Starting phenix.real_space_refine on Thu Feb 5 12:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.map" model { file = "/net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qpy_53288/02_2026/9qpy_53288.cif" } resolution = 4.3 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 81 5.16 5 C 10685 2.51 5 N 2950 2.21 5 O 3200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 16917 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5005 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 4683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4683 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 27, 'TRANS': 578} Chain breaks: 6 Chain: "C" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2235 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 268} Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 3987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 3983 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 502, 3983 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 1 bond proxies already assigned to first conformer: 4059 Chain: "A" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.40, per 1000 atoms: 0.26 Number of scatterers: 16917 At special positions: 0 Unit cell: (121.68, 126.88, 176.8, 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) S 81 16.00 Mg 1 11.99 O 3200 8.00 N 2950 7.00 C 10685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.04 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.04 Simple disulfide: pdb=" SG CYS C1595 " - pdb=" SG CYS C1673 " distance=2.03 Simple disulfide: pdb=" SG CYS C1618 " - pdb=" SG CYS C1742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1718 " - pdb=" SG CYS C1727 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 463 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 492 " - pdb=" SG CYS E 508 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 600 " distance=2.03 Simple disulfide: pdb=" SG CYS E 638 " - pdb=" SG CYS E 665 " distance=2.03 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.03 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 NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG E 802 " - " ASN E 290 " " NAG E 803 " - " ASN E 467 " " NAG E 804 " - " ASN E 471 " NAG-THR " NAG B1803 " - " THR B1393 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 702.9 milliseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 33 sheets defined 22.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.531A pdb=" N ALA A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.521A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'B' and resid 996 through 1002 removed outlier: 3.833A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B1002 " --> pdb=" O GLY B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1040 through 1058 Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1109 removed outlier: 3.838A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B1102 " --> pdb=" O GLU B1098 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1156 removed outlier: 4.195A pdb=" N ALA B1154 " --> pdb=" O HIS B1150 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B1155 " --> pdb=" O HIS B1151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B1156 " --> pdb=" O GLY B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1186 Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 removed outlier: 3.632A pdb=" N ILE B1262 " --> pdb=" O PRO B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.704A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 3.769A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'C' and resid 1612 through 1619 Processing helix chain 'C' and resid 1720 through 1724 Processing helix chain 'C' and resid 1726 through 1740 Processing helix chain 'D' and resid 58 through 61 removed outlier: 3.809A pdb=" N LYS D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'E' and resid 266 through 286 removed outlier: 3.510A pdb=" N ILE E 284 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 315 through 326 removed outlier: 3.528A pdb=" N ALA E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 removed outlier: 4.136A pdb=" N HIS E 331 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 358 removed outlier: 3.760A pdb=" N ALA E 342 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 384 through 396 removed outlier: 4.251A pdb=" N ALA E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 393 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 394 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE E 395 " --> pdb=" O HIS E 391 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 396 " --> pdb=" O ILE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 404 removed outlier: 3.689A pdb=" N ASN E 403 " --> pdb=" O GLN E 400 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP E 404 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 427 removed outlier: 3.518A pdb=" N LEU E 423 " --> pdb=" O ASP E 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 426 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 451 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.574A pdb=" N CYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 549 through 553 Processing helix chain 'E' and resid 585 through 592 Processing helix chain 'E' and resid 599 through 608 Processing helix chain 'E' and resid 631 through 640 removed outlier: 3.768A pdb=" N THR E 636 " --> pdb=" O GLY E 632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 637 " --> pdb=" O VAL E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 645 Processing helix chain 'E' and resid 675 through 679 Processing helix chain 'E' and resid 735 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 removed outlier: 3.752A pdb=" N ALA A 83 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 41 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 44 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 22 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 655 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 27 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.544A pdb=" N VAL A 31 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.813A pdb=" N PHE A 198 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 192 removed outlier: 3.881A pdb=" N ARG A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 214 