Starting phenix.real_space_refine on Thu Mar 5 17:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr6_24653/03_2026/7rr6_24653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr6_24653/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rr6_24653/03_2026/7rr6_24653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr6_24653/03_2026/7rr6_24653.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr6_24653/03_2026/7rr6_24653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr6_24653/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 276 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: 183 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: 272 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: 5.38, per 1000 atoms: 0.23 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: 2.15 Conformation dependent library (CDL) restraints added in 979.7 milliseconds 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: 0.96 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: 5.66 Time building geometry restraints manager: 2.83 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: 14170 35.13 - 70.27: 386 70.27 - 105.40: 28 105.40 - 140.54: 6 140.54 - 175.67: 7 Dihedral angle restraints: 14597 sinusoidal: 5839 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 14594 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: 3.860 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.350 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 16.026 175.670 8977 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 covalent geometry : bond 0.00831 (24216) covalent geometry : angle 1.21111 (32739) hydrogen bonds : bond 0.17590 ( 1406) hydrogen bonds : angle 7.73097 ( 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 : 0.844 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: 0.1482 time to fit residues: 105.4775 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 : 0.739 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3696 r_free = 0.3696 target = 0.129350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099015 restraints weight = 35729.140| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.39 r_work: 0.3149 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1532 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= 0.142 Angle : 0.576 10.072 32739 Z= 0.302 Chirality : 0.043 0.169 3824 Planarity : 0.004 0.056 4127 Dihedral : 14.107 179.209 3720 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.21 % Allowed : 8.57 % Favored : 90.21 % 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: -0.01 (0.16), residues: 3051 helix: 0.95 (0.13), residues: 1634 sheet: -1.44 (0.25), residues: 400 loop : -0.82 (0.20), residues: 1017 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 covalent geometry : bond 0.00325 (24216) covalent geometry : angle 0.57602 (32739) hydrogen bonds : bond 0.04219 ( 1406) hydrogen bonds : angle 5.18023 ( 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 348 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 318 time to evaluate : 0.879 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: 0.8804 (ttp) cc_final: 0.8380 (ttm) REVERT: B 468 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7604 (ttt-90) REVERT: B 525 HIS cc_start: 0.8157 (t70) cc_final: 0.7942 (t-90) REVERT: B 745 ASP cc_start: 0.8403 (t0) cc_final: 0.8179 (t0) REVERT: B 825 MET cc_start: 0.8961 (mtt) cc_final: 0.8602 (mtt) REVERT: C 712 MET cc_start: 0.8014 (tpp) cc_final: 0.7692 (tpp) REVERT: C 841 MET cc_start: 0.8877 (mtp) cc_final: 0.8558 (mtm) REVERT: A 174 ASP cc_start: 0.7649 (t70) cc_final: 0.7432 (t0) REVERT: A 355 MET cc_start: 0.8542 (mtm) cc_final: 0.8156 (mtm) REVERT: A 932 LEU cc_start: 0.7677 (mt) cc_final: 0.7473 (mt) outliers start: 30 outliers final: 20 residues processed: 335 average time/residue: 0.1383 time to fit residues: 77.8319 Evaluate side-chains 305 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 354 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 47 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 81 ASN B 298 ASN C 74 ASN C 81 ASN C 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094688 restraints weight = 36060.709| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.38 r_work: 0.3069 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24216 