Starting phenix.real_space_refine on Fri Sep 19 02:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.map" model { file = "/net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb8_49221/09_2025/9nb8_49221.cif" } resolution = 4.0 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= 0.011 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 21 9.91 5 Fe 2 7.16 5 S 215 5.16 5 C 13716 2.51 5 N 3967 2.21 5 O 4250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22171 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6494 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 24, 'TRANS': 833} Chain breaks: 1 Chain: "B" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5684 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 23, 'TRANS': 727} Chain breaks: 1 Chain: "C" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5684 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 23, 'TRANS': 727} Chain breaks: 1 Chain: "D" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "F" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2024 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CA': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.26 Number of scatterers: 22171 At special positions: 0 Unit cell: (137.64, 144.3, 158.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 21 19.99 S 215 16.00 O 4250 8.00 N 3967 7.00 C 13716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=91, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 472 " distance=2.02 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 693 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 818 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 972 " distance=2.03 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1028 " distance=2.03 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 462 " distance=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 452 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 547 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 818 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 869 " distance=2.03 Simple disulfide: pdb=" SG CYS B 864 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 895 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 972 " distance=2.03 Simple disulfide: pdb=" SG CYS B 954 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1028 " distance=2.03 Simple disulfide: pdb=" SG CYS B 998 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 355 " distance=2.04 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 452 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 547 " - pdb=" SG CYS C 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 672 " distance=2.02 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 662 " distance=2.02 Simple disulfide: pdb=" SG CYS C 693 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 818 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 869 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C 895 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 972 " distance=2.03 Simple disulfide: pdb=" SG CYS C 954 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1028 " distance=2.02 Simple disulfide: pdb=" SG CYS C 998 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 250 " - pdb=" SG CYS F 281 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 322 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 22.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.621A pdb=" N CYS A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.070A pdb=" N LYS A 346 " --> pdb=" O TRP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.804A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 749 through 760 removed outlier: 4.457A pdb=" N VAL A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.778A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.519A pdb=" N ASP B 572 " --> pdb=" O HIS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.983A pdb=" N ALA B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.555A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 removed outlier: 3.509A pdb=" N LEU B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 Processing helix chain 'B' and resid 959 through 971 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.545A pdb=" N ASP B1007 " --> pdb=" O SER B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.778A pdb=" N ASP B1023 " --> pdb=" O HIS B1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.608A pdb=" N GLU C 359 " --> pdb=" O ASN C 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 360 " --> pdb=" O HIS C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 403 through 414 removed outlier: 4.327A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 removed outlier: 4.298A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 613 through 624 removed outlier: 3.911A pdb=" N VAL C 619 " --> pdb=" O GLU C 615 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 749 through 760 removed outlier: 4.149A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 756 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 868 Processing helix chain 'C' and resid 901 through 905 Processing helix chain 'C' and resid 959 through 971 removed outlier: 4.059A pdb=" N VAL C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 967 " --> pdb=" O ALA C 963 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 970 " --> pdb=" O VAL C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1023 Processing helix chain 'D' and resid 4 through 19 Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.656A pdb=" N THR D 42 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE D 44 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.689A pdb=" N ALA D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 96 through 114 removed outlier: 4.177A pdb=" N LYS D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.650A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.844A