Starting phenix.real_space_refine on Mon Jan 13 16:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzl_18777/01_2025/8qzl_18777_trim.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.058 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: 6 Type Number sf(0) Gaussians S 132 5.16 5 Cl 2 4.86 5 C 15057 2.51 5 N 3851 2.21 5 O 4322 1.98 5 H 23721 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 1.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 15660 Classifications: {'peptide': 1021} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 973} Chain breaks: 2 Chain: "B" Number of atoms: 15707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 15707 Classifications: {'peptide': 1025} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 977} Chain breaks: 1 Chain: "C" Number of atoms: 15672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 15672 Classifications: {'peptide': 1023} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 975} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'WQW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'WQW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.36, per 1000 atoms: 0.37 Number of scatterers: 47085 At special positions: 0 Unit cell: (115.506, 122.202, 143.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 132 16.00 O 4322 8.00 N 3851 7.00 C 15057 6.00 H 23721 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.23 Conformation dependent library (CDL) restraints added in 2.9 seconds 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 26 sheets defined 59.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.113A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.818A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 118 Proline residue: A 116 - end of helix No H-bonds generated for 'chain 'A' and resid 113 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.639A pdb=" N ILE A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.638A pdb=" N ASN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.603A pdb=" N ALA A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.645A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 386 removed outlier: 4.124A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix removed outlier: 3.738A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.826A pdb=" N ILE A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.675A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.871A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 463 through 496 removed outlier: 3.612A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 536 removed outlier: 4.592A pdb=" N ASN A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 582 through 598 removed outlier: 3.608A pdb=" N THR A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 642 through 654 removed outlier: 3.533A pdb=" N TYR A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.549A pdb=" N GLN A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 741 through 751 Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 835 through 849 removed outlier: 3.691A pdb=" N ALA A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 868 Processing helix chain 'A' and resid 870 through 892 removed outlier: 4.430A pdb=" N ALA A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 875 " --> pdb=" O GLN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 902 removed outlier: 4.133A pdb=" N SER A 899 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 900 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 919 removed outlier: 4.011A pdb=" N GLY A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 954 removed outlier: 3.795A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 986 removed outlier: 5.065A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Proline residue: A 973 - end of helix Processing helix chain 'A' and resid 986 through 991 Processing helix chain 'A' and resid 995 through 1015 removed outlier: 3.843A pdb=" N GLY A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1032 Proline residue: A1022 - end of helix removed outlier: 3.864A pdb=" N ARG A1029 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.582A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.568A pdb=" N VAL B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.555A pdb=" N ILE B 166 " --> pdb=" O MET B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.647A pdb=" N ASN B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.804A pdb=" N ALA B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 4.143A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.567A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix removed outlier: 3.617A pdb=" N PHE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.508A pdb=" N PHE B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 423 removed outlier: 4.470A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.546A pdb=" N THR B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 488 removed outlier: 3.629A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.776A pdb=" N TRP