30) REVERT: D 1396 GLN cc_start: 0.8160 (pt0) cc_final: 0.7641 (mt0) REVERT: D 1441 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7592 (mmp-170) REVERT: D 1600 LYS cc_start: 0.6718 (mptp) cc_final: 0.6241 (mmmt) REVERT: B 387 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7734 (mmm) REVERT: B 410 TYR cc_start: 0.7573 (t80) cc_final: 0.7170 (t80) REVERT: B 422 TYR cc_start: 0.7201 (m-80) cc_final: 0.6759 (m-80) REVERT: B 454 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7553 (mmmm) REVERT: B 569 ILE cc_start: 0.7703 (mm) cc_final: 0.7444 (mp) REVERT: B 587 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8191 (tttm) REVERT: B 616 GLN cc_start: 0.7426 (tp40) cc_final: 0.6991 (tp-100) REVERT: B 619 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7432 (tttp) REVERT: B 639 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7153 (mmtm) REVERT: B 652 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7174 (ttmm) REVERT: B 658 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7168 (mtm110) REVERT: B 754 GLU cc_start: 0.7779 (tp30) cc_final: 0.7511 (tt0) REVERT: P 368 ARG cc_start: 0.4601 (ttm170) cc_final: 0.3810 (ttp80) REVERT: P 403 ARG cc_start: 0.1758 (OUTLIER) cc_final: 0.1412 (ttp-110) REVERT: E 35 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7344 (mtt90) REVERT: E 125 LEU cc_start: 0.6882 (mm) cc_final: 0.6638 (mt) REVERT: E 171 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 211 GLU cc_start: 0.8141 (tt0) cc_final: 0.7886 (tp30) REVERT: E 240 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: E 305 LYS cc_start: 0.7937 (tttp) cc_final: 0.7230 (mptt) REVERT: E 430 GLU cc_start: 0.8162 (pm20) cc_final: 0.7852 (pm20) REVERT: E 453 ASN cc_start: 0.8112 (m-40) cc_final: 0.7863 (m-40) REVERT: E 478 ARG cc_start: 0.8466 (tpm170) cc_final: 0.7832 (tpt-90) REVERT: E 513 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8114 (t0) REVERT: E 571 GLU cc_start: 0.5810 (tt0) cc_final: 0.5481 (tp30) REVERT: E 659 GLU cc_start: 0.7666 (mp0) cc_final: 0.7387 (mm-30) REVERT: E 977 GLU cc_start: 0.6541 (tt0) cc_final: 0.6030 (tt0) REVERT: E 1015 MET cc_start: 0.4742 (pmm) cc_final: 0.4035 (mmp) REVERT: E 1018 MET cc_start: 0.2072 (OUTLIER) cc_final: 0.1106 (tmt) REVERT: E 1241 LEU cc_start: 0.4664 (OUTLIER) cc_final: 0.4253 (tm) REVERT: E 1347 MET cc_start: 0.7022 (ttt) cc_final: 0.6784 (ttt) REVERT: E 1396 GLN cc_start: 0.8138 (pt0) cc_final: 0.7855 (pt0) REVERT: E 1431 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8185 (tttm) REVERT: E 1455 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6514 (pp20) REVERT: E 1563 MET cc_start: 0.7554 (mtp) cc_final: 0.7057 (mmt) REVERT: E 1567 GLN cc_start: 0.6130 (tt0) cc_final: 0.5891 (tm-30) REVERT: E 1598 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: E 1629 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: C 104 LYS cc_start: 0.7308 (tttt) cc_final: 0.6631 (mtpt) REVERT: C 159 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (m) REVERT: C 240 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: C 249 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8369 (mtmm) REVERT: C 258 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8267 (mtp180) REVERT: C 299 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8409 (tp30) REVERT: C 313 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.5838 (p0) REVERT: C 373 MET cc_start: 0.9491 (mtt) cc_final: 0.9180 (mtp) REVERT: C 427 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8365 (mmtt) REVERT: C 513 ASP cc_start: 0.8891 (m-30) cc_final: 0.8529 (m-30) REVERT: C 661 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8078 (mm-40) outliers start: 118 outliers final: 58 residues processed: 384 average time/residue: 0.7273 time to fit residues: 324.3010 Evaluate side-chains 373 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1343 SER Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1656 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 658 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 581 MET Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1018 MET Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1046 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1367 ILE Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1426 ASP Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1618 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 15 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 354 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 208 optimal weight: 0.0670 chunk 278 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN D1312 HIS D1327 ASN D1396 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN C 126 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112494 restraints weight = 32886.244| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.43 r_work: 0.3009 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30131 Z= 0.094 Angle : 0.500 8.991 40835 Z= 0.265 Chirality : 0.045 0.348 4613 Planarity : 0.004 0.057 5243 Dihedral : 4.929 57.003 4172 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.20 % Allowed : 23.26 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.25 (0.14), residues: 3668 helix: 0.74 (0.22), residues: 629 sheet: 1.38 (0.14), residues: 1235 loop : -0.94 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 481 TYR 0.019 0.001 TYR D1543 PHE 0.012 0.001 PHE C 112 TRP 0.018 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00221 (30099) covalent geometry : angle 0.49696 (40764) SS BOND : bond 0.00262 ( 25) SS BOND : angle 0.64058 ( 50) hydrogen bonds : bond 0.03074 ( 1083) hydrogen bonds : angle 4.65014 ( 3033) link_BETA1-4 : bond 0.00653 ( 1) link_BETA1-4 : angle 1.28822 ( 3) link_NAG-ASN : bond 0.00620 ( 6) link_NAG-ASN : angle 2.49926 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 308 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7795 (tptt) cc_final: 0.7372 (tppt) REVERT: D 858 GLN cc_start: 0.8201 (mt0) cc_final: 0.7732 (tt0) REVERT: D 909 GLU cc_start: 0.7975 (tp30) cc_final: 0.7528 (tt0) REVERT: D 959 LYS cc_start: 0.7908 (tttt) cc_final: 