pdb=" N VAL E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.699A pdb=" N PHE E 46 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 58 Processing helix chain 'E' and resid 58 through 78 removed outlier: 3.658A pdb=" N PHE E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 97 removed outlier: 3.542A pdb=" N PHE E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 Processing helix chain 'E' and resid 124 through 146 removed outlier: 3.771A pdb=" N LYS E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 removed outlier: 3.714A pdb=" N LEU F 145 " --> pdb=" O THR F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 removed outlier: 3.510A pdb=" N ILE F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) Proline residue: F 160 - end of helix Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.600A pdb=" N CYS F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 347 removed outlier: 3.954A pdb=" N ASP F 338 " --> pdb=" O THR F 334 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.660A pdb=" N VAL A 269 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 278 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.660A pdb=" N VAL A 269 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 278 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 363 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 removed outlier: 7.226A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.800A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 481 removed outlier: 3.973A pdb=" N GLU A 477 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 575 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE A 527 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 576 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 586 removed outlier: 6.488A pdb=" N VAL A 596 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TRP A 646 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER A 606 " --> pdb=" O TRP A 646 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 586 Processing sheet with id=AB2, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB3, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AB4, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.737A pdb=" N GLY A 730 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 816 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 815 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA A 768 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 817 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.513A pdb=" N ARG A 838 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP A 922 " --> pdb=" O ASN A 876 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 876 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 924 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 874 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.513A pdb=" N ARG A 838 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 839 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 850 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A 889 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR A 849 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 929 through 932 Processing sheet with id=AB8, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.502A pdb=" N LEU A 976 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A1027 " --> pdb=" O LEU A 976 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.593A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP B 329 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 289 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'B' and resid 372 through 377 removed outlier: 3.608A pdb=" N ILE B 470 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 421 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 397 removed outlier: 6.299A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B 439 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 438 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 456 " --> pdb=" O PHE B 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 480 through 481 removed outlier: 3.636A pdb=" N SER B 526 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AC6, first strand: chain 'B' and resid 501 through 502 removed outlier: 6.738A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.509A pdb=" N GLY B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.749A pdb=" N GLY B 594 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 680 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 649 through 650 removed outlier: 3.869A pdb=" N MET B 649 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 665 " --> pdb=" O MET B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.627A pdb=" N VAL B 816 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 817 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 822 through 827 removed outlier: 3.543A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 825 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 822 through 827 removed outlier: 3.543A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 825 " --> pdb=" O GLU B 840 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 837 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.438A pdb=" N ALA B1025 " --> pdb=" O ALA B 978 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA B 978 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN B1027 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 929 through 932 removed outlier: 7.070A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP B 992 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 952 " --> pdb=" O TRP B 992 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 266 through 268 removed outlier: 4.022A pdb=" N VAL C 281 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY C 288 