B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.823A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 557 " --> pdb=" O TRP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 601 removed outlier: 3.632A pdb=" N TYR B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 638 through 641 removed outlier: 3.946A pdb=" N ASN B 641 " --> pdb=" O GLY B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 706 removed outlier: 3.676A pdb=" N ALA B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 741 through 753 removed outlier: 3.968A pdb=" N THR B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 779 removed outlier: 3.986A pdb=" N ARG B 779 " --> pdb=" O ALA B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 781 through 787 removed outlier: 3.546A pdb=" N GLY B 786 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 803 No H-bonds generated for 'chain 'B' and resid 800 through 803' Processing helix chain 'B' and resid 835 through 848 removed outlier: 3.616A pdb=" N GLU B 844 " --> pdb=" O MET B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 869 removed outlier: 3.843A pdb=" N LEU B 867 " --> pdb=" O TYR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 892 removed outlier: 4.500A pdb=" N ALA B 874 " --> pdb=" O ASN B 870 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 876 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 902 removed outlier: 3.977A pdb=" N VAL B 900 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 919 removed outlier: 4.006A pdb=" N GLY B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 911 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 955 removed outlier: 3.564A pdb=" N LEU B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 970 Processing helix chain 'B' and resid 971 through 985 Processing helix chain 'B' and resid 986 through 991 Processing helix chain 'B' and resid 995 through 1032 removed outlier: 3.796A pdb=" N GLN B 999 " --> pdb=" O GLY B 995 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B1012 " --> pdb=" O GLY B1008 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B1019 " --> pdb=" O ILE B1015 " (cutoff:3.500A) Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.032A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.562A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 removed outlier: 3.845A pdb=" N THR C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.523A pdb=" N VAL C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.705A pdb=" N GLN C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.545A pdb=" N VAL C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.588A pdb=" N PHE C 246 " --> pdb=" O ASN C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.561A pdb=" N THR C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 329 through 360 removed outlier: 4.000A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 4.305A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 Processing helix chain 'C' and resid 391 through 403 removed outlier: 4.419A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 422 removed outlier: 4.324A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.874A pdb=" N ARG C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 454 through 458 removed outlier: 3.542A pdb=" N PHE C 458 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.877A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 removed outlier: 3.875A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 536 removed outlier: 3.684A pdb=" N TRP C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 529 " --> pdb=" O HIS C 525 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 532 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.624A pdb=" N VAL C 542 " --> pdb=" O GLY C 538 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR C 544 " --> pdb=" O TYR C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 594 removed outlier: 3.509A pdb=" N THR C 586 " --> pdb=" O THR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 642 through 655 removed outlier: 3.544A pdb=" N TYR C 653 " --> pdb=" O ARG C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 706 Processing helix chain 'C' and resid 731 through 738 Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 775 through 779 removed outlier: 3.584A pdb=" N TYR C 778 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG C 779 " --> pdb=" O ALA C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 779' Processing helix chain 'C' and resid 781 through 787 removed outlier: 3.501A pdb=" N GLY C 786 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 849 removed outlier: 3.562A pdb=" N GLU C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 849 " --> pdb=" O GLU C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 871 removed outlier: 3.606A pdb=" N TYR C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 892 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 903 through 918 removed outlier: 4.260A pdb=" N GLY C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 954 removed outlier: 3.634A pdb=" N ILE C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 