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.131A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 252 through 253 removed outlier: 5.121A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.591A pdb=" N SER A 301 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.557A pdb=" N ALA A 355 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.644A pdb=" N ALA A 388 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 417 through 424 removed outlier: 3.659A pdb=" N SER A 447 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 476 removed outlier: 3.525A pdb=" N SER A 474 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 494 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 476 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 492 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 527 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 514 through 522 removed outlier: 5.349A pdb=" N ILE A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 511 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 519 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 507 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 514 through 522 removed outlier: 5.349A pdb=" N ILE A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 511 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 519 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 507 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.989A pdb=" N LEU B 795 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.922A pdb=" N ARG B 785 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 597 " --> pdb=" O VAL B 789 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 811 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.922A pdb=" N ARG B 785 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 597 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 774 through 775 removed outlier: 3.517A pdb=" N VAL B 927 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 911 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 833 through 836 removed outlier: 3.633A pdb=" N VAL B 854 " --> pdb=" O HIS B 836 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 850 through 851 Processing sheet with id=AC3, first strand: chain 'B' and resid 875 through 876 removed outlier: 3.607A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.582A pdb=" N ALA B 938 " --> pdb=" O VAL B1386 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B1380 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B1376 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER B 976 " --> pdb=" O PHE B1360 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B1360 " --> pdb=" O SER B 976 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 removed outlier: 3.552A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B1329 " --> pdb=" O LEU B1344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B1340 " --> pdb=" O SER B1333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.519A pdb=" N GLN B1398 " --> pdb=" O TRP C1473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.761A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C1516 " --> pdb=" O LEU C1523 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C1558 " --> pdb=" O ARG C1564 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG C1564 " --> pdb=" O ASP C1558 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1701 through 1702 removed outlier: 8.624A pdb=" N TYR C1701 " --> pdb=" O MET C1664 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN C1666 " --> pdb=" O TYR C1701 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C1665 " --> pdb=" O THR C1645 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C1645 " --> pdb=" O ARG C1665 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C1667 " --> pdb=" O PHE C1643 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU C1642 " --> pdb=" O SER C1636 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C1636 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C1644 " --> pdb=" O GLU C1634 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU C1634 " --> pdb=" O GLU C1644 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C1646 " --> pdb=" O LEU C1632 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C1632 " --> pdb=" O LYS C1646 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C1648 " --> pdb=" O LYS C1630 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LYS C1630 " --> pdb=" O THR C1648 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C1650 " --> pdb=" O GLN C1628 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN C1628 " --> pdb=" O VAL C1650 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY C1687 " --> pdb=" O TYR C1625 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C1627 " --> pdb=" O ILE C1685 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.756A pdb=" N LEU D 20 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 77 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS D 22 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 65 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.198A pdb=" N TRP D 32 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 88 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 245 through 246 removed outlier: 6.620A pdb=" N ILE E 245 " --> pdb=" O ASP E 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.387A pdb=" N LEU E 253 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA E 294 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 255 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE E 296 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 257 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 298 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU E 259 " --> pdb=" O PHE E 298 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN E 254 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE E 372 " --> pdb=" O ASN E 254 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR E 256 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU E 374 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU E 258 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE E 437 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA E 410 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU E 439 " --> pdb=" O ALA E 410 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLY E 412 " --> pdb=" O LEU E 439 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 527 through 533 removed outlier: 6.064A pdb=" N TRP E 529 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP E 524 " --> pdb=" O TRP E 529 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY E 523 " --> pdb=" O HIS E 481 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N HIS E 481 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU E 564 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA E 538 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS E 566 " --> pdb=" O GLU E 536 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 612 through 618 Processing sheet with id=AD6, first strand: chain 'E' and resid 682 through 687 removed outlier: 6.822A pdb=" N LEU E 685 " --> pdb=" O GLN E 693 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN E 693 " --> pdb=" O LEU E 685 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 687 " --> pdb=" O PHE E 691 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE E 691 " --> pdb=" O ARG E 687 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL E 697 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE E 730 " --> pdb=" O VAL E 697 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1650 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: 3.83 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5630 1.35 - 1.48: 4125 1.48 - 1.61: 7385 1.61 - 1.73: 0 1.73 - 1.86: 127 Bond restraints: 17267 Sorted by residual: bond pdb=" CA THR B 805 " pdb=" CB THR B 805 " ideal model delta sigma weight residual 1.527 1.560 -0.033 1.75e-02 3.27e+03 3.64e+00 bond pdb=" CB CYS C1588 " pdb=" SG CYS C1588 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB CYS B 876 " pdb=" SG CYS B 876 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CB CYS C1595 " pdb=" SG CYS C1595 " ideal model delta sigma weight residual 1.808 1.759 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CA ILE B 969 " pdb=" CB ILE B 969 " ideal model delta sigma weight residual 1.537 1.520 0.017 1.29e-02 6.01e+03 1.72e+00 ... (remaining 17262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 23252 3.14 - 6.29: 130 6.29 - 9.43: 17 9.43 - 12.58: 1 12.58 - 15.72: 1 Bond angle restraints: 23401 Sorted by residual: angle pdb=" CA CYS C1583 " pdb=" CB CYS C1583 " pdb=" SG CYS C1583 " ideal model delta sigma weight residual 114.40 130.12 -15.72 2.30e+00 1.89e-01 4.67e+01 angle pdb=" C VAL C1587 " pdb=" N CYS C1588 " pdb=" CA CYS C1588 " ideal model delta sigma weight residual 122.73 115.78 6.95 1.62e+00 3.81e-01 1.84e+01 angle pdb=" N CYS C1583 " pdb=" CA CYS C1583 " pdb=" C CYS C1583 " ideal model delta sigma weight residual 111.03 115.25 -4.22 1.11e+00 8.12e-01 1.45e+01 angle pdb=" C LEU C1582 " pdb=" N CYS C1583 " pdb=" CA CYS C1583 " ideal model delta sigma weight residual 120.63 115.85 4.78 1.36e+00 5.41e-01 1.23e+01 angle pdb=" CA MET E 349 " pdb=" CB MET E 349 " pdb=" CG MET E 349 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 23396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 9749 16.99 - 33.98: 650 33.98 - 50.98: 106 50.98 - 67.97: 18 67.97 - 84.96: 15 Dihedral angle restraints: 10538 sinusoidal: 4330 harmonic: 6208 Sorted by residual: dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 36.53 56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 44.60 48.40 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA CYS C1595 " pdb=" C CYS C1595 " pdb=" N PRO C1596 " pdb=" CA PRO C1596 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 10535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2308 0.067 - 0.134: 310 0.134 - 0.202: 13 0.202 - 0.269: 4 0.269 - 0.336: 1 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CA CYS C1583 " pdb=" N CYS C1583 " pdb=" C CYS C1583 " pdb=" CB CYS C1583 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C1 NAG E 803 " pdb=" ND2 ASN E 467 " pdb=" C2 NAG E 803 " pdb=" O5 NAG E 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG E 802 " pdb=" ND2 ASN E 290 " pdb=" C2 NAG E 802 " pdb=" O5 NAG E 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2633 not shown) Planarity restraints: 3038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 806 " 0.020 2.00e-02 2.50e+03 1.84e-02 8.42e+00 pdb=" CG TRP B 806 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 806 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 806 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 806 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 806 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 806 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 806 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 806 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 806 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 738 " -0.016 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP E 738 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP E 738 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 738 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 738 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 738 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 738 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 738 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 738 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 738 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 256 " 0.012 2.00e-02 2.50e+03 1.44e-02 4.17e+00 pdb=" CG TYR E 256 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 256 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 256 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 256 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 256 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 256 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 256 " 0.001 2.00e-02 2.50e+03 ... (remaining 3035 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 209 2.58 - 3.16: 14101 3.16 - 3.74: 26369 3.74 - 4.32: 34746 4.32 - 4.90: 56935 Nonbonded interactions: 132360 Sorted by model distance: nonbonded pdb=" OG1 THR E 337 " pdb="MG MG E 801 " model vdw 1.995 2.170 nonbonded pdb=" O VAL C1744 " pdb="MG MG E 801 " model vdw 2.098 2.170 nonbonded pdb=" OG SER E 262 " pdb="MG MG E 801 " model vdw 2.175 2.170 nonbonded pdb=" OG SER E 266 " pdb=" OD1 ASN E 268 " model vdw 2.191 3.040 nonbonded pdb=" O ASN A 151 " pdb=" NE2 GLN A 