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AE1, first strand: chain 'C' and resid 372 through 376 removed outlier: 6.824A pdb=" N VAL C 386 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 397 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N LEU C 437 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 396 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU C 439 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.559A pdb=" N ILE C 470 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 477 through 481 removed outlier: 3.548A pdb=" N SER C 526 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 477 through 481 removed outlier: 6.679A pdb=" N VAL C 491 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 502 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP C 541 " --> pdb=" O TRP C 499 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 501 " --> pdb=" O TRP C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 583 through 586 Processing sheet with id=AE6, first strand: chain 'C' and resid 720 through 722 removed outlier: 6.969A pdb=" N VAL C 732 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE C 743 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TRP C 782 " --> pdb=" O TRP C 740 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR C 742 " --> pdb=" O TRP C 782 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 765 through 769 removed outlier: 3.735A pdb=" N ASN C 767 " --> pdb=" O ILE C 817 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AE9, first strand: chain 'C' and resid 824 through 827 removed outlier: 6.787A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP C 889 " --> pdb=" O TRP C 847 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 849 " --> pdb=" O TRP C 889 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 929 through 932 Processing sheet with id=AF2, first strand: chain 'C' and resid 929 through 932 removed outlier: 3.792A pdb=" N ALA C1025 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C1027 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 977 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 107 through 108 removed outlier: 4.205A pdb=" N LYS F 238 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL F 219 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS F 303 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 223 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA F 299 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE F 300 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR F 311 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP F 304 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR F 309 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 315 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 170 through 171 removed outlier: 3.894A pdb=" N LYS F 192 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS F 176 " --> pdb=" O LYS F 192 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1839 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: 4.98 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 8419 1.38 - 1.55: 14000 1.55 - 1.72: 7 1.72 - 1.89: 245 1.89 - 2.06: 8 Bond restraints: 22679 Sorted by residual: bond pdb=" CA GLN C 425 " pdb=" C GLN C 425 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.31e-02 5.83e+03 5.55e+00 bond pdb=" CA TYR A 427 " pdb=" C TYR A 427 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.37e-02 5.33e+03 3.37e+00 bond pdb=" CB CYS A 258 " pdb=" SG CYS A 258 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" CA GLN A 425 " pdb=" C GLN A 425 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.28e-02 6.10e+03 2.44e+00 bond pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 1.522 1.503 0.019 1.24e-02 6.50e+03 2.30e+00 ... (remaining 22674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 30299 2.21 - 4.42: 408 4.42 - 6.62: 47 6.62 - 8.83: 15 8.83 - 11.04: 2 Bond angle restraints: 30771 Sorted by residual: angle pdb=" N VAL B 426 " pdb=" CA VAL B 426 " pdb=" C VAL B 426 " ideal model delta sigma weight residual 108.11 116.08 -7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" N VAL C 426 " pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 108.11 114.91 -6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" CA CYS A 258 " pdb=" CB CYS A 258 " pdb=" SG CYS A 258 " ideal model delta sigma weight residual 114.40 125.44 -11.04 2.30e+00 1.89e-01 2.30e+01 angle pdb=" N LYS B 625 " pdb=" CA LYS B 625 " pdb=" C LYS B 625 " ideal model delta sigma weight residual 113.23 107.73 5.50 1.22e+00 6.72e-01 2.03e+01 angle pdb=" C CYS A 592 " pdb=" N GLU A 593 " pdb=" CA GLU A 593 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 ... (remaining 30766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11729 17.99 - 35.99: 1298 35.99 - 53.98: 345 53.98 - 71.98: 45 71.98 - 89.97: 20 Dihedral angle restraints: 13437 sinusoidal: 5345 harmonic: 8092 Sorted by residual: dihedral pdb=" CB CYS C 693 " pdb=" SG CYS C 693 " pdb=" SG CYS C 713 " pdb=" CB CYS C 713 " ideal model delta sinusoidal sigma weight residual -86.00 0.