Z= 0.222 Angle : 0.579 8.827 32739 Z= 0.302 Chirality : 0.044 0.161 3824 Planarity : 0.004 0.057 4127 Dihedral : 12.861 174.958 3720 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.78 % Allowed : 11.12 % Favored : 87.10 % 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: 0.26 (0.16), residues: 3051 helix: 1.18 (0.13), residues: 1639 sheet: -1.32 (0.26), residues: 384 loop : -0.76 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 637 TYR 0.019 0.002 TYR A 49 PHE 0.021 0.002 PHE C 11 TRP 0.012 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00532 (24216) covalent geometry : angle 0.57918 (32739) hydrogen bonds : bond 0.04198 ( 1406) hydrogen bonds : angle 4.91329 ( 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 348 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.791 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: 0.8646 (t80) cc_final: 0.8363 (t80) REVERT: B 468 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7491 (ttt-90) REVERT: B 478 MET cc_start: 0.7789 (tmm) cc_final: 0.7539 (tmm) REVERT: B 525 HIS cc_start: 0.8278 (t70) cc_final: 0.8037 (t-90) REVERT: B 825 MET cc_start: 0.9043 (mtt) cc_final: 0.8695 (mtt) REVERT: C 712 MET cc_start: 0.8093 (tpp) cc_final: 0.7848 (tpp) REVERT: A 174 ASP cc_start: 0.7768 (t70) cc_final: 0.7475 (t0) REVERT: A 355 MET cc_start: 0.8498 (mtm) cc_final: 0.8088 (mtm) outliers start: 44 outliers final: 28 residues processed: 323 average time/residue: 0.1451 time to fit residues: 77.8556 Evaluate side-chains 310 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 MET 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 354 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 644 VAL 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 65 ILE 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 Chi-restraints excluded: chain A residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 286 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097932 restraints weight = 35702.765| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.38 r_work: 0.3127 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24216 Z= 0.118 Angle : 0.503 7.986 32739 Z= 0.261 Chirality : 0.041 0.157 3824 Planarity : 0.004 0.056 4127 Dihedral : 12.108 173.819 3717 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.54 % Allowed : 12.13 % Favored : 86.33 % 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: 0.57 (0.16), residues: 3051 helix: 1.45 (0.13), residues: 1633 sheet: -1.26 (0.26), residues: 382 loop : -0.60 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.017 0.001 TYR C 541 PHE 0.016 0.001 PHE C 885 TRP 0.013 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00273 (24216) covalent geometry : angle 0.50313 (32739) hydrogen bonds : bond 0.03540 ( 1406) hydrogen bonds : angle 4.68669 ( 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 352 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 327 TYR cc_start: 0.8637 (t80) cc_final: 0.8409 (t80) REVERT: B 456 MET cc_start: 0.8718 (ttp) cc_final: 0.8446 (ttm) REVERT: B 468 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7494 (ttt-90) REVERT: B 478 MET cc_start: 0.7748 (tmm) cc_final: 0.7495 (tmm) REVERT: B 825 MET cc_start: 0.8991 (mtt) cc_final: 0.8612 (mtt) REVERT: C 89 GLN cc_start: 0.8110 (mt0) cc_final: 0.7839 (mt0) REVERT: C 124 GLN cc_start: 0.8234 (tp40) cc_final: 0.7790 (tm-30) REVERT: C 712 MET cc_start: 0.7955 (tpp) cc_final: 0.7593 (tpp) REVERT: C 841 MET cc_start: 0.8867 (mtp) cc_final: 0.8569 (mtm) REVERT: C 892 TYR cc_start: 0.8401 (m-10) cc_final: 0.8196 (m-80) REVERT: C 947 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 174 ASP cc_start: 0.7699 (t70) cc_final: 0.7425 (t0) REVERT: A 355 MET cc_start: 0.8461 (mtm) cc_final: 0.8108 (mtm) REVERT: A 367 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8530 (mp) outliers start: 38 outliers final: 22 residues processed: 333 average time/residue: 0.1356 time to fit residues: 76.1276 Evaluate side-chains 317 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 180 SER Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR 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 407 ASP 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 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: 1.9990 