154 " model vdw 2.193 3.120 ... (remaining 132355 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.003 0.055 17290 Z= 0.133 Angle : 0.694 15.723 23453 Z= 0.341 Chirality : 0.045 0.336 2636 Planarity : 0.004 0.055 3032 Dihedral : 11.610 84.960 6486 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.20 (0.19), residues: 2128 helix: 0.90 (0.26), residues: 418 sheet: 0.18 (0.21), residues: 650 loop : -0.69 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1674 TYR 0.034 0.002 TYR B1066 PHE 0.024 0.002 PHE C1640 TRP 0.049 0.002 TRP B 806 HIS 0.009 0.001 HIS B1271 Details of bonding type rmsd covalent geometry : bond 0.00294 (17267) covalent geometry : angle 0.67154 (23401) SS BOND : bond 0.00579 ( 16) SS BOND : angle 2.92670 ( 32) hydrogen bonds : bond 0.25051 ( 588) hydrogen bonds : angle 8.72613 ( 1650) link_NAG-ASN : bond 0.01071 ( 6) link_NAG-ASN : angle 5.13104 ( 18) link_NAG-THR : bond 0.00028 ( 1) link_NAG-THR : angle 2.03335 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.9131 (mmm) cc_final: 0.8855 (mmm) REVERT: A 352 MET cc_start: 0.8848 (pmm) cc_final: 0.8391 (pmm) REVERT: B 780 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 781 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 839 LEU cc_start: 0.8689 (mm) cc_final: 0.8449 (mt) REVERT: B 1176 ASN cc_start: 0.9195 (m-40) cc_final: 0.8927 (t0) REVERT: B 1217 LEU cc_start: 0.8763 (tp) cc_final: 0.8504 (tt) REVERT: C 1555 THR cc_start: 0.8917 (m) cc_final: 0.8475 (p) REVERT: C 1597 ARG cc_start: 0.7285 (ttt-90) cc_final: 0.6791 (ttt180) REVERT: C 1625 TYR cc_start: 0.8639 (p90) cc_final: 0.8361 (p90) REVERT: C 1675 LEU cc_start: 0.7979 (tp) cc_final: 0.7671 (tp) REVERT: E 306 MET cc_start: 0.5990 (tpt) cc_final: 0.5373 (tpp) REVERT: E 362 MET cc_start: 0.7197 (mmp) cc_final: 0.6638 (ppp) REVERT: E 364 TRP cc_start: 0.7556 (t60) cc_final: 0.7290 (t60) REVERT: E 425 GLU cc_start: 0.7309 (mp0) cc_final: 0.6865 (mp0) REVERT: E 452 MET cc_start: 0.7567 (mmm) cc_final: 0.6966 (mmm) REVERT: E 454 ASP cc_start: 0.6666 (t0) cc_final: 0.6397 (t0) REVERT: E 537 LYS cc_start: 0.4721 (ptmt) cc_final: 0.4395 (ttmt) REVERT: E 572 LYS cc_start: 0.6970 (mptt) cc_final: 0.6184 (tptt) REVERT: E 601 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8200 (mmt180) REVERT: E 648 MET cc_start: 0.4120 (ptt) cc_final: 0.2202 (tpp) REVERT: E 715 LYS cc_start: 0.4455 (pttm) cc_final: 0.4201 (tptm) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1347 time to fit residues: 42.0371 Evaluate side-chains 152 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 154 GLN A 504 HIS A 620 ASN ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1111 GLN B1112 GLN B1118 GLN ** B1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN B1191 HIS B1359 GLN C1542 GLN D 73 ASN E 248 GLN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN E 515 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069984 restraints weight = 68583.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068997 restraints weight = 46677.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069831 restraints weight = 35469.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070049 restraints weight = 30337.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070044 restraints weight = 28253.289| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 17290 Z= 0.245 Angle : 0.717 11.951 23453 Z= 0.365 Chirality : 0.046 0.257 2636 Planarity : 0.005 0.052 3032 Dihedral : 5.578 59.154 2476 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 0.11 % Allowed : 5.60 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.52 (0.18), residues: 2128 helix: 0.91 (0.26), residues: 420 sheet: -0.13 (0.21), residues: 653 loop : -0.97 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 402 TYR 0.019 0.002 TYR C1468 PHE 0.025 0.002 PHE D 33 TRP 0.034 0.002 TRP E 738 HIS 0.009 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00552 (17267) covalent geometry : angle 0.70445 (23401) SS BOND : bond 0.00487 ( 16) SS BOND : angle 1.58185 ( 32) hydrogen bonds : bond 0.04939 ( 588) hydrogen bonds : angle 6.27552 ( 1650) link_NAG-ASN : bond 0.00763 ( 6) link_NAG-ASN : angle 4.45651 ( 18) link_NAG-THR : bond 0.00120 ( 1) link_NAG-THR : angle 2.10851 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8410 (t0) cc_final: 0.8199 (t70) REVERT: A 352 MET cc_start: 0.8716 (pmm) cc_final: 0.8303 (pmm) REVERT: A 502 PHE cc_start: 0.8005 (p90) cc_final: 0.7733 (p90) REVERT: B 780 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8336 (mm-30) REVERT: B 1054 MET cc_start: 0.8958 (tpt) cc_final: 0.8621 (tpp) REVERT: B 1128 MET cc_start: 0.7086 (ptm) cc_final: 0.6818 (ptt) REVERT: B 1166 GLN cc_start: 0.9318 (tp40) cc_final: 0.9036 (pp30) REVERT: C 1625 TYR cc_start: 0.8642 (p90) cc_final: 0.8264 (p90) REVERT: D 66 ILE cc_start: 0.9011 (mt) cc_final: 0.8622 (tp) REVERT: E 306 MET cc_start: 0.5933 (tpt) cc_final: 0.5519 (tpp) REVERT: E 364 TRP cc_start: 0.7579 (t60) cc_final: 0.7377 (t60) REVERT: E 373 LEU cc_start: 0.7420 (mm) cc_final: 0.7125 (mt) REVERT: E 425 GLU cc_start: 0.7365 (mp0) cc_final: 0.6926 (mp0) REVERT: E 454 ASP cc_start: 0.6556 (t0) cc_final: 0.6254 (t0) REVERT: E 480 TRP cc_start: 0.7834 (p90) cc_final: 0.7608 (p90) REVERT: E 537 LYS cc_start: 0.4002 (ptmt) cc_final: 0.3522 (ttmt) REVERT: E 572 LYS cc_start: 0.7001 (mptt) cc_final: 0.6221 (mmtt) REVERT: E 601 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8238 (mmt180) REVERT: E 648 MET cc_start: 0.3839 (ptt) cc_final: 0.2108 (tpp) REVERT: E 715 LYS cc_start: 0.4416 (pttm) cc_final: 0.4045 (tptm) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1288 time to fit residues: 34.7194 Evaluate side-chains 131 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN C1542 GLN D 73 ASN D 115 GLN E 248 GLN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071069 restraints weight = 74150.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068981 restraints weight = 56870.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069563 restraints weight = 47881.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069763 restraints weight = 40830.