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C 398 " pdb=" SG CYS C 398 " pdb=" SG CYS C 462 " pdb=" CB CYS C 462 " ideal model delta sinusoidal sigma weight residual 93.00 177.72 -84.72 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 516 " pdb=" SG CYS C 516 " pdb=" SG CYS C 577 " pdb=" CB CYS C 577 " ideal model delta sinusoidal sigma weight residual 93.00 171.82 -78.82 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 13434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2497 0.045 - 0.090: 579 0.090 - 0.135: 173 0.135 - 0.180: 6 0.180 - 0.224: 1 Chirality restraints: 3256 Sorted by residual: chirality pdb=" CG LEU E 69 " pdb=" CB LEU E 69 " pdb=" CD1 LEU E 69 " pdb=" CD2 LEU E 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLN C 686 " pdb=" N GLN C 686 " pdb=" C GLN C 686 " pdb=" CB GLN C 686 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CG LEU A 519 " pdb=" CB LEU A 519 " pdb=" CD1 LEU A 519 " pdb=" CD2 LEU A 519 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 3253 not shown) Planarity restraints: 4018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 847 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.66e+00 pdb=" CG TRP C 847 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 847 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 847 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP C 847 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 847 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 847 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 847 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 847 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 847 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 898 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 899 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 424 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C TYR A 424 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR A 424 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 425 " 0.012 2.00e-02 2.50e+03 ... (remaining 4015 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 527 2.66 - 3.22: 22254 3.22 - 3.78: 35447 3.78 - 4.34: 46478 4.34 - 4.90: 73033 Nonbonded interactions: 177739 Sorted by model distance: nonbonded pdb=" O ASP B 891 " pdb=" OG SER B 907 " model vdw 2.101 3.040 nonbonded pdb=" NH2 ARG A 198 " pdb=" O ASN A 231 " model vdw 2.104 3.120 nonbonded pdb=" O SER B 423 " pdb=" OG1 THR B 471 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP D 7 " pdb=" OG SER D 125 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP B 926 " pdb=" N ASN B 927 " model vdw 2.165 3.120 ... (remaining 177734 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 263 through 1205) selection = (chain 'B' and resid 263 through 1205) selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.840 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.299 22772 Z= 0.165 Angle : 0.651 11.039 30953 Z= 0.352 Chirality : 0.042 0.224 3256 Planarity : 0.004 0.053 4018 Dihedral : 15.487 89.969 8008 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.02 % Allowed : 15.68 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.65 (0.15), residues: 2886 helix: 0.80 (0.22), residues: 522 sheet: -1.05 (0.34), residues: 233 loop : -0.70 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 517 TYR 0.019 0.002 TYR F 287 PHE 0.014 0.002 PHE C 842 TRP 0.039 0.002 TRP C 847 HIS 0.013 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00353 (22679) covalent geometry : angle 0.64896 (30771) SS BOND : bond 0.00267 ( 91) SS BOND : angle 0.92378 ( 182) hydrogen bonds : bond 0.25511 ( 633) hydrogen bonds : angle 8.88325 ( 1839) Misc. bond : bond 0.21176 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5692 (tmm) cc_final: 0.5400 (tmm) REVERT: A 188 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: A 427 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: A 649 MET cc_start: 0.6208 (ttt) cc_final: 0.5615 (tpp) REVERT: A 754 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7693 (t-90) REVERT: B 649 MET cc_start: 0.8133 (ptt) cc_final: 0.7483 (ptt) REVERT: B 659 MET cc_start: 0.8604 (tmm) cc_final: 0.8183 (tmm) REVERT: B 914 LEU cc_start: 0.9030 (tp) cc_final: 0.8747 (tt) REVERT: C 509 LEU cc_start: 0.8875 (pt) cc_final: 0.8475 (mt) REVERT: C 583 ILE cc_start: 0.8578 (mm) cc_final: 0.8319 (mm) REVERT: E 20 ASN cc_start: 0.8479 (p0) cc_final: 0.8071 (p0) REVERT: E 86 PHE cc_start: 0.7537 (m-80) cc_final: 0.6900 (m-80) REVERT: E 100 ASP cc_start: 0.8888 (t70) cc_final: 0.8645 (t70) REVERT: E 101 PRO cc_start: 0.8933 (Cg_exo) cc_final: 0.8585 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7417 (mp0) cc_final: 0.7176 (mp0) REVERT: E 104 PHE cc_start: 0.8364 (m-80) cc_final: 0.8020 (m-80) REVERT: F 204 MET cc_start: 0.8373 (tmm) cc_final: 0.8069 (tmm) REVERT: F 218 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7368 (tpp80) REVERT: F 284 MET cc_start: 0.4328 (ppp) cc_final: 0.3963 (ppp) REVERT: F 330 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6460 (p90) outliers start: 48 outliers final: 35 residues processed: 259 average time/residue: 0.1389 time to fit residues: 59.1142 Evaluate side-chains 250 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 475 HIS ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 754 HIS F 123 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.095930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081736 restraints weight = 92923.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.082771 restraints weight = 65297.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.083741 restraints weight = 48270.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084033 restraints weight = 41047.