Starting phenix.real_space_refine on Sat Jul 4 23:14:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr6_24653/07_2026/7rr6_24653.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 132 5.16 5 C 15413 2.51 5 N 3824 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7756 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7752 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7658 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 7, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 197 Unusual residues: {'D12': 4, 'PTY': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Unusual residues: {'D12': 4, 'PTY': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 3, 'PTY:plan-1': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 5.76, per 1000 atoms: 0.24 Number of scatterers: 23821 At special positions: 0 Unit cell: (121.049, 115.124, 145.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 15 15.00 O 4437 8.00 N 3824 7.00 C 15413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 57.3% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.702A pdb=" N PHE B 5 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.526A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) 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 161 removed outlier: 3.508A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.698A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 298 through 313 Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.685A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 386 Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.336A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 435 Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 487 removed outlier: 3.610A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.808A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 535 Processing helix chain 'B' and resid 538 through 557 removed outlier: 3.797A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 Processing helix chain 'B' and resid 643 through 656 Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 836 through 848 Processing helix chain 'B' and resid 861 through 870 Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.047A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 920 removed outlier: 4.182A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 956 Processing helix chain 'B' and resid 959 through 991 removed outlier: 3.634A pdb=" N ALA B 963 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix removed outlier: 4.254A pdb=" N LEU B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1014 removed outlier: 4.257A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1033 Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 8 through 30 removed outlier: 4.682A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.616A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.791A pdb=" N GLN C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.531A pdb=" N ILE C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.637A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 3.714A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.978A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 401 through 423 removed outlier: 4.260A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 453 through 458 removed outlier: 4.111A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.772A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.947A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 535 removed outlier: 3.616A pdb=" N LEU C 535 " --> pdb=" O VAL C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 708 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.582A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.829A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 893 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 896 through 902 Processing helix chain 'C' and resid 904 through 920 removed outlier: 4.040A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 3.568A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 972 through 991 removed outlier: 3.873A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 999 through 1014 removed outlier: 4.056A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 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 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.809A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.762A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.919A pdb=" N VAL A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 402 through 424 removed outlier: 4.671A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 450 removed outlier: 3.702A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.570A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 463 through 496 removed outlier: 4.688A 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 516 through 535 removed outlier: 3.823A