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070359 restraints weight = 33329.406| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17290 Z= 0.183 Angle : 0.630 11.509 23453 Z= 0.320 Chirality : 0.043 0.237 2636 Planarity : 0.004 0.040 3032 Dihedral : 5.407 59.614 2476 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.52 (0.18), residues: 2128 helix: 1.00 (0.26), residues: 413 sheet: -0.14 (0.20), residues: 654 loop : -0.99 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1722 TYR 0.014 0.002 TYR B1053 PHE 0.023 0.002 PHE B1144 TRP 0.025 0.002 TRP E 738 HIS 0.007 0.001 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.00407 (17267) covalent geometry : angle 0.61594 (23401) SS BOND : bond 0.00639 ( 16) SS BOND : angle 1.58189 ( 32) hydrogen bonds : bond 0.04476 ( 588) hydrogen bonds : angle 5.96200 ( 1650) link_NAG-ASN : bond 0.01017 ( 6) link_NAG-ASN : angle 4.32151 ( 18) link_NAG-THR : bond 0.00231 ( 1) link_NAG-THR : angle 2.12043 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8742 (pmm) cc_final: 0.8255 (pmm) REVERT: A 502 PHE cc_start: 0.7991 (p90) cc_final: 0.7558 (p90) REVERT: B 1054 MET cc_start: 0.8949 (tpt) cc_final: 0.8648 (tpp) REVERT: B 1057 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8612 (tm-30) REVERT: B 1066 TYR cc_start: 0.7165 (m-10) cc_final: 0.6780 (m-10) REVERT: B 1128 MET cc_start: 0.7392 (ptm) cc_final: 0.7165 (ptt) REVERT: B 1166 GLN cc_start: 0.9302 (tp40) cc_final: 0.9036 (pp30) REVERT: C 1597 ARG cc_start: 0.7201 (ttt-90) cc_final: 0.6729 (ttt180) REVERT: C 1614 MET cc_start: 0.7911 (tpt) cc_final: 0.7702 (tpt) REVERT: D 43 PHE cc_start: 0.8777 (p90) cc_final: 0.8463 (p90) REVERT: D 66 ILE cc_start: 0.8967 (mt) cc_final: 0.8729 (pt) REVERT: D 72 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9184 (mmtm) REVERT: E 306 MET cc_start: 0.6084 (tpt) cc_final: 0.5591 (tpp) REVERT: E 373 LEU cc_start: 0.7385 (mm) cc_final: 0.7153 (mt) REVERT: E 425 GLU cc_start: 0.7411 (mp0) cc_final: 0.6977 (mp0) REVERT: E 454 ASP cc_start: 0.6378 (t0) cc_final: 0.6101 (t0) REVERT: E 480 TRP cc_start: 0.7931 (p90) cc_final: 0.7604 (p90) REVERT: E 537 LYS cc_start: 0.4665 (ptmt) cc_final: 0.4157 (ttmt) REVERT: E 572 LYS cc_start: 0.6636 (mptt) cc_final: 0.5872 (mmtt) REVERT: E 601 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8330 (mmt180) REVERT: E 648 MET cc_start: 0.3634 (ptt) cc_final: 0.2091 (tpp) REVERT: E 715 LYS cc_start: 0.4422 (pttm) cc_final: 0.3995 (tptm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1409 time to fit residues: 35.4391 Evaluate side-chains 126 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 150 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 43 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1359 GLN D 73 ASN E 246 GLN E 248 GLN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069838 restraints weight = 67609.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067972 restraints weight = 59036.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068868 restraints weight = 42305.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069711 restraints weight = 32155.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069661 restraints weight = 28476.348| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17290 Z= 0.156 Angle : 0.604 10.765 23453 Z= 0.306 Chirality : 0.043 0.213 2636 Planarity : 0.004 0.053 3032 Dihedral : 5.319 59.242 2476 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.48 (0.18), residues: 2128 helix: 1.15 (0.26), residues: 413 sheet: -0.17 (0.21), residues: 647 loop : -0.98 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 852 TYR 0.016 0.001 TYR D 29 PHE 0.019 0.001 PHE B1144 TRP 0.011 0.001 TRP E 699 HIS 0.007 0.001 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.00349 (17267) covalent geometry : angle 0.59123 (23401) SS BOND : bond 0.00407 ( 16) SS BOND : angle 1.44569 ( 32) hydrogen bonds : bond 0.03897 ( 588) hydrogen bonds : angle 5.68409 ( 1650) link_NAG-ASN : bond 0.00529 ( 6) link_NAG-ASN : angle 4.03965 ( 18) link_NAG-THR : bond 0.00206 ( 1) link_NAG-THR : angle 1.66017 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8112 (t70) cc_final: 0.7768 (t70) REVERT: A 352 MET cc_start: 0.8686 (pmm) cc_final: 0.8211 (pmm) REVERT: A 502 PHE cc_start: 0.8023 (p90) cc_final: 0.7622 (p90) REVERT: B 1054 MET cc_start: 0.8979 (tpt) cc_final: 0.8460 (tpp) REVERT: B 1066 TYR cc_start: 0.7243 (m-10) cc_final: 0.6924 (m-10) REVERT: B 1128 MET cc_start: 0.7456 (ptm) cc_final: 0.7031 (ptt) REVERT: B 1295 PHE cc_start: 0.8304 (t80) cc_final: 0.7959 (t80) REVERT: D 43 PHE cc_start: 0.8720 (p90) cc_final: 0.8443 (p90) REVERT: D 66 ILE cc_start: 0.8938 (mt) cc_final: 0.8725 (pt) REVERT: D 72 LYS cc_start: 0.9439 (mmtm) cc_final: 0.9223 (mmtm) REVERT: E 306 MET cc_start: 0.6013 (tpt) cc_final: 0.5502 (tpp) REVERT: E 425 GLU cc_start: 0.7350 (mp0) cc_final: 0.6881 (mp0) REVERT: E 454 ASP cc_start: 0.6673 (t0) cc_final: 0.6339 (t0) REVERT: E 480 TRP cc_start: 0.7967 (p90) cc_final: 0.7619 (p90) REVERT: E 537 LYS cc_start: 0.4733 (ptmt) cc_final: 0.4277 (ttmt) REVERT: E 572 LYS cc_start: 0.6748 (mptt) cc_final: 0.5963 (mmtm) REVERT: E 601 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8339 (mmt180) REVERT: E 648 MET cc_start: 0.3305 (ptt) cc_final: 0.1855 (tpp) REVERT: E 715 LYS cc_start: 0.4424 (pttm) cc_final: 0.3973 (tptm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1292 time to fit residues: 33.2768 Evaluate side-chains 128 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 267 GLN A 580 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 HIS C1542 GLN D 73 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.095329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068934 restraints weight = 66844.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067992 restraints weight = 53780.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068301 restraints weight = 40963.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068632 restraints weight = 34890.