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084004 restraints weight = 37125.022| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 22772 Z= 0.167 Angle : 0.623 9.624 30953 Z= 0.329 Chirality : 0.043 0.169 3256 Planarity : 0.004 0.050 4018 Dihedral : 7.024 83.574 3152 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 2.78 % Allowed : 16.39 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.57 (0.15), residues: 2886 helix: 1.21 (0.23), residues: 546 sheet: -0.83 (0.29), residues: 304 loop : -0.78 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 374 TYR 0.023 0.002 TYR F 330 PHE 0.012 0.001 PHE F 280 TRP 0.019 0.001 TRP B 450 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00373 (22679) covalent geometry : angle 0.62070 (30771) SS BOND : bond 0.00317 ( 91) SS BOND : angle 0.95789 ( 182) hydrogen bonds : bond 0.04575 ( 633) hydrogen bonds : angle 5.83227 ( 1839) Misc. bond : bond 0.18265 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7501 (t0) cc_final: 0.7094 (p0) REVERT: A 188 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: A 339 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: A 649 MET cc_start: 0.5826 (ttt) cc_final: 0.5215 (tpp) REVERT: A 688 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: A 754 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7902 (t-90) REVERT: A 813 ASP cc_start: 0.6265 (OUTLIER) cc_final: 0.6056 (m-30) REVERT: B 649 MET cc_start: 0.7809 (ptt) cc_final: 0.7275 (ptt) REVERT: B 914 LEU cc_start: 0.8925 (tp) cc_final: 0.8595 (tt) REVERT: C 318 ARG cc_start: 0.7132 (ppt170) cc_final: 0.6691 (ptt90) REVERT: C 612 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: C 876 ASN cc_start: 0.7939 (p0) cc_final: 0.7587 (p0) REVERT: C 970 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8522 (tp) REVERT: D 76 ASP cc_start: 0.7740 (t0) cc_final: 0.6783 (t0) REVERT: E 20 ASN cc_start: 0.8604 (p0) cc_final: 0.8077 (p0) REVERT: E 101 PRO cc_start: 0.8833 (Cg_exo) cc_final: 0.8542 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7640 (mp0) cc_final: 0.7322 (mp0) REVERT: E 118 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7692 (m-70) REVERT: F 218 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7901 (tpp-160) REVERT: F 284 MET cc_start: 0.4627 (ppp) cc_final: 0.4375 (ppp) REVERT: F 319 ASP cc_start: 0.7733 (p0) cc_final: 0.7389 (p0) REVERT: F 330 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6533 (p90) outliers start: 66 outliers final: 31 residues processed: 294 average time/residue: 0.1358 time to fit residues: 65.4791 Evaluate side-chains 253 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 12 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 286 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN B 495 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 754 HIS C 773 HIS F 123 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.082808 restraints weight = 92656.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084273 restraints weight = 63022.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085567 restraints weight = 46627.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085764 restraints weight = 38708.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.085797 restraints weight = 33253.116| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 22772 Z= 0.122 Angle : 0.578 8.389 30953 Z= 0.302 Chirality : 0.042 0.162 3256 Planarity : 0.004 0.054 4018 Dihedral : 6.241 82.447 3105 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 3.62 % Allowed : 17.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.51 (0.15), residues: 2886 helix: 1.35 (0.23), residues: 545 sheet: -0.84 (0.30), residues: 297 loop : -0.76 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 825 TYR 0.021 0.001 TYR F 330 PHE 0.034 0.001 PHE E 104 TRP 0.028 0.001 TRP C 847 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00275 (22679) covalent geometry : angle 0.57694 (30771) SS BOND : bond 0.00319 ( 91) SS BOND : angle 0.79819 ( 182) hydrogen bonds : bond 0.03752 ( 633) hydrogen bonds : angle 5.27316 ( 1839) Misc. bond : bond 0.12082 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: A 339 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: A 754 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7857 (t-90) REVERT: B 649 MET cc_start: 0.7853 (ptt) cc_final: 0.7238 (ptt) REVERT: B 659 MET cc_start: 0.8607 (tmm) cc_final: 0.8225 (tmm) REVERT: B 914 LEU cc_start: 0.8818 (tp) cc_final: 0.8598 (tt) REVERT: B 927 ASN cc_start: 0.8373 (t0) cc_final: 0.8150 (t0) REVERT: C 280 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6479 (pm20) REVERT: C 295 TRP cc_start: 0.1944 (OUTLIER) cc_final: 0.0875 (t-100) REVERT: C 373 LEU cc_start: 0.8934 (tt) cc_final: 0.8712 (tp) REVERT: C 564 GLU cc_start: 0.8332 (mt-10) cc_final: 0.6944 (pp20) REVERT: C 612 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7680 (m-10) REVERT: C 840 GLU cc_start: 0.5703 (mp0) cc_final: 0.5298 (mm-30) REVERT: D 76 ASP cc_start: 0.7713 (t0) cc_final: 0.6718 (t0) REVERT: D 141 TYR cc_start: 0.7802 (t80) cc_final: 0.7255 (t80) REVERT: E 8 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7648 (mt-10) REVERT: E 20 ASN cc_start: 0.8538 (p0) cc_final: 0.8115 (p0) REVERT: E 100 ASP cc_start: 0.8905 (t70) cc_final: 0.8664 (t70) REVERT: E 101 PRO cc_start: 0.8653 (Cg_exo) cc_final: 0.8255 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7528 (mp0) cc_final: 0.7168 (mp0) REVERT: E 104 PHE cc_start: 0.8209 (m-80) cc_final: 0.7999 (m-80) REVERT: E 118 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7408 (m170) REVERT: E 145 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6626 (tptt) REVERT: F 204 MET cc_start: 0.8502 (tmm) cc_final: 0.8222 (tmm) REVERT: F 218 ARG cc_start: 0.8091 (tpp-160) cc_final: 0.7839 (tpp-160) REVERT: F 293 TYR cc_start: 0.8425 (m-10) cc_final: 0.8195 (m-10) REVERT: F 330 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6484 (p90) outliers start: 86 outliers final: 41 residues processed: 310 average time/residue: 0.1360 time to fit residues: 69.5969 Evaluate side-chains 273 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 128 optimal weight: 0.0570 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 0.0470 chunk 161 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS F 136 GLN F 144 ASN F 272 GLN ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082281 restraints weight = 92658.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.083706 restraints weight = 61494.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.084630 restraints weight = 46611.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085321 restraints weight = 38732.