979 removed outlier: 3.605A pdb=" N VAL C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 995 through 1016 removed outlier: 4.263A pdb=" N GLN C 999 " --> pdb=" O GLY C 995 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C1001 " --> pdb=" O GLY C 997 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C1009 " --> pdb=" O GLY C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1031 Proline residue: C1022 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.646A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 80 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 823 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.080A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 327 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY A 141 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYR A 325 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 143 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE A 323 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.317A pdb=" N TYR A 182 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 769 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 759 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 772 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR A 757 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.867A pdb=" N ALA A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER A 233 " --> pdb=" O PHE B 726 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 728 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 235 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 730 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.193A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.537A pdb=" N SER A 607 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 572 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 825 through 828 removed outlier: 4.482A pdb=" N ASP A 680 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 811 removed outlier: 4.461A pdb=" N SER C 233 " --> pdb=" O PRO A 724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 791 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.786A pdb=" N THR B 87 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 89 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER B 80 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N MET B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B 93 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 80 " --> pdb=" O ARG B 817 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 177 removed outlier: 7.331A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 272 removed outlier: 3.639A pdb=" N GLY B 271 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR B 182 " --> pdb=" O VAL B 767 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B 769 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN B 759 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 772 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR B 757 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.686A pdb=" N SER B 233 " --> pdb=" O PHE C 726 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE C 728 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 235 " --> pdb=" O ILE C 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 Processing sheet with id=AB7, first strand: chain 'B' and resid 605 through 609 removed outlier: 6.697A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR B 623 " --> pdb=" O GLY B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 605 through 609 removed outlier: 6.697A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 663 " --> pdb=" O MET B 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 712 through 717 removed outlier: 5.199A pdb=" N GLY B 714 " --> pdb=" O GLN B 829 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B 829 " --> pdb=" O GLY B 714 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 789 through 791 Processing sheet with id=AC2, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.965A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 80 " --> pdb=" O ARG C 817 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.281A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 143 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.281A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 286 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 610 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER C 629 " --> pdb=" O GLU C 606 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA C 610 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN C 612 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR C 623 " --> pdb=" O ASN C 612 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 575 " --> pdb=" O GLY C 624 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 576 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.215A pdb=" N TYR C 182 " --> pdb=" O VAL C 767 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS C 769 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG C 766 " --> pdb=" O ILE C 762 