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.068756 restraints weight = 30865.174| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17290 Z= 0.180 Angle : 0.613 9.962 23453 Z= 0.310 Chirality : 0.043 0.205 2636 Planarity : 0.004 0.059 3032 Dihedral : 5.401 59.519 2476 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.52 (0.18), residues: 2128 helix: 1.22 (0.26), residues: 411 sheet: -0.23 (0.21), residues: 652 loop : -1.01 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1722 TYR 0.017 0.002 TYR D 29 PHE 0.025 0.002 PHE C1733 TRP 0.018 0.001 TRP C1708 HIS 0.004 0.001 HIS E 451 Details of bonding type rmsd covalent geometry : bond 0.00403 (17267) covalent geometry : angle 0.60094 (23401) SS BOND : bond 0.00540 ( 16) SS BOND : angle 1.60332 ( 32) hydrogen bonds : bond 0.03802 ( 588) hydrogen bonds : angle 5.56313 ( 1650) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 3.78593 ( 18) link_NAG-THR : bond 0.00291 ( 1) link_NAG-THR : angle 1.99342 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8180 (t70) cc_final: 0.7793 (t70) REVERT: A 352 MET cc_start: 0.8728 (pmm) cc_final: 0.8046 (ppp) REVERT: A 502 PHE cc_start: 0.7980 (p90) cc_final: 0.7500 (p90) REVERT: B 1054 MET cc_start: 0.8915 (tpt) cc_final: 0.8384 (tpp) REVERT: B 1057 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 1128 MET cc_start: 0.7524 (ptm) cc_final: 0.7121 (ptt) REVERT: B 1271 HIS cc_start: 0.8798 (t-170) cc_final: 0.8597 (t-170) REVERT: C 1614 MET cc_start: 0.7960 (tpt) cc_final: 0.6538 (ppp) REVERT: C 1733 PHE cc_start: 0.6800 (t80) cc_final: 0.6408 (t80) REVERT: D 43 PHE cc_start: 0.8665 (p90) cc_final: 0.8395 (p90) REVERT: D 66 ILE cc_start: 0.8936 (mt) cc_final: 0.8729 (pt) REVERT: D 72 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9243 (mmtm) REVERT: E 245 ILE cc_start: 0.9169 (mt) cc_final: 0.8858 (mm) REVERT: E 306 MET cc_start: 0.6130 (tpt) cc_final: 0.5595 (tpp) REVERT: E 425 GLU cc_start: 0.7349 (mp0) cc_final: 0.6841 (mp0) REVERT: E 454 ASP cc_start: 0.6642 (t0) cc_final: 0.5643 (p0) REVERT: E 480 TRP cc_start: 0.8014 (p90) cc_final: 0.7623 (p90) REVERT: E 537 LYS cc_start: 0.4541 (ptmt) cc_final: 0.4083 (ttmt) REVERT: E 572 LYS cc_start: 0.6790 (mptt) cc_final: 0.5985 (mmtp) REVERT: E 601 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8335 (mmt180) REVERT: E 648 MET cc_start: 0.3160 (ptt) cc_final: 0.1779 (tpp) REVERT: E 715 LYS cc_start: 0.4272 (pttm) cc_final: 0.3844 (tptm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1058 time to fit residues: 26.7795 Evaluate side-chains 131 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 137 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 70 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 267 GLN A 616 HIS B1118 GLN ** B1275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1359 GLN D 73 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 736 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070103 restraints weight = 67410.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.069273 restraints weight = 52611.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069936 restraints weight = 40188.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070061 restraints weight = 35255.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070332 restraints weight = 29309.379| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17290 Z= 0.113 Angle : 0.592 10.670 23453 Z= 0.297 Chirality : 0.043 0.211 2636 Planarity : 0.004 0.062 3032 Dihedral : 5.243 57.761 2476 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.39 (0.18), residues: 2128 helix: 1.20 (0.26), residues: 411 sheet: -0.12 (0.21), residues: 657 loop : -0.90 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1722 TYR 0.018 0.001 TYR D 29 PHE 0.021 0.001 PHE C1733 TRP 0.019 0.001 TRP C1708 HIS 0.007 0.001 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.00250 (17267) covalent geometry : angle 0.58055 (23401) SS BOND : bond 0.00438 ( 16) SS BOND : angle 1.53151 ( 32) hydrogen bonds : bond 0.03560 ( 588) hydrogen bonds : angle 5.34263 ( 1650) link_NAG-ASN : bond 0.00475 ( 6) link_NAG-ASN : angle 3.77402 ( 18) link_NAG-THR : bond 0.00360 ( 1) link_NAG-THR : angle 1.53173 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8155 (t70) cc_final: 0.7782 (t70) REVERT: A 501 THR cc_start: 0.7997 (p) cc_final: 0.7794 (t) REVERT: A 502 PHE cc_start: 0.7966 (p90) cc_final: 0.7468 (p90) REVERT: B 1054 MET cc_start: 0.8918 (tpt) cc_final: 0.8336 (tpp) REVERT: B 1057 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 1128 MET cc_start: 0.7449 (ptm) cc_final: 0.7075 (ptt) REVERT: C 1614 MET cc_start: 0.7781 (tpt) cc_final: 0.6445 (ppp) REVERT: C 1733 PHE cc_start: 0.6732 (t80) cc_final: 0.6345 (t80) REVERT: D 43 PHE cc_start: 0.8553 (p90) cc_final: 0.8279 (p90) REVERT: D 66 ILE cc_start: 0.8897 (mt) cc_final: 0.8658 (pt) REVERT: D 72 LYS cc_start: 0.9462 (mmtm) cc_final: 0.9251 (mmtm) REVERT: E 245 ILE cc_start: 0.9178 (mt) cc_final: 0.8908 (mm) REVERT: E 306 MET cc_start: 0.6046 (tpt) cc_final: 0.5493 (tpp) REVERT: E 425 GLU cc_start: 0.7465 (mp0) cc_final: 0.7200 (mp0) REVERT: E 454 ASP cc_start: 0.6624 (t0) cc_final: 0.5587 (p0) REVERT: E 480 TRP cc_start: 0.7898 (p90) cc_final: 0.7580 (p90) REVERT: E 515 HIS cc_start: 0.5902 (p-80) cc_final: 0.5697 (p-80) REVERT: E 537 LYS cc_start: 0.4578 (ptmt) cc_final: 0.4065 (ttmt) REVERT: E 572 LYS cc_start: 0.6733 (mptt) cc_final: 0.5962 (mmtp) REVERT: E 586 MET cc_start: 0.7803 (tmm) cc_final: 0.7450 (tmm) REVERT: E 601 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8332 (mmt180) REVERT: E 648 MET cc_start: 0.3280 (ptt) cc_final: 0.2029 (tpp) REVERT: E 715 LYS cc_start: 0.4241 (pttm) cc_final: 0.3825 (tptm) REVERT: E 750 LEU cc_start: 0.3406 (mt) cc_final: 0.3189 (mt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1177 time to fit residues: 30.6420 Evaluate side-chains 137 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 33 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 192 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS ** E 515 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 = 0.3741 r_free = 0.3741 target = 0.097008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071403 restraints weight = 75854.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069308 restraints weight = 48509.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070110 restraints weight = 41390.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070498 restraints weight = 32189.