0.7480 (tmtm) REVERT: D 1030 GLU cc_start: 0.7300 (tm-30) cc_final: 0.7077 (tt0) REVERT: D 1061 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: D 1105 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8005 (tttm) REVERT: D 1110 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: D 1119 GLN cc_start: 0.8156 (pt0) cc_final: 0.7849 (pt0) REVERT: D 1159 GLU cc_start: 0.7636 (pt0) cc_final: 0.7146 (tp30) REVERT: D 1174 ASP cc_start: 0.7751 (m-30) cc_final: 0.7406 (m-30) REVERT: D 1295 ASP cc_start: 0.7214 (p0) cc_final: 0.6966 (p0) REVERT: D 1299 GLN cc_start: 0.7155 (tp40) cc_final: 0.6929 (tp40) REVERT: D 1310 ARG cc_start: 0.6958 (mmm160) cc_final: 0.6515 (ttp80) REVERT: D 1314 GLU cc_start: 0.7547 (mp0) cc_final: 0.7233 (mm-30) REVERT: D 1396 GLN cc_start: 0.8150 (pt0) cc_final: 0.7654 (mt0) REVERT: D 1441 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7491 (mmp-170) REVERT: D 1600 LYS cc_start: 0.6674 (mptp) cc_final: 0.6220 (mmmt) REVERT: B 387 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: B 410 TYR cc_start: 0.7579 (t80) cc_final: 0.7088 (t80) REVERT: B 422 TYR cc_start: 0.7157 (m-80) cc_final: 0.6702 (m-80) REVERT: B 454 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7596 (mmmm) REVERT: B 569 ILE cc_start: 0.7792 (mm) cc_final: 0.7590 (mp) REVERT: B 587 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8194 (tttm) REVERT: B 616 GLN cc_start: 0.7465 (tp40) cc_final: 0.7016 (tp-100) REVERT: B 619 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7329 (tttp) REVERT: B 754 GLU cc_start: 0.7739 (tp30) cc_final: 0.7461 (tt0) REVERT: P 403 ARG cc_start: 0.1765 (OUTLIER) cc_final: 0.1436 (ttp-110) REVERT: E 35 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7301 (mtt90) REVERT: E 125 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6623 (mt) REVERT: E 171 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7690 (mm-30) REVERT: E 211 GLU cc_start: 0.8122 (tt0) cc_final: 0.7879 (tp30) REVERT: E 305 LYS cc_start: 0.7903 (tttp) cc_final: 0.7180 (mptt) REVERT: E 430 GLU cc_start: 0.8194 (pm20) cc_final: 0.7783 (pm20) REVERT: E 453 ASN cc_start: 0.8019 (m-40) cc_final: 0.7770 (m-40) REVERT: E 478 ARG cc_start: 0.8432 (tpm170) cc_final: 0.7817 (tpt-90) REVERT: E 513 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8117 (t0) REVERT: E 537 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8590 (pt) REVERT: E 571 GLU cc_start: 0.5816 (tt0) cc_final: 0.5547 (tp30) REVERT: E 576 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8880 (m) REVERT: E 659 GLU cc_start: 0.7684 (mp0) cc_final: 0.7394 (mm-30) REVERT: E 977 GLU cc_start: 0.6547 (tt0) cc_final: 0.6028 (tt0) REVERT: E 1015 MET cc_start: 0.4744 (pmm) cc_final: 0.4089 (mmp) REVERT: E 1018 MET cc_start: 0.2282 (OUTLIER) cc_final: 0.1357 (tmt) REVERT: E 1181 MET cc_start: 0.4073 (mmt) cc_final: 0.3665 (mpp) REVERT: E 1241 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4235 (tm) REVERT: E 1391 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7328 (tmt90) REVERT: E 1431 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8196 (tttm) REVERT: E 1455 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: E 1535 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6090 (pttm) REVERT: E 1563 MET cc_start: 0.7480 (mtp) cc_final: 0.6994 (mmt) REVERT: E 1567 GLN cc_start: 0.6055 (tt0) cc_final: 0.5827 (tm-30) REVERT: E 1603 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6795 (tp) REVERT: E 1629 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: C 104 LYS cc_start: 0.7257 (tttt) cc_final: 0.6599 (mtpt) REVERT: C 159 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (m) REVERT: C 205 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8727 (tppt) REVERT: C 240 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: C 249 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8375 (mtmm) REVERT: C 258 ARG cc_start: 0.8568 (ttm170) cc_final: 0.8252 (mtp180) REVERT: C 299 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: C 373 MET cc_start: 0.9502 (mtt) cc_final: 0.9193 (mtp) REVERT: C 433 GLU cc_start: 0.8387 (tp30) cc_final: 0.8105 (tp30) REVERT: C 513 ASP cc_start: 0.8884 (m-30) cc_final: 0.8531 (m-30) REVERT: C 615 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8758 (mtmt) REVERT: C 661 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8063 (mm-40) outliers start: 105 outliers final: 44 residues processed: 383 average time/residue: 0.7654 time to fit residues: 340.2997 Evaluate side-chains 362 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 296 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1656 MET Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1018 MET Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1367 ILE Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 355 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 351 optimal weight: 0.3980 chunk 286 optimal weight: 9.9990 chunk 357 optimal weight: 1.9990 chunk 364 optimal weight: 0.0050 chunk 329 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN D1033 GLN D1327 ASN D1630 HIS ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN C 126 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111927 restraints weight = 32401.666| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.67 r_work: 0.2978 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 30131 Z= 0.100 Angle : 0.502 8.928 40835 Z= 0.265 Chirality : 0.045 0.342 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.770 57.438 4169 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.57 % Allowed : 22.86 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.36 (0.14), residues: 3668 helix: 0.96 (0.22), residues: 623 sheet: 1.37 (0.14), residues: 1252 loop : -0.87 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 330 TYR 0.020 0.001 TYR E 209 PHE 0.013 0.001 PHE C 112 TRP 0.018 0.001 TRP E1605 HIS 0.005 0.001 HIS D1312 Details of bonding type rmsd covalent geometry : bond 0.00241 (30099) covalent geometry : angle 0.49967 (40764) SS BOND : bond 0.00238 ( 25) SS BOND : angle 0.64520 ( 50) hydrogen bonds : bond 0.03128 ( 