pdb=" N LEU A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 4.322A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.500A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 655 Processing helix chain 'A' and resid 691 through 708 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 842 through 848 removed outlier: 4.075A pdb=" N ALA A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 869 removed outlier: 3.656A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 893 Processing helix chain 'A' and resid 896 through 903 removed outlier: 3.891A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 919 removed outlier: 3.778A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 954 removed outlier: 3.515A pdb=" N THR A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 removed outlier: 3.587A pdb=" N LEU A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 971 Processing helix chain 'A' and resid 972 through 986 removed outlier: 3.565A pdb=" N VAL A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 992 Processing helix chain 'A' and resid 996 through 1017 removed outlier: 3.567A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1027 Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.556A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 81 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.206A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 140 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR B 327 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 141 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR B 325 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE B 143 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 323 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 268 removed outlier: 3.727A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.818A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 731 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.734A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 713 through 718 removed outlier: 5.387A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 805 through 812 removed outlier: 4.650A pdb=" N SER A 233 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.620A pdb=" N SER C 46 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.753A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.927A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 574 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.472A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG C 767 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 763 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS C 769 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP C 761 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 771 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 215 through 219 removed outlier: 4.160A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.533A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 713 through 714 Processing sheet with id=AB7, first strand: chain 'C' and resid 790 through 792 Processing sheet with id=AB8, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.545A pdb=" N ALA A 47 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.364A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.545A pdb=" N ALA A 47 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.364A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 714 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.133A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 327 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 141 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR A 325 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 143 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE A 323 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.133A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 627 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.471A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 763 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS A 769 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP A 761 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 771 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AC5, first strand: chain 'A' and resid 790 through 792 1434 hydrogen bonds defined for protein. 