chunk 177 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 240 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 74 ASN C 274 ASN A 106 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097282 restraints weight = 35765.839| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.39 r_work: 0.3113 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2149 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= 0.129 Angle : 0.506 8.328 32739 Z= 0.260 Chirality : 0.041 0.153 3824 Planarity : 0.004 0.056 4127 Dihedral : 11.647 179.874 3717 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.82 % Allowed : 12.49 % Favored : 85.69 % 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: 0.67 (0.16), residues: 3051 helix: 1.51 (0.13), residues: 1635 sheet: -1.19 (0.27), residues: 372 loop : -0.54 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.017 0.001 TYR C 541 PHE 0.018 0.001 PHE A 459 TRP 0.011 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00303 (24216) covalent geometry : angle 0.50610 (32739) hydrogen bonds : bond 0.03479 ( 1406) hydrogen bonds : angle 4.59544 ( 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 347 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 414 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 456 MET cc_start: 0.8708 (ttp) cc_final: 0.8243 (ttm) REVERT: B 478 MET cc_start: 0.7701 (tmm) cc_final: 0.7443 (tmm) REVERT: B 825 MET cc_start: 0.9006 (mtt) cc_final: 0.8620 (mtt) REVERT: C 124 GLN cc_start: 0.8208 (tp40) cc_final: 0.7748 (tm-30) REVERT: C 712 MET cc_start: 0.8003 (tpp) cc_final: 0.7772 (tpp) REVERT: C 841 MET cc_start: 0.8865 (mtp) cc_final: 0.8589 (mtm) REVERT: C 947 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 29 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8526 (ttmt) REVERT: A 174 ASP cc_start: 0.7727 (t70) cc_final: 0.7440 (t0) REVERT: A 355 MET cc_start: 0.8412 (mtm) cc_final: 0.8053 (mtm) REVERT: A 367 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8515 (mp) outliers start: 45 outliers final: 30 residues processed: 327 average time/residue: 0.1292 time to fit residues: 71.8816 Evaluate side-chains 324 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 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 29 LYS 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 407 ASP Chi-restraints excluded: chain A residue 420 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 159 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 118 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 290 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 285 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 74 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099142 restraints weight = 35856.838| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.41 r_work: 0.3133 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24216 Z= 0.105 Angle : 0.487 7.688 32739 Z= 0.250 Chirality : 0.041 0.152 3824 Planarity : 0.003 0.054 4127 Dihedral : 11.011 165.873 3717 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.86 % Allowed : 12.98 % Favored : 85.16 % 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: 1644 sheet: -1.04 (0.26), residues: 387 loop : -0.51 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.017 0.001 TYR C 541 PHE 0.026 0.001 PHE A 459 TRP 0.011 0.001 TRP A 789 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00236 (24216) covalent geometry : angle 0.48716 (32739) hydrogen bonds : bond 0.03241 ( 1406) hydrogen bonds : angle 4.47658 ( 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 365 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.7988 (m-30) cc_final: 0.7715 (m-30) REVERT: B 346 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 414 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 478 MET cc_start: 0.7731 (tmm) cc_final: 0.7505 (tmm) REVERT: B 573 MET cc_start: 0.8851 (mmp) cc_final: 0.8585 (mmt) REVERT: B 681 ASP cc_start: 0.8134 (t0) cc_final: 0.7386 (t70) REVERT: B 826 GLU cc_start: 0.8776 (tt0) cc_final: 0.8330 (tt0) REVERT: C 69 MET cc_start: 0.8773 (mmp) cc_final: 0.8568 (mmp) REVERT: C 124 GLN cc_start: 0.8182 (tp40) cc_final: 0.7760 (tm-30) REVERT: C 184 MET cc_start: 0.9135 (tpp) cc_final: 0.8883 (tpt) REVERT: C 712 MET cc_start: 0.7935 (tpp) cc_final: 0.7714 (tpp) REVERT: C 841 MET cc_start: 0.8870 (mtp) cc_final: 0.8586 (mtm) REVERT: C 947 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 174 ASP cc_start: 0.7723 (t70) cc_final: 0.7465 (t0) REVERT: A 355 MET cc_start: 0.8405 (mtm) cc_final: 0.8057 (mtm) REVERT: A 367 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8448 (mp) outliers start: 46 outliers final: 33 residues processed: 344 average time/residue: 0.1346 time to fit residues: 78.3429 Evaluate side-chains 333 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 607 GLU 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 274 ASN Chi-restraints excluded: chain C residue 354 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 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 407 ASP 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 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: 0.9990 chunk 120 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 249 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 274 ASN C 284 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097193 restraints weight = 35852.682| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.39 r_work: 0.3102 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24216 Z= 0.148 Angle : 0.509 8.245 32739 Z= 0.261 Chirality : 0.042 0.151 3824 Planarity : 0.004 0.054 4127 Dihedral : 10.807 161.174 3717 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.90 % Allowed : 13.99 % Favored : 84.11 % 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: 0.79 (0.16), residues: 3051 helix: 1.60 (0.13), residues: 1642 sheet: -1.06 (0.26), residues: 384 loop : -0.49 (0.20), residues: 1025 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 0.027 0.001 PHE A 459 TRP 0.009 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00352 (24216) covalent geometry : angle 0.50901 (32739) hydrogen bonds : bond 0.03423 ( 1406) hydrogen bonds : angle 4.50089 ( 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 347 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.825 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: 0.8046 (m-30) cc_final: 0.7729 (m-30) REVERT: B 456 MET cc_start: 0.8660 (ttp) cc_final: 0.8360 (ttm) REVERT: B 468 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7432 (ttt-90) REVERT: B 478 MET cc_start: 0.7729 (tmm) cc_final: 0.7454 (tmm) REVERT: B 825 MET cc_start: 0.9022 (mtt) cc_final: 0.8630 (mtt) REVERT: B 826 GLU cc_start: 0.8798 (tt0) cc_final: 0.8412 (tt0) REVERT: C 69 MET cc_start: 0.8815 (mmp) cc_final: 0.8604 (mmp) REVERT: C 274 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8776 (p0) REVERT: C 712 MET cc_start: 0.7971 (tpp) cc_final: 0.7749 (tpp) REVERT: C 947 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 174 ASP cc_start: 0.7759 (t70) cc_final: 0.7435 (t0) REVERT: A 355 MET cc_start: 0.8421 (mtm) cc_final: 0.8038 (mtm) REVERT: A 367 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 480 LEU cc_start: 0.8491 (mt) cc_final: 0.8257 (mt) outliers start: 47 outliers final: 34 residues processed: 328 average time/residue: 0.1409 time to fit residues: 78.8823 Evaluate side-chains 329 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 274 ASN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 410 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 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 976 LEU 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: 0.5980 chunk 51 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 196 optimal weight: 0.0060 chunk 183 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 274 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098465 restraints weight = 35832.570| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.40 r_work: 0.3136 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2446 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= 0.109 Angle : 0.493 8.458 32739 Z= 0.252 Chirality : 0.041 0.150 3824 Planarity : 0.003 0.054 4127 Dihedral : 10.458 157.651 3717 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.74 % Allowed : 14.36 % Favored : 83.91 % 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: 0.84 (0.16), residues: 3051 helix: 1.62 (0.13), residues: 1646 sheet: -1.02 (0.26), residues: 383 loop : -0.46 (0.20), residues: 1022 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 