1083) hydrogen bonds : angle 4.57942 ( 3033) link_BETA1-4 : bond 0.00656 ( 1) link_BETA1-4 : angle 1.27625 ( 3) link_NAG-ASN : bond 0.00622 ( 6) link_NAG-ASN : angle 2.43774 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 308 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7752 (tptt) cc_final: 0.7336 (ttmt) REVERT: D 789 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8466 (ttmt) REVERT: D 858 GLN cc_start: 0.8193 (mt0) cc_final: 0.7743 (tt0) REVERT: D 909 GLU cc_start: 0.7985 (tp30) cc_final: 0.7648 (tt0) REVERT: D 959 LYS cc_start: 0.8020 (tttt) cc_final: 0.7579 (tmtm) REVERT: D 1030 GLU cc_start: 0.7300 (tm-30) cc_final: 0.7095 (tt0) REVERT: D 1061 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: D 1097 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8324 (t) REVERT: D 1098 GLN cc_start: 0.7896 (tp40) cc_final: 0.7667 (tp40) REVERT: D 1105 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8012 (tttm) REVERT: D 1110 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: D 1119 GLN cc_start: 0.8136 (pt0) cc_final: 0.7841 (pt0) REVERT: D 1159 GLU cc_start: 0.7599 (pt0) cc_final: 0.7096 (tp30) REVERT: D 1174 ASP cc_start: 0.7659 (m-30) cc_final: 0.7274 (m-30) REVERT: D 1292 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4691 (tp) REVERT: D 1295 ASP cc_start: 0.7265 (p0) cc_final: 0.7057 (p0) REVERT: D 1299 GLN cc_start: 0.7117 (tp40) cc_final: 0.6835 (tp40) REVERT: D 1310 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6559 (ttp80) REVERT: D 1314 GLU cc_start: 0.7602 (mp0) cc_final: 0.7248 (mm-30) REVERT: D 1317 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8030 (m) REVERT: D 1396 GLN cc_start: 0.8144 (pt0) cc_final: 0.7651 (mt0) REVERT: D 1441 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7442 (mmp-170) REVERT: D 1455 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: D 1600 LYS cc_start: 0.6871 (mptp) cc_final: 0.6242 (mtpt) REVERT: B 325 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7703 (p) REVERT: B 404 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 410 TYR cc_start: 0.7582 (t80) cc_final: 0.7182 (t80) REVERT: B 422 TYR cc_start: 0.7187 (m-80) cc_final: 0.6750 (m-80) REVERT: B 454 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7510 (mmmm) REVERT: B 587 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8204 (tttm) REVERT: B 616 GLN cc_start: 0.7513 (tp40) cc_final: 0.7040 (tp-100) REVERT: B 619 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7155 (tptt) REVERT: B 754 GLU cc_start: 0.7753 (tp30) cc_final: 0.7457 (tt0) REVERT: P 403 ARG cc_start: 0.1734 (OUTLIER) cc_final: 0.1455 (ttp-110) REVERT: E 35 ARG cc_start: 0.7584 (mtm180) cc_final: 0.7292 (mtt90) REVERT: E 125 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6408 (mt) REVERT: E 126 GLN cc_start: 0.7129 (mp10) cc_final: 0.6491 (mt0) REVERT: E 171 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7677 (mm-30) REVERT: E 211 GLU cc_start: 0.8126 (tt0) cc_final: 0.7852 (tp30) REVERT: E 240 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: E 305 LYS cc_start: 0.7788 (tttp) cc_final: 0.7192 (mptt) REVERT: E 430 GLU cc_start: 0.8248 (pm20) cc_final: 0.7866 (pm20) REVERT: E 478 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7772 (tpt-90) REVERT: E 513 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8211 (t0) REVERT: E 537 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8591 (pt) REVERT: E 571 GLU cc_start: 0.5755 (tt0) cc_final: 0.5483 (tp30) REVERT: E 576 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8891 (m) REVERT: E 659 GLU cc_start: 0.7667 (mp0) cc_final: 0.7389 (mm-30) REVERT: E 977 GLU cc_start: 0.6598 (tt0) cc_final: 0.6092 (tt0) REVERT: E 1015 MET cc_start: 0.4810 (pmm) cc_final: 0.4118 (mmp) REVERT: E 1018 MET cc_start: 0.2298 (OUTLIER) cc_final: 0.1416 (tmt) REVERT: E 1181 MET cc_start: 0.3987 (mmt) cc_final: 0.3598 (mpp) REVERT: E 1241 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4249 (tm) REVERT: E 1391 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7328 (tmt90) REVERT: E 1393 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7302 (mtp85) REVERT: E 1431 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8167 (tttm) REVERT: E 1455 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6515 (pp20) REVERT: E 1535 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6107 (pttm) REVERT: E 1563 MET cc_start: 0.7505 (mtp) cc_final: 0.7039 (mmt) REVERT: E 1567 GLN cc_start: 0.6060 (tt0) cc_final: 0.5807 (tm-30) REVERT: E 1598 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: E 1603 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6872 (tp) REVERT: E 1624 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6542 (tptm) REVERT: E 1629 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: C 44 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 104 LYS cc_start: 0.7256 (tttt) cc_final: 0.6597 (mtmt) REVERT: C 205 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8795 (tppt) REVERT: C 240 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: C 249 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8414 (mttp) REVERT: C 258 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8269 (mtp180) REVERT: C 299 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: C 406 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8756 (t) REVERT: C 433 GLU cc_start: 0.8424 (tp30) cc_final: 0.8150 (tp30) REVERT: C 513 ASP cc_start: 0.8909 (m-30) cc_final: 0.8584 (m-30) REVERT: C 615 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8781 (mtmt) REVERT: C 661 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8023 (mm-40) outliers start: 117 outliers final: 60 residues processed: 390 average time/residue: 0.7535 time to fit residues: 341.1092 Evaluate side-chains 385 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 294 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1595 LYS Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1018 MET Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1046 LEU Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1199 MET Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1624 