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.085634 restraints weight = 34090.802| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 22772 Z= 0.122 Angle : 0.571 8.444 30953 Z= 0.296 Chirality : 0.042 0.156 3256 Planarity : 0.004 0.054 4018 Dihedral : 6.077 81.590 3100 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 3.79 % Allowed : 18.50 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.49 (0.15), residues: 2886 helix: 1.38 (0.23), residues: 543 sheet: -0.84 (0.30), residues: 285 loop : -0.75 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 412 TYR 0.021 0.001 TYR F 330 PHE 0.025 0.001 PHE E 104 TRP 0.019 0.001 TRP C 612 HIS 0.011 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00277 (22679) covalent geometry : angle 0.56978 (30771) SS BOND : bond 0.00253 ( 91) SS BOND : angle 0.68827 ( 182) hydrogen bonds : bond 0.03341 ( 633) hydrogen bonds : angle 5.00709 ( 1839) Misc. bond : bond 0.10056 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 241 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: A 339 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: A 649 MET cc_start: 0.6388 (tpp) cc_final: 0.5417 (tpp) REVERT: A 754 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: B 649 MET cc_start: 0.7982 (ptt) cc_final: 0.7167 (ptt) REVERT: B 914 LEU cc_start: 0.8806 (tp) cc_final: 0.8598 (tt) REVERT: B 927 ASN cc_start: 0.8438 (t0) cc_final: 0.8161 (t0) REVERT: C 280 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6473 (pm20) REVERT: C 295 TRP cc_start: 0.2038 (OUTLIER) cc_final: 0.1031 (t-100) REVERT: C 318 ARG cc_start: 0.7103 (ppt170) cc_final: 0.6773 (ptt90) REVERT: C 373 LEU cc_start: 0.8917 (tt) cc_final: 0.8716 (tp) REVERT: C 564 GLU cc_start: 0.8352 (mt-10) cc_final: 0.6931 (pp20) REVERT: C 612 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: D 76 ASP cc_start: 0.7745 (t0) cc_final: 0.6734 (t0) REVERT: D 141 TYR cc_start: 0.7816 (t80) cc_final: 0.7307 (t80) REVERT: E 8 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7723 (mt-10) REVERT: E 20 ASN cc_start: 0.8654 (p0) cc_final: 0.8305 (p0) REVERT: E 100 ASP cc_start: 0.8939 (t70) cc_final: 0.8564 (t70) REVERT: E 101 PRO cc_start: 0.8730 (Cg_exo) cc_final: 0.8357 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7517 (mp0) cc_final: 0.7108 (mp0) REVERT: E 104 PHE cc_start: 0.8236 (m-80) cc_final: 0.7924 (m-80) REVERT: E 118 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7433 (m-70) REVERT: F 218 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7831 (tpp-160) REVERT: F 284 MET cc_start: 0.4176 (ppp) cc_final: 0.3907 (ppp) REVERT: F 319 ASP cc_start: 0.8085 (p0) cc_final: 0.7617 (p0) outliers start: 90 outliers final: 62 residues processed: 304 average time/residue: 0.1243 time to fit residues: 63.0016 Evaluate side-chains 290 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 274 optimal weight: 0.0870 chunk 285 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.095773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081438 restraints weight = 92242.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082469 restraints weight = 64666.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.083869 restraints weight = 48201.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.083948 restraints weight = 40591.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.083964 restraints weight = 35804.875| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 22772 Z= 0.148 Angle : 0.587 8.887 30953 Z= 0.305 Chirality : 0.042 0.173 3256 Planarity : 0.004 0.054 4018 Dihedral : 6.097 81.399 3100 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 3.96 % Allowed : 19.47 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.57 (0.15), residues: 2886 helix: 1.41 (0.23), residues: 544 sheet: -0.97 (0.30), residues: 290 loop : -0.81 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.023 0.002 TYR F 330 PHE 0.016 0.001 PHE E 104 TRP 0.041 0.001 TRP C 847 HIS 0.011 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00339 (22679) covalent geometry : angle 0.58619 (30771) SS BOND : bond 0.00290 ( 91) SS BOND : angle 0.72601 ( 182) hydrogen bonds : bond 0.03307 ( 633) hydrogen bonds : angle 4.98359 ( 1839) Misc. bond : bond 0.13722 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 241 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 339 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: A 623 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8086 (tt0) REVERT: A 649 MET cc_start: 0.6361 (tpp) cc_final: 0.5345 (tpp) REVERT: A 721 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 754 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7851 (t-90) REVERT: B 649 MET cc_start: 0.8068 (ptt) cc_final: 0.7312 (ptt) REVERT: B 659 MET cc_start: 0.8679 (tmm) cc_final: 0.8432 (tmm) REVERT: B 914 LEU cc_start: 0.8822 (tp) cc_final: 0.8284 (tt) REVERT: B 927 ASN cc_start: 0.8434 (t0) cc_final: 0.8147 (t0) REVERT: C 280 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6486 (pm20) REVERT: C 295 TRP cc_start: 0.1948 (OUTLIER) cc_final: 0.0889 (t-100) REVERT: C 373 LEU cc_start: 0.8938 (tt) cc_final: 0.8725 (tp) REVERT: C 564 GLU cc_start: 0.8328 (mt-10) cc_final: 0.6788 (pp20) REVERT: C 612 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: C 649 MET cc_start: 0.8086 (ttp) cc_final: 0.7476 (mtp) REVERT: D 76 ASP cc_start: 0.7835 (t0) cc_final: 0.6727 (t0) REVERT: D 141 TYR cc_start: 0.7912 (t80) cc_final: 0.7450 (t80) REVERT: E 8 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 20 ASN cc_start: 0.8634 (p0) cc_final: 0.8311 (p0) REVERT: E 100 ASP cc_start: 0.8993 (t70) cc_final: 0.8512 (t70) REVERT: E 102 GLU cc_start: 0.7528 (mp0) cc_final: 0.7199 (mp0) REVERT: E 104 PHE cc_start: 0.8332 (m-80) cc_final: 0.7988 (m-80) REVERT: E 118 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7381 (m170) REVERT: F 218 ARG cc_start: 0.8195 (tpp-160) cc_final: 0.7867 (tpp-160) REVERT: F 247 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: F 284 MET cc_start: 0.4573 (ppp) cc_final: 0.4270 (ppp) REVERT: F 319 ASP cc_start: 0.8087 (p0) cc_final: 0.7745 (p0) outliers start: 94 outliers final: 70 residues processed: 308 average time/residue: 0.1254 time to fit residues: 64.6808 Evaluate side-chains 301 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 223 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 201 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 161 optimal weight: 0.0070 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080367 restraints weight = 92985.