4134 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: 6.19 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3888 1.30 - 1.44: 5859 1.44 - 1.57: 14181 1.57 - 1.70: 30 1.70 - 1.83: 258 Bond restraints: 24216 Sorted by residual: bond pdb=" C ARG B 973 " pdb=" O ARG B 973 " ideal model delta sigma weight residual 1.244 1.185 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" N PRO B 318 " pdb=" CD PRO B 318 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.31e+01 bond pdb=" C GLU C 130 " pdb=" N LYS C 131 " ideal model delta sigma weight residual 1.330 1.393 -0.063 1.32e-02 5.74e+03 2.30e+01 bond pdb=" C GLY C 998 " pdb=" O GLY C 998 " ideal model delta sigma weight residual 1.233 1.286 -0.053 1.13e-02 7.83e+03 2.21e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.237 1.176 0.062 1.32e-02 5.74e+03 2.19e+01 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 29685 2.08 - 4.16: 2588 4.16 - 6.24: 391 6.24 - 8.32: 50 8.32 - 10.40: 25 Bond angle restraints: 32739 Sorted by residual: angle pdb=" N GLN B 255 " pdb=" CA GLN B 255 " pdb=" C GLN B 255 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.17e+00 7.31e-01 6.14e+01 angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 111.62 105.50 6.12 7.90e-01 1.60e+00 5.99e+01 angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 111.90 105.67 6.23 8.10e-01 1.52e+00 5.91e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 113.41 104.19 9.22 1.22e+00 6.72e-01 5.71e+01 angle pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 120.83 125.26 -4.43 5.90e-01 2.87e+00 5.64e+01 ... (remaining 32734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 14120 35.13 - 70.27: 352 70.27 - 105.40: 22 105.40 - 140.54: 6 140.54 - 175.67: 7 Dihedral angle restraints: 14507 sinusoidal: 5749 harmonic: 8758 Sorted by residual: dihedral pdb=" C ASP B 153 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " ideal model delta harmonic sigma weight residual -122.60 -135.50 12.90 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" C GLU B 414 " pdb=" N GLU B 414 " pdb=" CA GLU B 414 " pdb=" CB GLU B 414 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C THR B 489 " pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual -122.00 -133.90 11.90 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 14504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3333 0.114 - 0.228: 419 0.228 - 0.342: 60 0.342 - 0.456: 10 0.456 - 0.571: 2 Chirality restraints: 3824 Sorted by residual: chirality pdb=" CB VAL A 905 " pdb=" CA VAL A 905 " pdb=" CG1 VAL A 905 " pdb=" CG2 VAL A 905 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" C6 PTY A1103 " pdb=" C1 PTY A1103 " pdb=" C5 PTY A1103 " pdb=" O7 PTY A1103 " both_signs ideal model delta sigma weight residual False 2.49 2.01 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" C6 PTY A1109 " pdb=" C1 PTY A1109 " pdb=" C5 PTY A1109 " pdb=" O7 PTY A1109 " both_signs ideal model delta sigma weight residual False 2.49 2.05 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 3821 not shown) Planarity restraints: 4127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 412 " -0.028 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C VAL C 412 " 0.097 2.00e-02 2.50e+03 pdb=" O VAL C 412 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL C 413 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 443 " 0.025 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C VAL A 443 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A 443 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY A 444 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 403 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C GLY A 403 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY A 403 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU A 404 " 0.027 2.00e-02 2.50e+03 ... (remaining 4124 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 410 2.66 - 3.22: 23177 3.22 - 3.78: 37151 3.78 - 4.34: 53345 4.34 - 4.90: 87531 Nonbonded interactions: 201614 Sorted by model distance: nonbonded pdb=" O ASN C 81 " pdb=" OD1 ASN C 81 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 345 " pdb=" CG2 ILE A 348 " model vdw 2.205 3.460 nonbonded pdb=" OG SER A 836 " pdb=" OE2 GLU A 839 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP A 858 " pdb=" N TRP A 859 " model vdw 2.218 3.120 nonbonded pdb=" OD1 ASN A 415 " pdb=" OG SER A 434 " model vdw 2.242 3.040 ... (remaining 201609 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 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 478 or (resid 479 and (n \ ame N or name CA or name C or name CB )) or resid 480 through 500 or resid 516 t \ hrough 1033 or (resid 1102 and (name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37)) or (resid 1103 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18)) or (resid 1104 and (na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 \ or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or (resid 1105 and (name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)))) selection = (chain 'B' and (resid 1 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 449 or (resid 450 and (name N or \ name CA or name C or name CB or name OG )) or resid 451 through 500 or resid 51 \ 6 through 517 or (resid 518 and (name N or name CA or name C or name O or name C \ B )) or resid 519 through 524 or (resid 525 and (name N or name CA or name C or \ name O or name CB )) or resid 526 