LYS Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 6 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 246 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 708 GLN D 760 ASN D1119 GLN D1327 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111784 restraints weight = 32461.982| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.45 r_work: 0.2978 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30131 Z= 0.109 Angle : 0.516 10.798 40835 Z= 0.271 Chirality : 0.045 0.340 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.718 57.227 4165 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.38 % Allowed : 23.26 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.37 (0.14), residues: 3668 helix: 0.98 (0.22), residues: 629 sheet: 1.35 (0.14), residues: 1248 loop : -0.86 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 481 TYR 0.018 0.001 TYR D1543 PHE 0.013 0.001 PHE C 112 TRP 0.018 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00263 (30099) covalent geometry : angle 0.51285 (40764) SS BOND : bond 0.00250 ( 25) SS BOND : angle 0.62707 ( 50) hydrogen bonds : bond 0.03186 ( 1083) hydrogen bonds : angle 4.57909 ( 3033) link_BETA1-4 : bond 0.00803 ( 1) link_BETA1-4 : angle 1.36423 ( 3) link_NAG-ASN : bond 0.00610 ( 6) link_NAG-ASN : angle 2.42326 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 296 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7736 (tptt) cc_final: 0.7331 (ttmt) REVERT: D 789 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8484 (ttmt) REVERT: D 858 GLN cc_start: 0.8217 (mt0) cc_final: 0.7739 (tt0) REVERT: D 909 GLU cc_start: 0.7996 (tp30) cc_final: 0.7639 (tt0) REVERT: D 959 LYS cc_start: 0.8090 (tttt) cc_final: 0.7642 (tmtm) REVERT: D 1030 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7084 (tt0) REVERT: D 1061 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: D 1097 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8336 (t) REVERT: D 1098 GLN cc_start: 0.7887 (tp40) cc_final: 0.7665 (tp40) REVERT: D 1105 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8030 (tttm) REVERT: D 1110 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: D 1119 GLN cc_start: 0.8212 (pt0) cc_final: 0.7911 (pt0) REVERT: D 1159 GLU cc_start: 0.7626 (pt0) cc_final: 0.7107 (tp30) REVERT: D 1174 ASP cc_start: 0.7613 (m-30) cc_final: 0.7229 (m-30) REVERT: D 1299 GLN cc_start: 0.7177 (tp40) cc_final: 0.6917 (tp40) REVERT: D 1310 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6624 (ttp80) REVERT: D 1314 GLU cc_start: 0.7609 (mp0) cc_final: 0.7265 (mm-30) REVERT: D 1317 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8064 (m) REVERT: D 1328 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: D 1396 GLN cc_start: 0.8109 (pt0) cc_final: 0.7652 (mt0) REVERT: D 1441 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7444 (mmp-170) REVERT: D 1455 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8052 (pp20) REVERT: D 1600 LYS cc_start: 0.7001 (mptp) cc_final: 0.6320 (mtpt) REVERT: B 325 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 410 TYR cc_start: 0.7566 (t80) cc_final: 0.7114 (t80) REVERT: B 422 TYR cc_start: 0.7227 (m-80) cc_final: 0.6809 (m-80) REVERT: B 450 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (mm110) REVERT: B 454 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7537 (mmmm) REVERT: B 587 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8190 (tttm) REVERT: B 616 GLN cc_start: 0.7446 (tp40) cc_final: 0.7008 (tp-100) REVERT: B 619 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7197 (tptt) REVERT: B 754 GLU cc_start: 0.7749 (tp30) cc_final: 0.7460 (tt0) REVERT: P 403 ARG cc_start: 0.1845 (OUTLIER) cc_final: 0.1403 (ttp-110) REVERT: E 35 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7304 (mtt90) REVERT: E 171 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7655 (mm-30) REVERT: E 240 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: E 305 LYS cc_start: 0.7833 (tttp) cc_final: 0.7229 (mptt) REVERT: E 430 GLU cc_start: 0.8180 (pm20) cc_final: 0.7824 (pm20) REVERT: E 478 ARG cc_start: 0.8408 (tpm170) cc_final: 0.7799 (tpt-90) REVERT: E 513 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (t0) REVERT: E 571 GLU cc_start: 0.5754 (tt0) cc_final: 0.5518 (tp30) REVERT: E 576 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8891 (m) REVERT: E 659 GLU cc_start: 0.7675 (mp0) cc_final: 0.7424 (mm-30) REVERT: E 934 GLU cc_start: 0.7549 (pm20) cc_final: 0.6752 (tp30) REVERT: E 1015 MET cc_start: 0.4950 (pmm) cc_final: 0.3988 (mmp) REVERT: E 1181 MET cc_start: 0.4060 (mmt) cc_final: 0.3637 (mpp) REVERT: E 1199 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.2128 (tmm) REVERT: E 1241 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4232 (tm) REVERT: E 1391 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7331 (tmt90) REVERT: E 1431 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8164 (tttm) REVERT: E 1455 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: E 1535 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6115 (pttm) REVERT: E 1563 MET cc_start: 0.7524 (mtp) cc_final: 0.7197 (mmt) REVERT: E 1567 GLN cc_start: 0.5993 (tt0) cc_final: 0.5745 (tm-30) REVERT: E 1598 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: E 1603 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6845 (tp) REVERT: E 1624 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6588 (tptm) REVERT: E 1629 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: C 44 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 104 LYS cc_start: 0.7273 (tttt) cc_final: 0.6583 (mtmt) REVERT: C 205 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8770 (tppt) REVERT: C 240 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: C 249 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8387 (mttp) REVERT: C 258 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8269 (mtp180) REVERT: C 299 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: C 406 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8771 (t) REVERT: C 433 GLU cc_start: 0.8389 (tp30) cc_final: 