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070604 restraints weight = 28399.669| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17290 Z= 0.129 Angle : 0.594 10.770 23453 Z= 0.297 Chirality : 0.043 0.207 2636 Planarity : 0.004 0.052 3032 Dihedral : 5.203 57.910 2476 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.40 (0.19), residues: 2128 helix: 1.30 (0.26), residues: 411 sheet: -0.12 (0.21), residues: 650 loop : -0.94 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1722 TYR 0.027 0.002 TYR A 581 PHE 0.016 0.001 PHE C1733 TRP 0.035 0.001 TRP A 360 HIS 0.007 0.001 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.00290 (17267) covalent geometry : angle 0.58247 (23401) SS BOND : bond 0.00412 ( 16) SS BOND : angle 1.58423 ( 32) hydrogen bonds : bond 0.03497 ( 588) hydrogen bonds : angle 5.29009 ( 1650) link_NAG-ASN : bond 0.00492 ( 6) link_NAG-ASN : angle 3.63864 ( 18) link_NAG-THR : bond 0.00209 ( 1) link_NAG-THR : angle 1.38719 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8200 (t70) cc_final: 0.7849 (t70) REVERT: A 502 PHE cc_start: 0.7950 (p90) cc_final: 0.7459 (p90) REVERT: B 1054 MET cc_start: 0.8920 (tpt) cc_final: 0.8346 (tpp) REVERT: B 1057 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8463 (tm-30) REVERT: B 1128 MET cc_start: 0.7574 (ptm) cc_final: 0.7210 (ptt) REVERT: C 1614 MET cc_start: 0.7764 (tpt) cc_final: 0.6518 (ppp) REVERT: C 1733 PHE cc_start: 0.6739 (t80) cc_final: 0.6372 (t80) REVERT: D 43 PHE cc_start: 0.8481 (p90) cc_final: 0.8245 (p90) REVERT: D 66 ILE cc_start: 0.8848 (mt) cc_final: 0.8605 (pt) REVERT: E 245 ILE cc_start: 0.9196 (mt) cc_final: 0.8938 (mm) REVERT: E 306 MET cc_start: 0.6119 (tpt) cc_final: 0.5605 (tpp) REVERT: E 425 GLU cc_start: 0.7431 (mp0) cc_final: 0.7130 (mp0) REVERT: E 454 ASP cc_start: 0.6565 (t0) cc_final: 0.5482 (p0) REVERT: E 480 TRP cc_start: 0.7840 (p90) cc_final: 0.7598 (p90) REVERT: E 515 HIS cc_start: 0.5668 (p-80) cc_final: 0.5465 (p-80) REVERT: E 537 LYS cc_start: 0.4466 (ptmt) cc_final: 0.3932 (ttmt) REVERT: E 572 LYS cc_start: 0.6733 (mptt) cc_final: 0.5921 (mmtp) REVERT: E 648 MET cc_start: 0.3176 (ptt) cc_final: 0.1705 (ttm) REVERT: E 715 LYS cc_start: 0.4262 (pttm) cc_final: 0.3831 (tptm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1090 time to fit residues: 28.8238 Evaluate side-chains 125 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 107 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS B1176 ASN ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1359 GLN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070890 restraints weight = 94245.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.070242 restraints weight = 57466.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070543 restraints weight = 58764.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071066 restraints weight = 39014.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072000 restraints weight = 33139.006| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17290 Z= 0.151 Angle : 0.610 11.312 23453 Z= 0.306 Chirality : 0.043 0.204 2636 Planarity : 0.004 0.050 3032 Dihedral : 5.249 58.286 2476 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.46 (0.18), residues: 2128 helix: 1.24 (0.26), residues: 411 sheet: -0.17 (0.20), residues: 650 loop : -0.98 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1722 TYR 0.018 0.001 TYR D 29 PHE 0.015 0.001 PHE C1733 TRP 0.014 0.001 TRP A 360 HIS 0.009 0.001 HIS B1271 Details of bonding type rmsd covalent geometry : bond 0.00342 (17267) covalent geometry : angle 0.59377 (23401) SS BOND : bond 0.00395 ( 16) SS BOND : angle 1.43540 ( 32) hydrogen bonds : bond 0.03649 ( 588) hydrogen bonds : angle 5.29645 ( 1650) link_NAG-ASN : bond 0.00967 ( 6) link_NAG-ASN : angle 4.70264 ( 18) link_NAG-THR : bond 0.00208 ( 1) link_NAG-THR : angle 1.39642 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8801 (ttm) cc_final: 0.8560 (ttm) REVERT: A 193 MET cc_start: 0.9126 (mpp) cc_final: 0.8506 (mtp) REVERT: A 200 ASP cc_start: 0.7978 (t70) cc_final: 0.7613 (t70) REVERT: A 502 PHE cc_start: 0.8034 (p90) cc_final: 0.7481 (p90) REVERT: B 1015 MET cc_start: 0.8609 (mmp) cc_final: 0.8285 (mmt) REVERT: B 1053 TYR cc_start: 0.7792 (t80) cc_final: 0.7553 (t80) REVERT: B 1054 MET cc_start: 0.8807 (tpt) cc_final: 0.8434 (tpp) REVERT: B 1128 MET cc_start: 0.7633 (ptm) cc_final: 0.7290 (ptt) REVERT: C 1614 MET cc_start: 0.7649 (tpt) cc_final: 0.6466 (ppp) REVERT: C 1733 PHE cc_start: 0.6663 (t80) cc_final: 0.6335 (t80) REVERT: D 43 PHE cc_start: 0.8495 (p90) cc_final: 0.8267 (p90) REVERT: D 66 ILE cc_start: 0.8826 (mt) cc_final: 0.8592 (pt) REVERT: E 245 ILE cc_start: 0.9203 (mt) cc_final: 0.8937 (mm) REVERT: E 306 MET cc_start: 0.6237 (tpt) cc_final: 0.5692 (tpp) REVERT: E 425 GLU cc_start: 0.7482 (mp0) cc_final: 0.7180 (mp0) REVERT: E 454 ASP cc_start: 0.6278 (t0) cc_final: 0.5133 (p0) REVERT: E 480 TRP cc_start: 0.7869 (p90) cc_final: 0.7622 (p90) REVERT: E 537 LYS cc_start: 0.4541 (ptmt) cc_final: 0.4068 (ttmt) REVERT: E 572 LYS cc_start: 0.6687 (mptt) cc_final: 0.5926 (mmtp) REVERT: E 586 MET cc_start: 0.7747 (tmm) cc_final: 0.7443 (tmm) REVERT: E 648 MET cc_start: 0.3137 (ptt) cc_final: 0.1701 (ttm) REVERT: E 715 LYS cc_start: 0.4156 (pttm) cc_final: 0.3709 (tptm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1059 time to fit residues: 26.9837 Evaluate side-chains 128 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 203 optimal weight: 0.0980 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 160 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1700 GLN D 73 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070910 restraints weight = 67407.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068902 restraints weight = 50407.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069749 restraints weight = 40616.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069904 restraints weight = 34899.