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 or (resid 531 and (name N or n \ ame CA or name C or name O or name CB )) or resid 532 through 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 535 or (resid \ 536 and (name N or name CA or name C or name O or name CB )) or resid 537 or (re \ sid 538 and (name N or name CA or name C or name O or name CB )) or resid 539 or \ (resid 540 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 1 through 619 or (resid 620 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ )) or resid 621 through 846 or (re \ sid 847 through 848 and (name N or name CA or name C or name O or name CB )) or \ resid 849 through 954 or (resid 955 through 956 and (name N or name CA or name C \ or name O or name CB )) or resid 957 through 964 or (resid 965 and (name N or n \ ame CA or name C or name O or name CB )) or resid 966 through 968 or (resid 969 \ and (name N or name CA or name C or name O or name CB )) or resid 970 through 10 \ 25 or (resid 1026 through 1027 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1028 through 1030 or (resid 1031 through 1033 and (name N or na \ me CA or name C or name O or name CB )) or resid 1105 or (resid 1106 and (name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) or \ resid 1107 through 1108)) selection = (chain 'C' and (resid 1 through 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 449 or ( \ resid 450 and (name N or name CA or name C or name CB or name OG )) or resid 451 \ through 478 or (resid 479 and (name N or name CA or name C or name CB )) or res \ id 480 through 500 or resid 516 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 524 or (resid 525 and (n \ ame N or name CA or name C or name O or name CB )) or resid 526 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ or (resid 531 and (name N or name CA or name C or name O or name CB )) or resid \ 532 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 or (resid 538 and (name N or name CA or name C or name O \ or name CB )) or resid 539 or (resid 540 and (name N or name CA or name C or na \ me O or name CB )) or resid 541 through 619 or (resid 620 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 621 through 846 or (resid 847 through 848 and (name N or name CA or name \ C or name O or name CB )) or resid 849 through 954 or (resid 955 through 956 an \ d (name N or name CA or name C or name O or name CB )) or resid 957 through 964 \ or (resid 965 and (name N or name CA or name C or name O or name CB )) or resid \ 966 through 968 or (resid 969 and (name N or name CA or name C or name O or name \ CB )) or resid 970 through 1025 or (resid 1026 through 1027 and (name N or name \ CA or name C or name O or name CB )) or resid 1028 through 1030 or (resid 1031 \ through 1033 and (name N or name CA or name C or name O or name CB )) or (resid \ 1104 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37)) or (resid 1105 and (name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18)) or (resid 1106 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O1 \ 3 or name O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and \ (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name N \ 1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.200 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.008 0.069 24216 Z= 0.581 Angle : 1.211 10.402 32739 Z= 0.858 Chirality : 0.078 0.571 3824 Planarity : 0.006 0.056 4127 Dihedral : 15.643 175.670 8887 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 2.99 % Favored : 96.56 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 3051 helix: -0.05 (0.13), residues: 1597 sheet: -1.68 (0.25), residues: 408 loop : -1.36 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 818 TYR 0.058 0.002 TYR A 49 PHE 0.031 0.002 PHE A 358 TRP 0.028 0.002 TRP B 809 HIS 0.012 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.58 (24216) covalent geometry : angle 1.21111 / 0.86 (32739) hydrogen bonds : bond 0.17590 / 11.75 ( 1406) hydrogen bonds : angle 7.73097 / 5.62 ( 4134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 427 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 HIS cc_start: 0.8041 (t70) cc_final: 0.7840 (t-90) REVERT: B 407 ASP cc_start: 0.8236 (t70) cc_final: 0.7970 (t0) REVERT: B 573 MET cc_start: 0.7633 (mmt) cc_final: 0.7124 (mmt) REVERT: B 798 MET cc_start: 0.7342 (mtp) cc_final: 0.7133 (mmm) REVERT: A 174 ASP cc_start: 0.6700 (t70) cc_final: 0.5961 (t0) REVERT: A 904 VAL cc_start: 0.8603 (m) cc_final: 0.8150 (p) REVERT: A 1000 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7331 (tp-100) outliers start: 11 outliers final: 1 residues processed: 435 average time/residue: 0.1577 time to fit residues: 111.4232 Evaluate side-chains 289 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 683 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN B 231 ASN C 274 ASN C 928 GLN A 577 GLN A 584 GLN A1000 