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE C 762 " --> pdb=" O ARG C 766 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS C 768 " --> pdb=" O ASP C 760 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP C 760 " --> pdb=" O LYS C 768 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 770 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.692A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 712 through 717 removed outlier: 4.444A pdb=" N VAL C 715 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 827 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU C 825 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 828 " --> pdb=" O PHE C 679 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 679 " --> pdb=" O GLY C 828 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 791 1371 hydrogen bonds defined for protein. 3942 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: 16.66 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23715 1.03 - 1.23: 6 1.23 - 1.42: 9639 1.42 - 1.61: 13928 1.61 - 1.81: 260 Bond restraints: 47548 Sorted by residual: bond pdb=" N GLU C 423 " pdb=" H GLU C 423 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" N LYS A 954 " pdb=" H LYS A 954 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" N GLU A 955 " pdb=" CA GLU A 955 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.03e+00 bond pdb=" N GLU C 423 " pdb=" CA GLU C 423 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.25e-02 6.40e+03 5.92e+00 bond pdb=" N GLU A 955 " pdb=" H GLU A 955 " ideal model delta sigma weight residual 0.860 0.908 -0.048 2.00e-02 2.50e+03 5.82e+00 ... (remaining 47543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 85798 1.93 - 3.85: 345 3.85 - 5.78: 45 5.78 - 7.71: 4 7.71 - 9.64: 2 Bond angle restraints: 86194 Sorted by residual: angle pdb=" N VAL B 345 " pdb=" CA VAL B 345 " pdb=" C VAL B 345 " ideal model delta sigma weight residual 112.96 108.62 4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" CA GLU A 955 " pdb=" C GLU A 955 " pdb=" O GLU A 955 " ideal model delta sigma weight residual 120.55 116.84 3.71 1.06e+00 8.90e-01 1.22e+01 angle pdb=" N VAL A 715 " pdb=" CA VAL A 715 " pdb=" C VAL A 715 " ideal model delta sigma weight residual 109.34 102.41 6.93 2.08e+00 2.31e-01 1.11e+01 angle pdb=" C3 WQW A1101 " pdb=" N2 WQW A1101 " pdb=" C5 WQW A1101 " ideal model delta sigma weight residual 115.80 125.44 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N VAL B 265 " pdb=" CA VAL B 265 " pdb=" C VAL B 265 " ideal model delta sigma weight residual 113.20 110.18 3.02 9.60e-01 1.09e+00 9.91e+00 ... (remaining 86189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 21074 26.19 - 52.38: 1105 52.38 - 78.57: 180 78.57 - 104.76: 15 104.76 - 130.95: 5 Dihedral angle restraints: 22379 sinusoidal: 12270 harmonic: 10109 Sorted by residual: dihedral pdb=" N4 WQW C1101 " pdb=" C16 WQW C1101 " pdb=" C17 WQW C1101 " pdb=" N5 WQW C1101 " ideal model delta sinusoidal sigma weight residual -65.20 65.75 -130.95 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" N1 WQW C1101 " pdb=" C1 WQW C1101 " pdb=" C2 WQW C1101 " pdb=" N2 WQW C1101 " ideal model delta sinusoidal sigma weight residual -56.58 61.81 -118.39 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" N4 WQW C1101 " pdb=" C14 WQW C1101 " pdb=" C15 WQW C1101 " pdb=" N5 WQW C1101 " ideal model delta sinusoidal sigma weight residual 61.39 -56.61 118.00 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 22376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3361 0.063 - 0.126: 415 0.126 - 0.188: 7 0.188 - 0.251: 0 0.251 - 0.314: 1 Chirality restraints: 3784 Sorted by residual: chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU C 423 " pdb=" N GLU C 423 " pdb=" C GLU C 423 " pdb=" CB GLU C 423 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 3781 not shown) Planarity restraints: 7059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 958 " -0.025 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" N LEU A 959 " 0.082 2.00e-02 2.50e+03 pdb=" CA LEU A 959 " -0.021 2.00e-02 2.50e+03 pdb=" H LEU A 959 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 986 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO B 987 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 955 " -0.018 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" N GLY A 956 " 0.059 2.00e-02 2.50e+03 pdb=" CA GLY A 956 " -0.015 2.00e-02 2.50e+03 pdb=" H GLY A 956 " -0.026 2.00e-02 2.50e+03 ... (remaining 7056 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2111 2.19 - 2.79: 95949 2.79 - 3.39: 131215 3.39 - 4.00: 169336 4.00 - 4.60: 265143 Nonbonded interactions: 663754 Sorted by model distance: nonbonded pdb=" OD1 ASP A 153 " pdb=" HH TYR A 182 " model vdw 1.583 2.450 nonbonded pdb=" HH TYR C 757 " pdb=" OD1 ASP C 760 " model vdw 1.595 2.450 nonbonded pdb=" O GLN A 360 " pdb="HD21 ASN A 361 " model vdw 1.603 2.450 nonbonded pdb=" O GLY A 569 " pdb=" H LEU A 630 " model vdw 1.607 2.450 nonbonded pdb=" OD2 ASP A 729 " pdb="HH12 ARG A 807 " model vdw 1.624 2.450 ... (remaining 663749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 499 or resid 509 through 1031)) selection = (chain 'B' and (resid 1 through 499 or resid 509 through 672 or resid 678 throug \ h 1031)) selection = (chain 'C' and (resid 1 through 499 or (resid 509 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG \ 1 or name HG21 or name HG22 or name HG23)) or resid 510 through 672 or resid 678 \ through 1031)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.600 Extract box with map and model: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 75.590 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.002 0.041 23827 Z= 0.143 Angle : 0.461 9.637 32365 Z= 0.238 Chirality : 0.038 0.314 3784 Planarity : 0.003 0.098 4138 Dihedral : 14.788 130.953 8625 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 3055 helix: 0.60 (0.14), residues: 1583 sheet: -1.85 (0.27), residues: 359 loop : -0.41 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 788 HIS 0.012 0.001 HIS A 708 PHE 0.012 0.001 PHE B 761 TYR 0.009 0.001 TYR A 49 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 THR cc_start: 0.8912 (m) cc_final: 0.8536 (p) REVERT: C 365 THR cc_start: 0.8583 (m) cc_final: 0.8307 (m) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.5791 time to fit residues: 307.2870 Evaluate side-chains 275 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN C 125 GLN C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124916 restraints weight = 90457.650| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.88 r_work: 0.3475 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23827 Z= 0.249 Angle : 0.556 6.302 32365 Z= 0.303 Chirality : 0.041 0.153 3784 Planarity : 0.005 0.095 4138 Dihedral : 5.891 105.164 3299 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.48 % Allowed : 5.61 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3055 helix: 0.85 (0.13), residues: 1645 sheet: -1.81 (0.26), residues: 362 loop : -0.60 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 894 HIS 0.006 0.001 HIS A 525 PHE 0.018 0.001 PHE C 362 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 THR cc_start: 0.9025 (m) cc_final: 0.8620 (p) REVERT: B 487 ILE cc_start: 0.9056 (tt) cc_final: 0.8843 (pt) REVERT: B 891 TYR cc_start: 0.8185 (m-10) cc_final: 0.7780 (m-10) REVERT: C 365 THR cc_start: 0.8815 (m) cc_final: 0.8479 (m) outliers start: 12 outliers final: 7 residues processed: 301 average time/residue: 0.5979 time to fit residues: 294.5934 Evaluate side-chains 285 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 278 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 369 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 181 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126282 restraints weight = 91109.950| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.86 r_work: 0.3447 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23827 Z= 0.208 Angle : 0.503 9.027 32365 Z= 0.264 Chirality : 0.040 0.150 3784 Planarity : 0.004 0.060 4138 Dihedral : 4.960 88.139 3299 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.52 % Allowed : 7.45 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 3055 helix: 1.08 (0.13), residues: 1649 sheet: -1.83 (0.26), residues: 379 loop : -0.62 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 753 HIS 0.004 0.001 HIS C 525 PHE 0.021 0.001 PHE A 947 TYR 0.014 0.001 TYR A 157 ARG 0.006 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 THR cc_start: 0.9041 (m) cc_final: 0.8628 (p) REVERT: B 891 TYR cc_start: 0.8078 (m-10) cc_final: 0.7853 (m-10) REVERT: C 309 GLU cc_start: 0.8738 (tp30) cc_final: 0.8282 (tp30) REVERT: C 365 THR cc_start: 0.8758 (m) cc_final: 0.8423 (m) outliers start: 13 outliers final: 11 residues processed: 298 average time/residue: 0.5964 time to fit residues: 290.7512 Evaluate side-chains 280 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 816 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.144067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123389 restraints weight = 91302.510| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.87 r_work: 0.3391 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23827 Z= 0.331 Angle : 0.533 6.054 32365 Z= 0.284 Chirality : 0.041 0.143 3784 Planarity : 0.004 0.057 4138 Dihedral : 4.649 74.140 3299 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.84 % Allowed : 9.26 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3055 helix: 1.05 (0.13), residues: 1653 sheet: -1.98 (0.25), residues: 379 loop : -0.79 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 894 HIS 0.004 0.001 HIS B 338 PHE 0.016 0.001 PHE C 681 TYR 0.019 0.001 TYR A 157 ARG 0.007 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 891 TYR cc_start: 0.8131 (m-10) cc_final: 0.7861 (m-10) REVERT: C 309 GLU cc_start: 0.8723 (tp30) cc_final: 0.8259 (tp30) REVERT: C 365 THR cc_start: 0.8839 (m) cc_final: 0.8508 (m) REVERT: C 696 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7652 (mp10) outliers start: 21 outliers final: 18 residues processed: 287 average time/residue: 0.6013 time to