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070038 restraints weight = 29074.691| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17290 Z= 0.124 Angle : 0.606 10.540 23453 Z= 0.300 Chirality : 0.042 0.209 2636 Planarity : 0.004 0.048 3032 Dihedral : 5.205 57.502 2476 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.41 (0.19), residues: 2128 helix: 1.26 (0.26), residues: 411 sheet: -0.13 (0.21), residues: 650 loop : -0.94 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 355 TYR 0.019 0.001 TYR D 29 PHE 0.015 0.001 PHE B1144 TRP 0.010 0.001 TRP E 699 HIS 0.009 0.001 HIS B1271 Details of bonding type rmsd covalent geometry : bond 0.00281 (17267) covalent geometry : angle 0.59029 (23401) SS BOND : bond 0.00479 ( 16) SS BOND : angle 1.89236 ( 32) hydrogen bonds : bond 0.03404 ( 588) hydrogen bonds : angle 5.20550 ( 1650) link_NAG-ASN : bond 0.00509 ( 6) link_NAG-ASN : angle 4.26920 ( 18) link_NAG-THR : bond 0.00226 ( 1) link_NAG-THR : angle 1.37069 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.9165 (t0) cc_final: 0.8928 (t0) REVERT: A 193 MET cc_start: 0.9091 (mpp) cc_final: 0.8614 (mtp) REVERT: A 200 ASP cc_start: 0.8077 (t70) cc_final: 0.7484 (t70) REVERT: A 502 PHE cc_start: 0.7983 (p90) cc_final: 0.7495 (p90) REVERT: B 1054 MET cc_start: 0.8948 (tpt) cc_final: 0.8508 (tpp) REVERT: B 1128 MET cc_start: 0.7586 (ptm) cc_final: 0.7254 (ptt) REVERT: C 1614 MET cc_start: 0.7793 (tpt) cc_final: 0.6541 (ppp) REVERT: C 1733 PHE cc_start: 0.6752 (t80) cc_final: 0.6373 (t80) REVERT: D 30 MET cc_start: 0.8119 (pmm) cc_final: 0.7914 (pmm) REVERT: D 43 PHE cc_start: 0.8472 (p90) cc_final: 0.8213 (p90) REVERT: D 66 ILE cc_start: 0.8866 (mt) cc_final: 0.8572 (pt) REVERT: E 245 ILE cc_start: 0.9228 (mt) cc_final: 0.8974 (mm) REVERT: E 306 MET cc_start: 0.6262 (tpt) cc_final: 0.5664 (tpp) REVERT: E 425 GLU cc_start: 0.7469 (mp0) cc_final: 0.7149 (mp0) REVERT: E 454 ASP cc_start: 0.6212 (t0) cc_final: 0.4939 (p0) REVERT: E 480 TRP cc_start: 0.7937 (p90) cc_final: 0.7607 (p90) REVERT: E 537 LYS cc_start: 0.4651 (ptmt) cc_final: 0.4085 (ttmt) REVERT: E 572 LYS cc_start: 0.6795 (mptt) cc_final: 0.6039 (mmtp) REVERT: E 715 LYS cc_start: 0.4150 (pttm) cc_final: 0.3700 (tptm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1136 time to fit residues: 28.3891 Evaluate side-chains 124 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 178 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 117 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 97 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS B1359 GLN C1542 GLN D 73 ASN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071251 restraints weight = 66910.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069982 restraints weight = 42085.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070858 restraints weight = 34354.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071105 restraints weight = 27932.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071107 restraints weight = 25416.238| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17290 Z= 0.112 Angle : 0.616 10.399 23453 Z= 0.303 Chirality : 0.043 0.243 2636 Planarity : 0.004 0.052 3032 Dihedral : 5.179 56.872 2476 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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 (0.19), residues: 2128 helix: 1.26 (0.26), residues: 411 sheet: -0.12 (0.20), residues: 658 loop : -0.91 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 355 TYR 0.022 0.001 TYR B1053 PHE 0.023 0.001 PHE E 649 TRP 0.010 0.001 TRP A 360 HIS 0.008 0.001 HIS B1271 Details of bonding type rmsd covalent geometry : bond 0.00253 (17267) covalent geometry : angle 0.60295 (23401) SS BOND : bond 0.00351 ( 16) SS BOND : angle 1.77930 ( 32) hydrogen bonds : bond 0.03378 ( 588) hydrogen bonds : angle 5.12666 ( 1650) link_NAG-ASN : bond 0.00500 ( 6) link_NAG-ASN : angle 4.03459 ( 18) link_NAG-THR : bond 0.00235 ( 1) link_NAG-THR : angle 1.30077 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8414 (tp30) cc_final: 0.8177 (tp30) REVERT: A 180 ASN cc_start: 0.9162 (t0) cc_final: 0.8863 (t0) REVERT: A 193 MET cc_start: 0.9118 (mpp) cc_final: 0.8622 (mtp) REVERT: A 200 ASP cc_start: 0.8018 (t70) cc_final: 0.7724 (t70) REVERT: A 352 MET cc_start: 0.8308 (ppp) cc_final: 0.7946 (ppp) REVERT: A 353 GLU cc_start: 0.8827 (pm20) cc_final: 0.8518 (pm20) REVERT: A 502 PHE cc_start: 0.7919 (p90) cc_final: 0.7459 (p90) REVERT: B 1054 MET cc_start: 0.8987 (tpt) cc_final: 0.8540 (tpp) REVERT: B 1128 MET cc_start: 0.7553 (ptm) cc_final: 0.7230 (ptt) REVERT: B 1166 GLN cc_start: 0.9266 (tp40) cc_final: 0.8943 (mm-40) REVERT: B 1217 LEU cc_start: 0.8876 (mt) cc_final: 0.8596 (pp) REVERT: C 1614 MET cc_start: 0.7793 (tpt) cc_final: 0.6539 (ppp) REVERT: C 1733 PHE cc_start: 0.6712 (t80) cc_final: 0.6341 (t80) REVERT: D 43 PHE cc_start: 0.8495 (p90) cc_final: 0.8219 (p90) REVERT: D 66 ILE cc_start: 0.8842 (mt) cc_final: 0.8562 (pt) REVERT: E 245 ILE cc_start: 0.9245 (mt) cc_final: 0.8990 (mm) REVERT: E 306 MET cc_start: 0.6246 (tpt) cc_final: 0.5639 (tpp) REVERT: E 425 GLU cc_start: 0.7445 (mp0) cc_final: 0.7125 (mp0) REVERT: E 454 ASP cc_start: 0.6259 (t0) cc_final: 0.4941 (p0) REVERT: E 480 TRP cc_start: 0.7937 (p90) cc_final: 0.7572 (p90) REVERT: E 537 LYS cc_start: 0.4527 (ptmt) cc_final: 0.4198 (ttpp) REVERT: E 572 LYS cc_start: 0.6481 (mptt) cc_final: 0.5808 (mmtm) REVERT: E 648 MET cc_start: 0.5043 (ppp) cc_final: 0.3994 (tpp) REVERT: E 715 LYS cc_start: 0.4211 (pttm) cc_final: 0.3719 (tptm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1173 time to fit residues: 31.1034 Evaluate side-chains 131 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 809 HIS C1700 GLN D 73 ASN E 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071687 restraints weight = 76979.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069083 restraints weight = 55864.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069883 restraints weight = 50385.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070008 restraints weight = 41733.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070379 restraints weight = 33513.803| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17290 Z= 0.156 Angle : 0.627 10.310 23453 Z= 0.313 Chirality : 0.043 0.207 2636 Planarity : 0.004 0.050 3032 Dihedral : 5.349 57.682 2476 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 2128 helix: 1.26 (0.26), residues: 407 sheet: -0.14 (0.21), residues: 655 loop : -0.96 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 355 TYR 0.019 0.002 TYR D 29 PHE 0.017 0.002 PHE E 649 TRP 0.011 0.001 TRP E 699 HIS 0.010 0.001 HIS B1271 Details of bonding type rmsd covalent geometry : bond 0.00358 (17267) covalent geometry : angle 0.61481 (23401) SS BOND : bond 0.00356 ( 16) SS BOND : angle 1.70460 ( 32) hydrogen bonds : bond 0.03474 ( 588) hydrogen bonds : angle 5.23073 ( 1650) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 3.91840 ( 18) link_NAG-THR : bond 0.00213 ( 1) link_NAG-THR : angle 1.30484 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.21 seconds wall clock time: 44 minutes 11.85 seconds (2651.85 seconds total)