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099288 restraints weight = 35704.467| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.38 r_work: 0.3138 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24216 Z= 0.141 Angle : 0.575 10.273 32739 Z= 0.302 Chirality : 0.044 0.173 3824 Planarity : 0.004 0.056 4127 Dihedral : 13.208 179.782 3630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.21 % Allowed : 8.53 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 3051 helix: 0.96 (0.13), residues: 1632 sheet: -1.28 (0.26), residues: 396 loop : -0.86 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.017 0.001 TYR C 541 PHE 0.021 0.001 PHE C 11 TRP 0.012 0.001 TRP A 789 HIS 0.012 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24216) covalent geometry : angle 0.57547 / 0.30 (32739) hydrogen bonds : bond 0.04164 / 2.84 ( 1406) hydrogen bonds : angle 5.16818 / 3.78 ( 4134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 0.929 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 456 MET cc_start: 0.8801 (ttp) cc_final: 0.8572 (ttm) REVERT: B 468 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7601 (ttt-90) REVERT: B 525 HIS cc_start: 0.8163 (t70) cc_final: 0.7950 (t-90) REVERT: B 745 ASP cc_start: 0.8395 (t0) cc_final: 0.8174 (t0) REVERT: B 825 MET cc_start: 0.8955 (mtt) cc_final: 0.8599 (mtt) REVERT: C 712 MET cc_start: 0.8014 (tpp) cc_final: 0.7692 (tpp) REVERT: C 841 MET cc_start: 0.8879 (mtp) cc_final: 0.8554 (mtm) REVERT: A 174 ASP cc_start: 0.7649 (t70) cc_final: 0.7436 (t0) REVERT: A 355 MET cc_start: 0.8527 (mtm) cc_final: 0.8031 (mtm) outliers start: 30 outliers final: 20 residues processed: 339 average time/residue: 0.1433 time to fit residues: 81.5619 Evaluate side-chains 310 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 290 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 937 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 47 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 233 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 ASN B 81 ASN B 298 ASN C 74 ASN C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096979 restraints weight = 35888.517| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.40 r_work: 0.3101 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24216 Z= 0.159 Angle : 0.533 8.162 32739 Z= 0.278 Chirality : 0.042 0.161 3824 Planarity : 0.004 0.056 4127 Dihedral : 12.073 174.333 3630 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.42 % Allowed : 10.92 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 3051 helix: 1.29 (0.13), residues: 1638 sheet: -1.33 (0.26), residues: 393 loop : -0.72 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 637 TYR 0.017 0.001 TYR C 541 PHE 0.017 0.001 PHE C 11 TRP 0.011 0.001 TRP A 789 HIS 0.009 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (24216) covalent geometry : angle 0.53270 / 0.28 (32739) hydrogen bonds : bond 0.03911 / 2.67 ( 1406) hydrogen bonds : angle 4.83901 / 3.52 ( 4134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.841 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 327 TYR cc_start: 0.8633 (t80) cc_final: 0.8414 (t80) REVERT: B 468 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7552 (ttt-90) REVERT: B 478 MET cc_start: 0.7704 (tmm) cc_final: 0.7466 (tmm) REVERT: B 525 HIS cc_start: 0.8287 (t70) cc_final: 0.8049 (t-90) REVERT: B 825 MET cc_start: 0.9027 (mtt) cc_final: 0.8668 (mtt) REVERT: C 89 GLN cc_start: 0.7984 (mt0) cc_final: 0.7692 (mt0) REVERT: C 712 MET cc_start: 0.8044 (tpp) cc_final: 0.7670 (tpp) REVERT: A 174 ASP cc_start: 0.7730 (t70) cc_final: 0.7462 (t0) REVERT: A 355 MET cc_start: 0.8336 (mtm) cc_final: 0.8042 (mtm) outliers start: 35 outliers final: 23 residues processed: 324 average time/residue: 0.1465 time to fit residues: 78.3188 Evaluate side-chains 306 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 286 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 283 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN C 74 ASN C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098190 restraints weight = 35632.739| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.40 r_work: 0.3123 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24216 Z= 0.121 Angle : 0.499 7.652 32739 Z= 0.259 Chirality : 0.041 0.156 3824 Planarity : 0.004 0.055 4127 Dihedral : 11.293 170.430 3627 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.74 % Allowed : 11.69 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 3051 helix: 1.46 (0.13), residues: 1641 sheet: -1.18 (0.26), residues: 391 loop : -0.60 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 307 TYR 0.017 0.001 TYR C 541 PHE 0.017 0.001 PHE C 885 TRP 0.011 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (24216) covalent geometry : angle 0.49938 / 0.26 (32739) hydrogen bonds : bond 0.03492 / 2.39 ( 1406) hydrogen bonds : angle 4.64445 / 3.37 ( 4134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.913 