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081325 restraints weight = 64466.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.083071 restraints weight = 48271.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083150 restraints weight = 39149.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083190 restraints weight = 34361.091| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 22772 Z= 0.163 Angle : 0.596 10.208 30953 Z= 0.310 Chirality : 0.042 0.156 3256 Planarity : 0.004 0.055 4018 Dihedral : 6.187 81.389 3100 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 4.38 % Allowed : 19.64 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.65 (0.15), residues: 2886 helix: 1.39 (0.23), residues: 545 sheet: -1.16 (0.30), residues: 280 loop : -0.87 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 825 TYR 0.024 0.002 TYR F 330 PHE 0.014 0.002 PHE A 984 TRP 0.026 0.002 TRP C 847 HIS 0.012 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00371 (22679) covalent geometry : angle 0.59465 (30771) SS BOND : bond 0.00319 ( 91) SS BOND : angle 0.78170 ( 182) hydrogen bonds : bond 0.03280 ( 633) hydrogen bonds : angle 4.95774 ( 1839) Misc. bond : bond 0.16205 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 228 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: A 339 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: A 546 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 623 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8149 (tt0) REVERT: A 649 MET cc_start: 0.6296 (tpp) cc_final: 0.5256 (tpp) REVERT: A 754 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7858 (t-90) REVERT: A 927 ASN cc_start: 0.7877 (t0) cc_final: 0.7658 (t0) REVERT: B 649 MET cc_start: 0.7969 (ptt) cc_final: 0.7227 (ptt) REVERT: B 927 ASN cc_start: 0.8488 (t0) cc_final: 0.8179 (t0) REVERT: C 295 TRP cc_start: 0.1894 (OUTLIER) cc_final: 0.1042 (t-100) REVERT: C 564 GLU cc_start: 0.8358 (mt-10) cc_final: 0.6911 (pp20) REVERT: C 649 MET cc_start: 0.7957 (ttp) cc_final: 0.7494 (mtp) REVERT: D 74 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9141 (t) REVERT: D 76 ASP cc_start: 0.7968 (t0) cc_final: 0.6853 (t0) REVERT: E 8 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7781 (mt-10) REVERT: E 20 ASN cc_start: 0.8545 (p0) cc_final: 0.8217 (p0) REVERT: E 91 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7817 (mm-30) REVERT: E 104 PHE cc_start: 0.8344 (m-80) cc_final: 0.7966 (m-80) REVERT: E 118 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7395 (m170) REVERT: F 218 ARG cc_start: 0.8206 (tpp-160) cc_final: 0.7491 (tpp80) REVERT: F 247 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: F 284 MET cc_start: 0.4797 (ppp) cc_final: 0.4441 (ppp) REVERT: F 319 ASP cc_start: 0.8142 (p0) cc_final: 0.7801 (p0) outliers start: 104 outliers final: 75 residues processed: 301 average time/residue: 0.1271 time to fit residues: 64.3668 Evaluate side-chains 301 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 219 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083211 restraints weight = 95726.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084590 restraints weight = 65687.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084882 restraints weight = 45510.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.085101 restraints weight = 42141.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.085131 restraints weight = 38947.451| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 22772 Z= 0.118 Angle : 0.585 9.332 30953 Z= 0.302 Chirality : 0.042 0.163 3256 Planarity : 0.004 0.063 4018 Dihedral : 6.046 81.083 3096 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 3.79 % Allowed : 20.69 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.58 (0.15), residues: 2886 helix: 1.54 (0.23), residues: 545 sheet: -1.03 (0.30), residues: 292 loop : -0.86 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 825 TYR 0.021 0.001 TYR F 330 PHE 0.014 0.001 PHE A 984 TRP 0.021 0.001 TRP F 310 HIS 0.012 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00275 (22679) covalent geometry : angle 0.58291 (30771) SS BOND : bond 0.00229 ( 91) SS BOND : angle 0.83663 ( 182) hydrogen bonds : bond 0.03007 ( 633) hydrogen bonds : angle 4.76381 ( 1839) Misc. bond : bond 0.10117 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 230 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5893 (tmm) cc_final: 0.5578 (tmm) REVERT: A 188 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: A 546 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 597 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6289 (pm20) REVERT: A 623 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8105 (tt0) REVERT: A 649 MET cc_start: 0.6236 (tpp) cc_final: 0.5144 (tpp) REVERT: A 754 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7783 (t-90) REVERT: B 649 MET cc_start: 0.7902 (ptt) cc_final: 0.7220 (ptt) REVERT: B 927 ASN cc_start: 0.8473 (t0) cc_final: 0.8168 (t0) REVERT: C 295 TRP cc_start: 0.1752 (OUTLIER) cc_final: 0.0688 (t-100) REVERT: C 318 ARG cc_start: 0.6982 (ppt170) cc_final: 0.6569 (ptt90) REVERT: C 564 GLU cc_start: 0.8447 (mt-10) cc_final: 0.6953 (pp20) REVERT: C 649 MET cc_start: 0.8020 (ttp) cc_final: 0.7525 (mtp) REVERT: D 76 