0.8116 (tp30) REVERT: C 513 ASP cc_start: 0.8900 (m-30) cc_final: 0.8589 (m-30) REVERT: C 615 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8783 (mtmt) REVERT: C 661 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8118 (mm-40) outliers start: 111 outliers final: 64 residues processed: 374 average time/residue: 0.7279 time to fit residues: 314.7375 Evaluate side-chains 383 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 288 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1208 ASN Chi-restraints excluded: chain D residue 1310 ARG Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1328 GLU Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1595 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 438 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1199 MET Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1455 GLU Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1624 LYS Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 117 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN D1327 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 GLN P 365 GLN E1647 GLN C 126 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111050 restraints weight = 32461.724| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.2960 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30131 Z= 0.124 Angle : 0.536 10.723 40835 Z= 0.282 Chirality : 0.046 0.340 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.815 56.836 4165 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.57 % Allowed : 23.13 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.36 (0.14), residues: 3668 helix: 1.04 (0.22), residues: 623 sheet: 1.32 (0.14), residues: 1258 loop : -0.87 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 481 TYR 0.022 0.001 TYR E 209 PHE 0.015 0.001 PHE C 525 TRP 0.019 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00305 (30099) covalent geometry : angle 0.53292 (40764) SS BOND : bond 0.00282 ( 25) SS BOND : angle 0.68428 ( 50) hydrogen bonds : bond 0.03417 ( 1083) hydrogen bonds : angle 4.63917 ( 3033) link_BETA1-4 : bond 0.00589 ( 1) link_BETA1-4 : angle 1.29512 ( 3) link_NAG-ASN : bond 0.00622 ( 6) link_NAG-ASN : angle 2.42947 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 297 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7788 (tptt) cc_final: 0.7366 (ttmt) REVERT: D 789 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8499 (ttmt) REVERT: D 858 GLN cc_start: 0.8247 (mt0) cc_final: 0.7770 (tt0) REVERT: D 909 GLU cc_start: 0.8068 (tp30) cc_final: 0.7724 (tt0) REVERT: D 959 LYS cc_start: 0.8129 (tttt) cc_final: 0.7677 (tmtm) REVERT: D 1030 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7188 (tt0) REVERT: D 1061 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: D 1097 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8364 (t) REVERT: D 1098 GLN cc_start: 0.7953 (tp40) cc_final: 0.7731 (tp40) REVERT: D 1105 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8069 (tttm) REVERT: D 1110 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: D 1119 GLN cc_start: 0.8235 (pt0) cc_final: 0.7904 (pt0) REVERT: D 1159 GLU cc_start: 0.7682 (pt0) cc_final: 0.7195 (tp30) REVERT: D 1174 ASP cc_start: 0.7612 (m-30) cc_final: 0.7233 (m-30) REVERT: D 1310 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6582 (ttp80) REVERT: D 1314 GLU cc_start: 0.7609 (mp0) cc_final: 0.7283 (mm-30) REVERT: D 1317 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8103 (m) REVERT: D 1328 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: D 1396 GLN cc_start: 0.8135 (pt0) cc_final: 0.7678 (mt0) REVERT: D 1441 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7490 (mmp-170) REVERT: D 1455 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8017 (pp20) REVERT: D 1563 MET cc_start: 0.6098 (mmt) cc_final: 0.5834 (mmp) REVERT: D 1600 LYS cc_start: 0.7059 (mptp) cc_final: 0.6346 (mtpt) REVERT: B 387 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: B 410 TYR cc_start: 0.7550 (t80) cc_final: 0.7136 (t80) REVERT: B 422 TYR cc_start: 0.7273 (m-80) cc_final: 0.6855 (m-80) REVERT: B 433 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7354 (mt) REVERT: B 450 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7893 (mm110) REVERT: B 454 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7564 (mmmm) REVERT: B 587 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8241 (tttm) REVERT: B 616 GLN cc_start: 0.7491 (tp40) cc_final: 0.7078 (tp-100) REVERT: B 619 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7464 (tttp) REVERT: B 754 GLU cc_start: 0.7866 (tp30) cc_final: 0.7583 (tt0) REVERT: P 403 ARG cc_start: 0.1817 (OUTLIER) cc_final: 0.1310 (ttp-110) REVERT: P 453 ARG cc_start: 0.0469 (pmt-80) cc_final: -0.0233 (mtm-85) REVERT: E 35 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7324 (mtt90) REVERT: E 104 LYS cc_start: 0.7216 (tppt) cc_final: 0.6995 (mmtm) REVERT: E 125 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6567 (mt) REVERT: E 171 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7725 (mm-30) REVERT: E 177 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: E 240 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: E 305 LYS cc_start: 0.7870 (tttp) cc_final: 0.7272 (mptt) REVERT: E 430 GLU cc_start: 0.8235 (pm20) cc_final: 0.7920 (pm20) REVERT: E 478 ARG cc_start: 0.8438 (tpm170) cc_final: 0.7803 (tpt-90) REVERT: E 513 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8232 (t0) REVERT: E 537 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8634 (pt) REVERT: E 571 GLU cc_start: 0.5806 (tt0) cc_final: 0.5565 (tp30) REVERT: E 659 GLU cc_start: 0.7698 (mp0) cc_final: 0.7441 (mm-30) REVERT: E 1181 MET cc_start: 0.3881 (mmt) cc_final: 0.3507 (mpp) REVERT: E 1199 MET cc_start: 0.2744 (OUTLIER) cc_final: 0.2243 (tmm) REVERT: E 1241 LEU cc_start: 0.4651 (OUTLIER) cc_final: 0.4276 (tm) REVERT: E 1391 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7356 (tmt90) REVERT: E 1431 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8171 (tttm) REVERT: E 1535 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.5994 (pttm) REVERT: E 1563 MET cc_start: 0.7473 (mtp) cc_final: 0.7099 (mmt) REVERT: E 1567 GLN cc_start: 0.6008 (tt0) cc_final: 0.5765 (tm-30) REVERT: E 1598 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: E 1603 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6823 (tp) REVERT: E 1624 LYS cc_start: 0.7188 (pttp) cc_final: 0.6619 (tptm) REVERT: E 1629 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: C 44 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8622 (mt) REVERT: C 104 LYS cc_start: 0.7357 (tttt) cc_final: 0.6609 (mtmt) REVERT: C 205 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8783 (tppt) REVERT: C 240 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: C 249 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8408 (mttp) REVERT: C 258 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8281 (mtp180) REVERT: C 299 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: C 427 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mmtt) REVERT: C 433 GLU cc_start: 0.8421 (tp30) cc_final: 0.8144 (tp30) REVERT: C 513 ASP cc_start: 0.8899 (m-30) cc_final: 0.8592 (m-30) REVERT: C 615 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8798 (mtmt) outliers start: 117 outliers final: 70 residues processed: 378 average time/residue: 0.6954 time to fit residues: 303.6842 Evaluate side-chains 389 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 287 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1310 ARG Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1328 GLU Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 438 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1199 MET Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1618 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 145 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 280 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 369 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110455 restraints weight = 32392.704| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.57 r_work: 0.2949 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30131 Z= 0.133 Angle : 0.550 10.778 40835 Z= 0.288 Chirality : 0.046 0.341 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.860 56.897 4165 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.38 % Allowed : 23.62 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.36 (0.14), residues: 3668 helix: 1.04 (0.22), residues: 626 sheet: 1.31 (0.14), residues: 1256 loop : -0.87 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 330 TYR 0.018 0.001 TYR D1543 PHE 0.016 0.002 PHE C 525 TRP 0.019 0.001 TRP E1605 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00330 (30099) covalent geometry : angle 0.54753 (40764) SS BOND : bond 0.00301 ( 25) SS BOND : angle 0.70029 ( 50) hydrogen bonds : bond 0.03490 ( 1083) hydrogen bonds : angle 4.66224 ( 3033) link_BETA1-4 : bond 0.00783 ( 1) link_BETA1-4 : angle 1.41693 ( 3) link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 2.42589 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 288 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7753 (tptt) cc_final: 0.7317 (ttmt) REVERT: D 789 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8478 (ttmt) REVERT: D 858 GLN cc_start: 0.8256 (mt0) cc_final: 0.7765 (tt0) REVERT: D 909 GLU cc_start: 0.8121 (tp30) cc_final: 0.7756 (tt0) REVERT: D 959 LYS cc_start: 0.8099 (tttt) cc_final: 0.7633 (tmtm) REVERT: D 1061 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: D 1097 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8358 (t) REVERT: D 1098 GLN cc_start: 0.7965 (tp40) cc_final: 0.7731 (tp40) REVERT: D 1105 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8028 (tttm) REVERT: D 1110 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: D 1119 GLN cc_start: 0.8237 (pt0) cc_final: 0.7911 (pt0) REVERT: D 1159 GLU cc_start: 0.7646 (pt0) cc_final: 0.7131 (tp30) REVERT: D 1174 ASP cc_start: 0.7584 (m-30) cc_final: 0.7197 (m-30) REVERT: D 1310 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6448 (ttp80) REVERT: D 1314 GLU cc_start: 0.7396 (mp0) cc_final: 0.7073 (mm-30) REVERT: D 1317 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8061 (m) REVERT: D 1328 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: D 1396 GLN cc_start: 0.8194 (pt0) cc_final: 0.7712 (mt0) REVERT: D 1441 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7488 (mmp-170) REVERT: D 1455 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8023 (pp20) REVERT: D 1563 MET cc_start: 0.6008 (mmt) cc_final: 0.5780 (mmp) REVERT: D 1600 LYS cc_start: 0.6962 (mptp) cc_final: 0.6265 (mtpt) REVERT: B 325 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 387 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7670 (mmm) REVERT: B 410 TYR cc_start: 0.7551 (t80) cc_final: 0.7119 (t80) REVERT: B 422 TYR cc_start: 0.7242 (m-80) cc_final: 0.6820 (m-80) REVERT: B 433 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7336 (mt) REVERT: B 450 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7846 (mm110) REVERT: B 454 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7578 (mmmm) REVERT: B 587 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8219 (tttm) REVERT: B 616 GLN cc_start: 0.7450 (tp40) cc_final: 0.7000 (tp-100) REVERT: B 619 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7382 (tttp) REVERT: B 754 GLU cc_start: 0.7843 (tp30) cc_final: 0.7552 (tt0) REVERT: P 359 ARG cc_start: 0.3884 (OUTLIER) cc_final: 0.2826 (mmp-170) REVERT: P 403 ARG cc_start: 0.1852 (OUTLIER) cc_final: 0.1372 (ttp-110) REVERT: E 35 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7334 (mtt90) REVERT: E 104 LYS cc_start: 0.7187 (tppt) cc_final: 0.6970 (mmtm) REVERT: E 125 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6515 (mt) REVERT: E 171 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 177 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: E 240 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: E 305 LYS cc_start: 0.7840 (tttp) cc_final: 0.7217 (mptt) REVERT: E 430 GLU cc_start: 0.8316 (pm20) cc_final: 0.8045 (pm20) REVERT: E 478 ARG