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 456 MET cc_start: 0.8705 (ttp) cc_final: 0.8428 (ttm) REVERT: B 468 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7497 (ttt-90) REVERT: B 478 MET cc_start: 0.7712 (tmm) cc_final: 0.7461 (tmm) REVERT: B 825 MET cc_start: 0.9003 (mtt) cc_final: 0.8628 (mtt) REVERT: C 124 GLN cc_start: 0.8275 (tp40) cc_final: 0.7788 (tm-30) REVERT: C 712 MET cc_start: 0.7986 (tpp) cc_final: 0.7620 (tpp) REVERT: C 892 TYR cc_start: 0.8392 (m-10) cc_final: 0.8168 (m-80) REVERT: C 947 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 174 ASP cc_start: 0.7700 (t70) cc_final: 0.7420 (t0) REVERT: A 355 MET cc_start: 0.8240 (mtm) cc_final: 0.7912 (mtm) REVERT: A 367 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8476 (mp) outliers start: 43 outliers final: 27 residues processed: 336 average time/residue: 0.1438 time to fit residues: 81.2645 Evaluate side-chains 318 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 151 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN C 74 ASN C 274 ASN A 106 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097681 restraints weight = 35618.864| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.39 r_work: 0.3112 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24216 Z= 0.132 Angle : 0.500 8.014 32739 Z= 0.258 Chirality : 0.041 0.153 3824 Planarity : 0.004 0.056 4127 Dihedral : 10.863 168.161 3627 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.94 % Allowed : 12.33 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 3051 helix: 1.53 (0.13), residues: 1641 sheet: -1.20 (0.26), residues: 377 loop : -0.51 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.016 0.001 TYR C 541 PHE 0.016 0.001 PHE A 352 TRP 0.011 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (24216) covalent geometry : angle 0.50032 / 0.26 (32739) hydrogen bonds : bond 0.03454 / 2.36 ( 1406) hydrogen bonds : angle 4.57308 / 3.31 ( 4134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 456 MET cc_start: 0.8697 (ttp) cc_final: 0.8230 (ttm) REVERT: B 468 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7497 (ttt-90) REVERT: B 478 MET cc_start: 0.7684 (tmm) cc_final: 0.7429 (tmm) REVERT: B 825 MET cc_start: 0.9010 (mtt) cc_final: 0.8634 (mtt) REVERT: C 124 GLN cc_start: 0.8194 (tp40) cc_final: 0.7747 (tm-30) REVERT: C 712 MET cc_start: 0.8020 (tpp) cc_final: 0.7790 (tpp) REVERT: C 892 TYR cc_start: 0.8406 (m-10) cc_final: 0.8203 (m-80) REVERT: C 947 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 174 ASP cc_start: 0.7745 (t70) cc_final: 0.7456 (t0) REVERT: A 355 MET cc_start: 0.8205 (mtm) cc_final: 0.7880 (mtm) REVERT: A 367 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 459 PHE cc_start: 0.7385 (t80) cc_final: 0.7107 (t80) REVERT: A 1000 GLN cc_start: 0.7404 (tp40) cc_final: 0.7121 (tp40) outliers start: 48 outliers final: 30 residues processed: 329 average time/residue: 0.1327 time to fit residues: 73.4689 Evaluate side-chains 322 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 159 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 118 optimal weight: 0.0470 chunk 163 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 285 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098467 restraints weight = 35840.528| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.40 r_work: 0.3130 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24216 Z= 0.113 Angle : 0.491 7.960 32739 Z= 0.252 Chirality : 0.041 0.152 3824 Planarity : 0.003 0.055 4127 Dihedral : 10.423 164.919 3627 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.70 % Allowed : 12.70 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 3051 helix: 1.60 (0.13), residues: 1645 sheet: -1.05 (0.26), residues: 387 loop : -0.49 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.016 0.001 TYR C 541 PHE 0.017 0.001 PHE A 885 TRP 0.011 0.001 TRP A 789 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (24216) covalent geometry : angle 0.49149 / 0.25 (32739) hydrogen bonds : bond 0.03307 / 2.26 ( 1406) hydrogen bonds : angle 4.49761 / 3.25 ( 4134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 0.920 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 202 ASP cc_start: 0.7991 (m-30) cc_final: 0.7708 (m-30) REVERT: B 414 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 468 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7443 (ttt-90) REVERT: B 478 MET cc_start: 0.7717 (tmm) cc_final: 0.7441 (tmm) REVERT: B 573 MET cc_start: 0.8877 (mmp) cc_final: 0.8530 (mmt) REVERT: C 124 GLN cc_start: 0.8186 (tp40) cc_final: 0.7767 (tm-30) REVERT: C 712 MET cc_start: 0.7972 (tpp) cc_final: 0.7744 (tpp) REVERT: C 947 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 174 ASP cc_start: 0.7738 (t70) cc_final: 0.7476 (t0) REVERT: A 355 MET cc_start: 0.8226 (mtm) cc_final: 0.7921 (mtm) REVERT: A 367 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 