fit residues: 280.0652 Evaluate side-chains 285 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 69 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 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 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125354 restraints weight = 90455.554| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.81 r_work: 0.3440 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23827 Z= 0.219 Angle : 0.489 5.968 32365 Z= 0.256 Chirality : 0.040 0.143 3784 Planarity : 0.004 0.052 4138 Dihedral : 4.582 79.666 3299 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.84 % Allowed : 9.94 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3055 helix: 1.19 (0.13), residues: 1659 sheet: -1.93 (0.25), residues: 382 loop : -0.70 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 753 HIS 0.004 0.001 HIS C 524 PHE 0.014 0.001 PHE A 681 TYR 0.015 0.001 TYR A 157 ARG 0.004 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: A 838 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: B 37 THR cc_start: 0.9048 (m) cc_final: 0.8647 (p) REVERT: B 891 TYR cc_start: 0.8067 (m-10) cc_final: 0.7855 (m-10) REVERT: C 309 GLU cc_start: 0.8652 (tp30) cc_final: 0.8196 (tp30) REVERT: C 365 THR cc_start: 0.8814 (m) cc_final: 0.8484 (m) REVERT: C 696 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7650 (mp10) outliers start: 21 outliers final: 15 residues processed: 288 average time/residue: 0.5863 time to fit residues: 276.4561 Evaluate side-chains 288 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 215 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125715 restraints weight = 90240.446| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.86 r_work: 0.3421 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23827 Z= 0.201 Angle : 0.479 5.923 32365 Z= 0.250 Chirality : 0.039 0.147 3784 Planarity : 0.003 0.051 4138 Dihedral : 4.510 80.047 3299 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.84 % Allowed : 10.50 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 3055 helix: 1.30 (0.13), residues: 1659 sheet: -1.83 (0.25), residues: 384 loop : -0.68 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 753 HIS 0.003 0.001 HIS C 524 PHE 0.013 0.001 PHE A 681 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: A 838 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: B 37 THR cc_start: 0.9053 (m) cc_final: 0.8650 (p) REVERT: B 891 TYR cc_start: 0.8054 (m-10) cc_final: 0.7826 (m-10) REVERT: C 309 GLU cc_start: 0.8652 (tp30) cc_final: 0.8181 (tp30) REVERT: C 365 THR cc_start: 0.8812 (m) cc_final: 0.8485 (m) REVERT: C 696 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: C 865 GLU cc_start: 0.8091 (tt0) cc_final: 0.7785 (tt0) outliers start: 21 outliers final: 17 residues processed: 291 average time/residue: 0.6018 time to fit residues: 289.5296 Evaluate side-chains 289 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 266 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119828 restraints weight = 89634.142| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.78 r_work: 0.3261 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23827 Z= 0.239 Angle : 0.491 5.914 32365 Z= 0.256 Chirality : 0.040 0.156 3784 Planarity : 0.004 0.049 4138 Dihedral : 4.523 81.523 3299 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.96 % Allowed : 11.02 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 3055 helix: 1.32 (0.13), residues: 1660 sheet: -1.83 (0.25), residues: 384 loop : -0.70 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 753 HIS 0.003 0.001 HIS B 338 PHE 0.013 0.001 PHE A 681 TYR 0.016 0.001 TYR A 157 ARG 0.002 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: A 838 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: B 37 THR cc_start: 0.9059 (m) cc_final: 0.8666 (p) REVERT: B 696 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: B 891 TYR cc_start: 0.8047 (m-10) cc_final: 0.7845 (m-10) REVERT: C 309 GLU cc_start: 0.8687 (tp30) cc_final: 0.8172 (tp30) REVERT: C 365 THR cc_start: 0.8842 (m) cc_final: 0.8501 (m) REVERT: C 696 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7760 (mp10) outliers start: 24 outliers final: 20 residues processed: 288 average time/residue: 0.5934 time to fit residues: 278.3294 Evaluate side-chains 292 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 269 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121415 restraints weight = 89022.747| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.76 r_work: 0.2958 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23827 Z= 0.186 Angle : 0.471 5.869 32365 Z= 0.244 Chirality : 0.039 0.155 3784 Planarity : 0.003 0.049 4138 Dihedral : 4.450 82.319 3299 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.88 % Allowed : 11.14 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3055 helix: 1.45 (0.13), residues: 1660 sheet: -1.79 (0.25), residues: 390 loop : -0.62 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 753 HIS 0.004 0.001 HIS C 524 PHE 0.013 0.001 PHE A 681 TYR 0.018 0.001 TYR A 157 