0.028 0.001 PHE A 459 TRP 0.011 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00253 (24216) covalent geometry : angle 0.49343 (32739) hydrogen bonds : bond 0.03234 ( 1406) hydrogen bonds : angle 4.44525 ( 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: 43 poor density : 307 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8582 (mtp) cc_final: 0.8172 (mtt) REVERT: B 202 ASP cc_start: 0.8010 (m-30) cc_final: 0.7727 (m-30) REVERT: B 276 ASP cc_start: 0.8271 (m-30) cc_final: 0.7910 (m-30) REVERT: B 456 MET cc_start: 0.8636 (ttp) cc_final: 0.8146 (ttm) REVERT: B 478 MET cc_start: 0.7706 (tmm) cc_final: 0.7477 (tmm) REVERT: B 681 ASP cc_start: 0.8042 (t0) cc_final: 0.7300 (t70) REVERT: B 826 GLU cc_start: 0.8767 (tt0) cc_final: 0.8265 (tt0) REVERT: C 69 MET cc_start: 0.8828 (mmp) cc_final: 0.8605 (mmp) REVERT: C 124 GLN cc_start: 0.8212 (tp40) cc_final: 0.7785 (tm-30) REVERT: C 447 MET cc_start: 0.7869 (ttp) cc_final: 0.7643 (mtp) REVERT: C 516 PHE cc_start: 0.6356 (t80) cc_final: 0.6038 (t80) REVERT: C 712 MET cc_start: 0.7900 (tpp) cc_final: 0.7678 (tpp) REVERT: C 947 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7939 (tm-30) REVERT: A 174 ASP cc_start: 0.7669 (t70) cc_final: 0.7364 (t0) REVERT: A 355 MET cc_start: 0.8403 (mtm) cc_final: 0.8047 (mtm) REVERT: A 367 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 552 MET cc_start: 0.6829 (mmt) cc_final: 0.6469 (mmt) REVERT: A 902 MET cc_start: 0.8795 (mmm) cc_final: 0.8573 (mmm) outliers start: 43 outliers final: 32 residues processed: 334 average time/residue: 0.1362 time to fit residues: 77.2348 Evaluate side-chains 328 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 180 SER 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 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 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 672 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 924 ASP 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: 10.0000 chunk 267 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098124 restraints weight = 36030.107| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.40 r_work: 0.3117 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2501 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= 0.121 Angle : 0.497 8.454 32739 Z= 0.254 Chirality : 0.041 0.149 3824 Planarity : 0.004 0.056 4127 Dihedral : 10.091 153.935 3717 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.62 % Allowed : 14.64 % Favored : 83.74 % 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: 0.89 (0.16), residues: 3051 helix: 1.64 (0.13), residues: 1645 sheet: -0.94 (0.26), residues: 390 loop : -0.40 (0.21), residues: 1016 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 0.028 0.001 PHE A 459 TRP 0.010 0.001 TRP A 789 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00284 (24216) covalent geometry : angle 0.49707 (32739) hydrogen bonds : bond 0.03269 ( 1406) hydrogen bonds : angle 4.43579 ( 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: 40 poor density : 306 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8558 (mtp) cc_final: 0.8157 (mtt) REVERT: B 202 ASP cc_start: 0.7971 (m-30) cc_final: 0.7675 (m-30) REVERT: B 456 MET cc_start: 0.8642 (ttp) cc_final: 0.8155 (ttm) REVERT: B 478 MET cc_start: 0.7709 (tmm) cc_final: 0.7476 (tmm) REVERT: B 681 ASP cc_start: 0.8027 (t0) cc_final: 0.7248 (t70) REVERT: B 825 MET cc_start: 0.9008 (mtt) cc_final: 0.8620 (mtt) REVERT: B 826 GLU cc_start: 0.8770 (tt0) cc_final: 0.8259 (tt0) REVERT: C 69 MET cc_start: 0.8828 (mmp) cc_final: 0.8581 (mmp) REVERT: C 447 MET cc_start: 0.7964 (ttp) cc_final: 0.7743 (mtp) REVERT: C 516 PHE cc_start: 0.6419 (t80) cc_final: 0.6017 (t80) REVERT: C 712 MET cc_start: 0.7950 (tpp) cc_final: 0.7730 (tpp) REVERT: C 947 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 174 ASP cc_start: 0.7680 (t70) cc_final: 0.7378 (t0) REVERT: A 355 MET cc_start: 0.8389 (mtm) cc_final: 0.8034 (mtm) REVERT: A 367 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 552 MET cc_start: 0.6787 (mmt) cc_final: 0.6429 (mmt) REVERT: A 902 MET cc_start: 0.8790 (mmm) cc_final: 0.8571 (mmm) REVERT: A 918 PHE cc_start: 0.7757 (m-80) cc_final: 0.6972 (t80) REVERT: A 982 PHE cc_start: 0.7590 (t80) cc_final: 0.7301 (t80) outliers start: 40 outliers final: 31 residues processed: 332 average time/residue: 0.1383 time to fit residues: 78.1994 Evaluate side-chains 332 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 76 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 ILE 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 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 729 ILE 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: 0.0980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 280 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098184 restraints weight = 36075.011| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.40 r_work: 0.3120 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2539 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= 0.123 Angle : 0.503 8.549 32739 Z= 0.255 Chirality : 0.041 0.149 3824 Planarity : 0.004 0.054 4127 Dihedral : 9.831 150.768 3717 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.33 % Allowed : 15.20 % 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: 0.92 (0.16), residues: 3051 helix: 1.65 (0.13), residues: 1638 sheet: -0.89 (0.26), residues: 391 loop : -0.38 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.015 0.001 TYR C 541 PHE 0.028 0.001 PHE A 459 TRP 0.010 0.001 TRP A 789 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00292 (24216) covalent geometry : angle 0.50278 (32739) hydrogen bonds : bond 0.03281 ( 1406) hydrogen bonds : angle 4.43277 ( 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 339 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8568 (mtp) cc_final: 0.8169 (mtt) REVERT: B 202 ASP cc_start: 0.7977 (m-30) cc_final: 0.7683 (m-30) REVERT: B 346 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 456 MET cc_start: 0.8649 (ttp) cc_final: 0.8172 (ttm) REVERT: B 478 MET cc_start: 0.7659 (tmm) cc_final: 0.7427 (tmm) REVERT: B 681 ASP cc_start: 0.8034 (t0) cc_final: 0.7266 (t70) REVERT: B 826 GLU cc_start: 0.8762 (tt0) cc_final: 0.8237 (tt0) REVERT: C 69 MET cc_start: 0.8849 (mmp) cc_final: 0.8597 (mmp) REVERT: C 184 MET cc_start: 0.9126 (tpp) cc_final: 0.8900 (tpt) REVERT: C 447 MET cc_start: 0.7971 (ttp) cc_final: 0.7760 (mtp) REVERT: C 516 PHE cc_start: 0.6291 (t80) cc_final: 0.5868 (t80) REVERT: C 712 MET cc_start: 0.7938 (tpp) cc_final: 0.7721 (tpp) REVERT: C 947 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 174 ASP cc_start: 0.7672 (t70) cc_final: 0.7379 (t0) REVERT: A 355 MET cc_start: 0.8424 (mtm) cc_final: 0.8041 (mtm) REVERT: A 367 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 902 MET cc_start: 0.8797 (mmm) cc_final: 0.8578 (mmm) REVERT: A 918 PHE cc_start: 0.7772 (m-80) cc_final: 0.6991 (t80) REVERT: A 982 PHE cc_start: 0.7578 (t80) cc_final: 0.7327 (t80) outliers start: 33 outliers final: 29 residues processed: 327 average time/residue: 0.1421 time to fit residues: 78.7377 Evaluate side-chains 326 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 76 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 ILE 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 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 729 ILE 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: 0.9980 chunk 126 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098519 restraints weight = 35683.539| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.39 r_work: 0.3128 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2593 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= 0.116 Angle : 0.498 9.070 32739 Z= 0.252 Chirality : 0.041 0.149 3824 Planarity : 0.004 0.056 4127 Dihedral : 9.577 146.446 3717 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.42 % Allowed : 15.41 % Favored : 83.18 % 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: 0.95 (0.16), residues: 3051 helix: 1.67 (0.13), residues: 1646 sheet: -0.87 (0.26), residues: 383 loop : -0.39 (0.20), residues: 1022 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 0.028 0.001 PHE A 459 TRP 0.010 0.001 TRP A 789 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00272 (24216) covalent geometry : angle 0.49800 (32739) hydrogen bonds : bond 0.03224 ( 1406) hydrogen bonds : angle 4.40285 ( 4134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6503.60 seconds wall clock time: 111 minutes 45.88 seconds (6705.88 seconds total)