459 PHE cc_start: 0.7331 (t80) cc_final: 0.7062 (t80) outliers start: 42 outliers final: 27 residues processed: 335 average time/residue: 0.1248 time to fit residues: 70.5440 Evaluate side-chains 320 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 11 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 249 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098792 restraints weight = 35745.052| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.40 r_work: 0.3130 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24216 Z= 0.110 Angle : 0.486 8.680 32739 Z= 0.249 Chirality : 0.041 0.150 3824 Planarity : 0.003 0.056 4127 Dihedral : 9.998 161.020 3627 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.58 % Allowed : 13.75 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3051 helix: 1.65 (0.13), residues: 1647 sheet: -0.99 (0.26), residues: 387 loop : -0.45 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.016 0.001 TYR C 541 PHE 0.017 0.001 PHE C 885 TRP 0.010 0.001 TRP A 789 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (24216) covalent geometry : angle 0.48597 / 0.25 (32739) hydrogen bonds : bond 0.03225 / 2.20 ( 1406) hydrogen bonds : angle 4.44353 / 3.21 ( 4134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.757 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8569 (mtp) cc_final: 0.8158 (mtt) REVERT: B 202 ASP cc_start: 0.7992 (m-30) cc_final: 0.7717 (m-30) REVERT: B 280 GLU cc_start: 0.8166 (pt0) cc_final: 0.7921 (mt-10) REVERT: B 414 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 456 MET cc_start: 0.8599 (ttp) cc_final: 0.8298 (ttm) REVERT: B 468 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7445 (ttt-90) REVERT: B 478 MET cc_start: 0.7685 (tmm) cc_final: 0.7458 (tmm) REVERT: C 69 MET cc_start: 0.8824 (mmp) cc_final: 0.8608 (mmp) REVERT: C 124 GLN cc_start: 0.8186 (tp40) cc_final: 0.7762 (tm-30) REVERT: C 712 MET cc_start: 0.7942 (tpp) cc_final: 0.7723 (tpp) REVERT: C 947 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 174 ASP cc_start: 0.7794 (t70) cc_final: 0.7507 (t0) REVERT: A 355 MET cc_start: 0.8202 (mtm) cc_final: 0.7990 (mtm) REVERT: A 367 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 459 PHE cc_start: 0.7295 (t80) cc_final: 0.7033 (t80) REVERT: A 1000 GLN cc_start: 0.7407 (tp40) cc_final: 0.7075 (tp40) outliers start: 39 outliers final: 29 residues processed: 332 average time/residue: 0.1336 time to fit residues: 75.0673 Evaluate side-chains 327 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 289 optimal weight: 0.0030 chunk 253 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098993 restraints weight = 35755.785| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.39 r_work: 0.3130 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24216 Z= 0.112 Angle : 0.490 7.828 32739 Z= 0.249 Chirality : 0.040 0.149 3824 Planarity : 0.003 0.055 4127 Dihedral : 9.631 164.952 3627 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.62 % Allowed : 14.15 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 3051 helix: 1.68 (0.13), residues: 1647 sheet: -1.00 (0.26), residues: 383 loop : -0.40 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.015 0.001 TYR C 541 PHE 0.023 0.001 PHE A 885 TRP 0.010 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (24216) covalent geometry : angle 0.48975 / 0.25 (32739) hydrogen bonds : bond 0.03201 / 2.18 ( 1406) hydrogen bonds : angle 4.41524 / 3.19 ( 4134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.860 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8552 (mtp) cc_final: 0.8164 (mtt) REVERT: B 202 ASP cc_start: 0.7972 (m-30) cc_final: 0.7664 (m-30) REVERT: B 346 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 456 MET cc_start: 0.8610 (ttp) cc_final: 0.8312 (ttm) REVERT: B 468 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7416 (ttt-90) REVERT: B 478 MET cc_start: 0.7686 (tmm) cc_final: 0.7455 (tmm) REVERT: C 124 GLN cc_start: 0.8190 (tp40) cc_final: 0.7767 (tm-30) REVERT: C 712 MET cc_start: 0.7926 (tpp) cc_final: 0.7700 (tpp) REVERT: C 947 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 174 ASP cc_start: 0.7774 (t70) cc_final: 0.7454 (t0) REVERT: A 355 MET cc_start: 0.8258 (mtm) cc_final: 0.8028 (mtm) REVERT: A 367 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 459 PHE cc_start: 0.7279 (t80) cc_final: 0.7016 (t80) REVERT: A 567 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: A 918 PHE cc_start: 0.7624 (m-80) cc_final: 0.6838 (t80) REVERT: A 1000 GLN cc_start: 0.7323 (tp40) cc_final: 0.6995 (tp40) outliers start: 40 outliers final: 29 residues processed: 335 average time/residue: 0.1319 time to fit residues: 74.3310 Evaluate side-chains 328 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 970 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 266 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 830 GLN C 274 ASN C 284 