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: A 838 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7035 (pm20) REVERT: B 37 THR cc_start: 0.9166 (m) cc_final: 0.8741 (p) REVERT: B 696 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: B 891 TYR cc_start: 0.8002 (m-10) cc_final: 0.7780 (m-10) REVERT: C 309 GLU cc_start: 0.8632 (tp30) cc_final: 0.8027 (tp30) REVERT: C 365 THR cc_start: 0.8760 (m) cc_final: 0.8398 (m) REVERT: C 429 GLU cc_start: 0.8477 (tt0) cc_final: 0.8262 (tt0) REVERT: C 593 MET cc_start: 0.8352 (ttm) cc_final: 0.7952 (ttm) REVERT: C 696 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: C 865 GLU cc_start: 0.7961 (tt0) cc_final: 0.7591 (tt0) outliers start: 22 outliers final: 15 residues processed: 293 average time/residue: 0.6096 time to fit residues: 292.6275 Evaluate side-chains 294 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 227 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121860 restraints weight = 89128.744| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.77 r_work: 0.2963 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23827 Z= 0.172 Angle : 0.468 5.934 32365 Z= 0.242 Chirality : 0.039 0.165 3784 Planarity : 0.003 0.048 4138 Dihedral : 4.428 84.093 3299 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.92 % Allowed : 11.22 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 3055 helix: 1.55 (0.13), residues: 1659 sheet: -1.74 (0.25), residues: 388 loop : -0.60 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 753 HIS 0.004 0.001 HIS C 524 PHE 0.011 0.001 PHE A 681 TYR 0.017 0.001 TYR A 157 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8140 (m-10) REVERT: A 838 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: B 37 THR cc_start: 0.9162 (m) cc_final: 0.8743 (p) REVERT: B 696 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: B 891 TYR cc_start: 0.7995 (m-10) cc_final: 0.7766 (m-10) REVERT: C 124 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 309 GLU cc_start: 0.8613 (tp30) cc_final: 0.8027 (tp30) REVERT: C 365 THR cc_start: 0.8791 (m) cc_final: 0.8440 (m) REVERT: C 429 GLU cc_start: 0.8422 (tt0) cc_final: 0.8202 (tt0) REVERT: C 593 MET cc_start: 0.8364 (ttm) cc_final: 0.7955 (ttm) REVERT: C 865 GLU cc_start: 0.7964 (tt0) cc_final: 0.7575 (tt0) outliers start: 23 outliers final: 16 residues processed: 300 average time/residue: 0.5931 time to fit residues: 289.3350 Evaluate side-chains 294 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 217 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 268 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117970 restraints weight = 89744.948| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.80 r_work: 0.3332 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23827 Z= 0.164 Angle : 0.466 6.186 32365 Z= 0.240 Chirality : 0.039 0.168 3784 Planarity : 0.003 0.048 4138 Dihedral : 4.411 85.695 3299 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.68 % Allowed : 11.54 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 3055 helix: 1.63 (0.13), residues: 1659 sheet: -1.68 (0.25), residues: 388 loop : -0.56 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 753 HIS 0.004 0.001 HIS C 524 PHE 0.013 0.001 PHE A 947 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG C 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: A 838 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: B 37 THR cc_start: 0.9028 (m) cc_final: 0.8620 (p) REVERT: B 696 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: C 124 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8109 (tm-30) REVERT: C 309 GLU cc_start: 0.8636 (tp30) cc_final: 0.8156 (tp30) REVERT: C 365 THR cc_start: 0.8940 (m) cc_final: 0.8620 (m) REVERT: C 593 MET cc_start: 0.8427 (ttm) cc_final: 0.8036 (ttm) REVERT: C 865 GLU cc_start: 0.7943 (tt0) cc_final: 0.7591 (tt0) outliers start: 17 outliers final: 14 residues processed: 292 average time/residue: 0.6010 time to fit residues: 286.8007 Evaluate side-chains 296 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 279 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 974 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 220 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 286 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120404 restraints weight = 89337.120| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.75 r_work: 0.3305 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23827 Z= 0.269 Angle : 0.499 6.060 32365 Z= 0.260 Chirality : 0.040 0.183 3784 Planarity : 0.004 0.050 4138 Dihedral : 4.491 86.448 3299 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.76 % Allowed : 11.62 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 3055 helix: 1.54 (0.13), residues: 1659 sheet: -1.78 (0.25), residues: 390 loop : -0.65 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 894 HIS 0.003 0.001 HIS B 338 PHE 0.014 0.001 PHE C 681 TYR 0.018 0.001 TYR A 157 ARG 0.003 0.000 ARG C 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15165.19 seconds wall clock time: 259 minutes 15.07 seconds (15555.07 seconds total)