cc_start: 0.8437 (tpm170) cc_final: 0.7782 (tpt-90) REVERT: E 513 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8253 (t0) REVERT: E 537 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8639 (pt) REVERT: E 571 GLU cc_start: 0.5850 (tt0) cc_final: 0.5618 (tp30) REVERT: E 659 GLU cc_start: 0.7677 (mp0) cc_final: 0.7405 (mm-30) REVERT: E 1015 MET cc_start: 0.5235 (pmm) cc_final: 0.3816 (mmp) REVERT: E 1129 MET cc_start: 0.4675 (mmp) cc_final: 0.3398 (ppp) REVERT: E 1181 MET cc_start: 0.3909 (mmt) cc_final: 0.3556 (mpp) REVERT: E 1199 MET cc_start: 0.2700 (OUTLIER) cc_final: 0.2301 (tmm) REVERT: E 1241 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4274 (tm) REVERT: E 1431 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8118 (tttm) REVERT: E 1535 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.5969 (pttm) REVERT: E 1563 MET cc_start: 0.7429 (mtp) cc_final: 0.6816 (mmt) REVERT: E 1567 GLN cc_start: 0.6005 (tt0) cc_final: 0.5756 (tm-30) REVERT: E 1598 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: E 1603 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6870 (tp) REVERT: E 1624 LYS cc_start: 0.7162 (pttp) cc_final: 0.6601 (tptm) REVERT: E 1629 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: C 44 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8596 (mt) REVERT: C 104 LYS cc_start: 0.7362 (tttt) cc_final: 0.6582 (mtmt) REVERT: C 205 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8779 (tppt) REVERT: C 240 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: C 249 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8409 (mttp) REVERT: C 258 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8288 (mtp180) REVERT: C 299 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: C 427 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8353 (mmtt) REVERT: C 433 GLU cc_start: 0.8418 (tp30) cc_final: 0.8133 (tp30) REVERT: C 513 ASP cc_start: 0.8919 (m-30) cc_final: 0.8605 (m-30) REVERT: C 615 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8810 (mtmt) outliers start: 111 outliers final: 70 residues processed: 367 average time/residue: 0.7352 time to fit residues: 313.0313 Evaluate side-chains 391 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 287 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1130 ILE Chi-restraints excluded: chain D residue 1310 ARG Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1328 GLU Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 438 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 581 MET Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1199 MET Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1618 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 10 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN D1299 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** C 153 ASN ** 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 = 0.3967 r_free = 0.3967 target = 0.174569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110647 restraints weight = 32329.141| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.43 r_work: 0.2967 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30131 Z= 0.124 Angle : 0.546 14.526 40835 Z= 0.285 Chirality : 0.046 0.339 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.833 57.915 4165 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.51 % Allowed : 23.47 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.38 (0.14), residues: 3668 helix: 1.07 (0.22), residues: 625 sheet: 1.30 (0.14), residues: 1253 loop : -0.84 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 546 TYR 0.022 0.001 TYR E 209 PHE 0.015 0.001 PHE C 525 TRP 0.019 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00306 (30099) covalent geometry : angle 0.54345 (40764) SS BOND : bond 0.00285 ( 25) SS BOND : angle 0.67170 ( 50) hydrogen bonds : bond 0.03375 ( 1083) hydrogen bonds : angle 4.62809 ( 3033) link_BETA1-4 : bond 0.00794 ( 1) link_BETA1-4 : angle 1.47183 ( 3) link_NAG-ASN : bond 0.00623 ( 6) link_NAG-ASN : angle 2.40985 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 287 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 722 LYS cc_start: 0.7769 (tptt) cc_final: 0.7347 (ttmt) REVERT: D 789 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8471 (ttmt) REVERT: D 858 GLN cc_start: 0.8234 (mt0) cc_final: 0.7740 (tt0) REVERT: D 909 GLU cc_start: 0.8037 (tp30) cc_final: 0.7678 (tt0) REVERT: D 959 LYS cc_start: 0.8159 (tttt) cc_final: 0.7666 (tmtm) REVERT: D 1061 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: D 1097 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 1098 GLN cc_start: 0.7968 (tp40) cc_final: 0.7704 (tp40) REVERT: D 1105 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8037 (tttm) REVERT: D 1110 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: D 1119 GLN cc_start: 0.8232 (pt0) cc_final: 0.7912 (pt0) REVERT: D 1159 GLU cc_start: 0.7673 (pt0) cc_final: 0.7192 (tp30) REVERT: D 1174 ASP cc_start: 0.7570 (m-30) cc_final: 0.7175 (m-30) REVERT: D 1310 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6517 (ttp80) REVERT: D 1314 GLU cc_start: 0.7343 (mp0) cc_final: 0.7013 (mm-30) REVERT: D 1317 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8068 (m) REVERT: D 1328 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: D 1396 GLN cc_start: 0.8171 (pt0) cc_final: 0.7727 (mt0) REVERT: D 1441 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7477 (mmp-170) REVERT: D 1455 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: D 1600 LYS cc_start: 0.7041 (mptp) cc_final: 0.6343 (mtpt) REVERT: B 325 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 387 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: B 410 TYR cc_start: 0.7506 (t80) cc_final: 0.7118 (t80) REVERT: B 422 TYR cc_start: 0.7292 (m-80) cc_final: 0.6865 (m-80) REVERT: B 433 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7354 (mt) REVERT: B 450 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7843 (mm110) REVERT: B 454 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7609 (mmmm) REVERT: B 587 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8221 (tttm) REVERT: B 616 GLN cc_start: 0.7508 (tp40) cc_final: 0.7078 (tp-100) REVERT: B 619 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7461 (tttp) REVERT: B 754 GLU cc_start: 0.7869 (tp30) cc_final: 0.7602 (tt0) REVERT: P 359 ARG cc_start: 0.3755 (OUTLIER) cc_final: 0.2779 (mmp-170) REVERT: P 403 ARG cc_start: 0.1862 (OUTLIER) cc_final: 0.1390 (ttp-110) REVERT: E 35 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7427 (mtt90) REVERT: E 104 LYS cc_start: 0.7194 (tppt) cc_final: 0.6974 (mmtm) REVERT: E 116 VAL cc_start: 0.8535 (p) cc_final: 0.8238 (t) REVERT: E 125 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6550 (mt) REVERT: E 171 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 177 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: E 240 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: E 305 LYS cc_start: 0.7872 (tttp) cc_final: 0.7251 (mptt) REVERT: E 430 GLU cc_start: 0.8285 (pm20) cc_final: 0.8005 (pm20) REVERT: E 478 ARG cc_start: 0.8399 (tpm170) cc_final: 0.7778 (tpt-90) REVERT: E 513 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (t0) REVERT: E 537 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8633 (pt) REVERT: E 571 GLU cc_start: 0.5830 (tt0) cc_final: 0.5565 (tp30) REVERT: E 659 GLU cc_start: 0.7681 (mp0) cc_final: 0.7435 (mm-30) REVERT: E 1015 MET cc_start: 0.5154 (pmm) cc_final: 0.3742 (mmp) REVERT: E 1181 MET cc_start: 0.4035 (mmt) cc_final: 0.3674 (mpp) REVERT: E 1189 VAL cc_start: 0.2416 (OUTLIER) cc_final: 0.2198 (t) REVERT: E 1199 MET cc_start: 0.2778 (OUTLIER) cc_final: 0.2511 (tmm) REVERT: E 1241 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4279 (tm) REVERT: E 1391 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7291 (ttt90) REVERT: E 1431 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8158 (tttm) REVERT: E 1535 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5918 (pttm) REVERT: E 1563 MET cc_start: 0.7510 (mtp) cc_final: 0.6871 (mmt) REVERT: E 1567 GLN cc_start: 0.6017 (tt0) cc_final: 0.5780 (tm-30) REVERT: E 1598 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6273 (tm-30) REVERT: E 1603 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6844 (tp) REVERT: E 1624 LYS cc_start: 0.7186 (pttp) cc_final: 0.6633 (tptm) REVERT: E 1629 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: C 44 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8609 (mt) REVERT: C 104 LYS cc_start: 0.7384 (tttt) cc_final: 0.6604 (mtmt) REVERT: C 205 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (tppt) REVERT: C 240 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: C 249 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8399 (mttp) REVERT: C 258 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8267 (mtp180) REVERT: C 299 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: C 427 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (mmtt) REVERT: C 433 GLU cc_start: 0.8410 (tp30) cc_final: 0.8121 (tp30) REVERT: C 513 ASP cc_start: 0.8890 (m-30) cc_final: 0.8579 (m-30) REVERT: C 615 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8790 (mtmt) outliers start: 115 outliers final: 72 residues processed: 373 average time/residue: 0.7054 time to fit residues: 305.3723 Evaluate side-chains 392 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 285 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 928 SER Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1310 ARG Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1328 GLU Chi-restraints excluded: chain D residue 1441 ARG Chi-restraints excluded: chain D residue 1455 GLU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain P residue 403 ARG Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 438 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 MET Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 513 ASP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 581 MET Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 638 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1185 ARG Chi-restraints excluded: chain E residue 1189 VAL Chi-restraints excluded: chain E residue 1199 MET Chi-restraints excluded: chain E residue 1241 LEU Chi-restraints excluded: chain E residue 1284 LYS Chi-restraints excluded: chain E residue 1399 THR Chi-restraints excluded: chain E residue 1535 LYS Chi-restraints excluded: chain E residue 1569 ILE Chi-restraints excluded: chain E residue 1598 GLU Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1618 LEU Chi-restraints excluded: chain E residue 1629 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 615 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 328 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 760 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** 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 = 0.3979 r_free = 0.3979 target = 0.175933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111558 restraints weight = 32497.136| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.43 r_work: 0.2972 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30131 Z= 0.110 Angle : 0.534 13.863 40835 Z= 0.278 Chirality : 0.045 0.336 4613 Planarity : 0.004 0.054 5243 Dihedral : 4.773 58.679 4165 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.17 % Allowed : 23.80 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.43 (0.14), residues: 3668 helix: 1.12 (0.22), residues: 625 sheet: 1.33 (0.14), residues: 1252 loop : -0.81 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 546 TYR 0.026 0.001 TYR C 385 PHE 0.026 0.001 PHE D1584 TRP 0.019 0.001 TRP E1605 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00266 (30099) covalent geometry : angle 0.53177 (40764) SS BOND : bond 0.00251 ( 25) SS BOND : angle 0.62198 ( 50) hydrogen bonds : bond 0.03221 ( 1083) hydrogen bonds : angle 4.59117 ( 3033) link_BETA1-4 : bond 0.00790 ( 1) link_BETA1-4 : angle 1.46988 ( 3) link_NAG-ASN : bond 0.00627 ( 6) link_NAG-ASN : angle 2.39673 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14055.49 seconds wall clock time: 238 minutes 45.93 seconds (14325.93 seconds total)