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096004 restraints weight = 36120.598| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.39 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24216 Z= 0.189 Angle : 0.550 9.535 32739 Z= 0.279 Chirality : 0.043 0.151 3824 Planarity : 0.004 0.054 4127 Dihedral : 9.618 160.758 3627 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 14.48 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3051 helix: 1.57 (0.13), residues: 1644 sheet: -1.02 (0.26), residues: 393 loop : -0.42 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 973 TYR 0.016 0.001 TYR C 758 PHE 0.018 0.001 PHE C 885 TRP 0.007 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (24216) covalent geometry : angle 0.55044 / 0.28 (32739) hydrogen bonds : bond 0.03629 / 2.48 ( 1406) hydrogen bonds : angle 4.54452 / 3.29 ( 4134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 303 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 456 MET cc_start: 0.8702 (ttp) cc_final: 0.8234 (ttm) REVERT: B 478 MET cc_start: 0.7723 (tmm) cc_final: 0.7461 (tmm) REVERT: B 825 MET cc_start: 0.8970 (mtt) cc_final: 0.8572 (mtt) REVERT: C 516 PHE cc_start: 0.6374 (t80) cc_final: 0.6150 (t80) REVERT: C 712 MET cc_start: 0.7971 (tpp) cc_final: 0.7738 (tpp) REVERT: C 947 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 174 ASP cc_start: 0.7767 (t70) cc_final: 0.7403 (t0) REVERT: A 355 MET cc_start: 0.8359 (mtm) cc_final: 0.8037 (mtm) REVERT: A 367 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 459 PHE cc_start: 0.7271 (t80) cc_final: 0.7002 (t80) REVERT: A 1000 GLN cc_start: 0.7437 (tp40) cc_final: 0.7093 (tp40) outliers start: 43 outliers final: 33 residues processed: 329 average time/residue: 0.1366 time to fit residues: 75.7036 Evaluate side-chains 330 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 970 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 191 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 258 optimal weight: 0.0040 chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098240 restraints weight = 35987.434| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.39 r_work: 0.3133 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24216 Z= 0.114 Angle : 0.512 8.687 32739 Z= 0.259 Chirality : 0.041 0.151 3824 Planarity : 0.003 0.053 4127 Dihedral : 9.233 155.108 3627 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.58 % Allowed : 14.96 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 3051 helix: 1.64 (0.13), residues: 1643 sheet: -0.93 (0.26), residues: 383 loop : -0.39 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.018 0.001 TYR A 35 PHE 0.017 0.001 PHE C 885 TRP 0.013 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (24216) covalent geometry : angle 0.51231 / 0.26 (32739) hydrogen bonds : bond 0.03292 / 2.24 ( 1406) hydrogen bonds : angle 4.46393 / 3.23 ( 4134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 202 ASP cc_start: 0.8008 (m-30) cc_final: 0.7730 (m-30) REVERT: B 456 MET cc_start: 0.8662 (ttp) cc_final: 0.8377 (ttm) REVERT: B 478 MET cc_start: 0.7658 (tmm) cc_final: 0.7429 (tmm) REVERT: C 516 PHE cc_start: 0.6390 (t80) cc_final: 0.6146 (t80) REVERT: C 712 MET cc_start: 0.7903 (tpp) cc_final: 0.7676 (tpp) REVERT: C 947 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 174 ASP cc_start: 0.7707 (t70) cc_final: 0.7452 (t0) REVERT: A 355 MET cc_start: 0.8309 (mtm) cc_final: 0.8064 (mtm) REVERT: A 367 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 459 PHE cc_start: 0.7237 (t80) cc_final: 0.7010 (t80) REVERT: A 918 PHE cc_start: 0.7755 (m-80) cc_final: 0.6978 (t80) REVERT: A 1000 GLN cc_start: 0.7328 (tp40) cc_final: 0.6989 (tp40) outliers start: 39 outliers final: 30 residues processed: 324 average time/residue: 0.1224 time to fit residues: 67.2337 Evaluate side-chains 325 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 970 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098145 restraints weight = 35646.763| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.37 r_work: 0.3124 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 24216 Z= 0.157 Angle : 0.682 59.198 32739 Z= 0.377 Chirality : 0.041 0.149 3824 Planarity : 0.003 0.053 4127 Dihedral : 9.230 155.079 3627 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.37 % Allowed : 15.16 % Favored : 83.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 3051 helix: 1.64 (0.13), residues: 1643 sheet: -0.93 (0.26), residues: 383 loop : -0.39 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.016 0.001 TYR A 35 PHE 0.017 0.001 PHE C 885 TRP 0.012 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (24216) covalent geometry : angle 0.68186 / 0.38 (32739) hydrogen bonds : bond 0.03306 / 2.25 ( 1406) hydrogen bonds : angle 4.46402 / 3.23 ( 4134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6400.82 seconds wall clock time: 110 minutes 14.58 seconds (6614.58 seconds total)