ASP cc_start: 0.7820 (t0) cc_final: 0.6747 (t0) REVERT: D 117 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7726 (mm-30) REVERT: E 8 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7757 (mt-10) REVERT: E 20 ASN cc_start: 0.8627 (p0) cc_final: 0.7914 (p0) REVERT: E 100 ASP cc_start: 0.8943 (t70) cc_final: 0.8520 (t70) REVERT: E 102 GLU cc_start: 0.7407 (mp0) cc_final: 0.7153 (mp0) REVERT: E 104 PHE cc_start: 0.8292 (m-80) cc_final: 0.7958 (m-80) REVERT: E 118 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7305 (m170) REVERT: F 218 ARG cc_start: 0.8138 (tpp-160) cc_final: 0.7501 (tpp80) REVERT: F 284 MET cc_start: 0.4557 (ppp) cc_final: 0.4280 (ppp) REVERT: F 319 ASP cc_start: 0.8029 (p0) cc_final: 0.7748 (p0) outliers start: 90 outliers final: 64 residues processed: 296 average time/residue: 0.1222 time to fit residues: 60.1860 Evaluate side-chains 287 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 203 optimal weight: 4.9990 chunk 235 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 128 optimal weight: 0.0770 chunk 174 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.094255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079626 restraints weight = 92558.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081122 restraints weight = 64911.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081518 restraints weight = 46507.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081809 restraints weight = 43626.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.081871 restraints weight = 40458.303| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 22772 Z= 0.170 Angle : 0.613 9.152 30953 Z= 0.318 Chirality : 0.042 0.184 3256 Planarity : 0.004 0.055 4018 Dihedral : 6.226 81.704 3096 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 4.13 % Allowed : 20.94 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 2886 helix: 1.48 (0.23), residues: 545 sheet: -1.17 (0.29), residues: 300 loop : -0.92 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 584 TYR 0.024 0.002 TYR F 330 PHE 0.014 0.002 PHE A 979 TRP 0.020 0.002 TRP F 310 HIS 0.013 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00390 (22679) covalent geometry : angle 0.61138 (30771) SS BOND : bond 0.00328 ( 91) SS BOND : angle 0.87628 ( 182) hydrogen bonds : bond 0.03197 ( 633) hydrogen bonds : angle 4.88681 ( 1839) Misc. bond : bond 0.17254 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 214 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5905 (tmm) cc_final: 0.5607 (tmm) REVERT: A 188 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: A 546 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 597 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: A 623 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8105 (tt0) REVERT: A 649 MET cc_start: 0.6335 (tpp) cc_final: 0.5232 (tpp) REVERT: A 754 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7842 (t-90) REVERT: B 649 MET cc_start: 0.8010 (ptt) cc_final: 0.7267 (ptt) REVERT: B 927 ASN cc_start: 0.8484 (t0) cc_final: 0.8198 (t0) REVERT: C 295 TRP cc_start: 0.2039 (OUTLIER) cc_final: 0.1009 (t-100) REVERT: C 564 GLU cc_start: 0.8421 (mt-10) cc_final: 0.6950 (pp20) REVERT: C 583 ILE cc_start: 0.8521 (mm) cc_final: 0.8310 (mm) REVERT: C 649 MET cc_start: 0.8051 (ttp) cc_final: 0.7748 (mtp) REVERT: D 76 ASP cc_start: 0.7966 (t0) cc_final: 0.6899 (t0) REVERT: E 8 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7782 (mt-10) REVERT: E 20 ASN cc_start: 0.8585 (p0) cc_final: 0.8105 (p0) REVERT: E 100 ASP cc_start: 0.9047 (t70) cc_final: 0.8562 (t70) REVERT: E 104 PHE cc_start: 0.8392 (m-80) cc_final: 0.8000 (m-80) REVERT: E 118 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7352 (m170) REVERT: F 218 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7559 (tpp80) REVERT: F 247 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: F 284 MET cc_start: 0.4916 (ppp) cc_final: 0.4557 (ppp) REVERT: F 319 ASP cc_start: 0.8125 (p0) cc_final: 0.7677 (p0) REVERT: F 336 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7267 (pp) outliers start: 98 outliers final: 79 residues processed: 285 average time/residue: 0.1230 time to fit residues: 58.3276 Evaluate side-chains 297 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 211 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 871 ASP Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 932 GLN ** C 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.091936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.077401 restraints weight = 92728.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078430 restraints weight = 63829.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079697 restraints weight = 48963.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079808 restraints weight = 43248.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079824 restraints weight = 37142.869| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 22772 Z= 0.252 Angle : 0.702 11.012 30953 Z= 0.367 Chirality : 0.045 0.173 3256 Planarity : 0.005 0.093 4018 Dihedral : 6.732 84.025 3096 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 4.47 % Allowed : 20.90 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.99 (0.15), residues: 2886 helix: 1.18 (0.23), residues: 546 sheet: -1.35 (0.28), residues: 301 loop : -1.12 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 647 TYR 0.028 0.002 TYR F 330 PHE 0.018 0.002 PHE D 99 TRP 0.024 0.002 TRP B1013 HIS 0.012 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00565 (22679) covalent geometry : angle 0.69923 (30771) SS BOND : bond 0.00484 ( 91) SS BOND : angle 1.01758 ( 182) hydrogen bonds : bond 0.03722 ( 633) hydrogen bonds : angle 5.24086 ( 1839) Misc. bond : bond 0.32923 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 213 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5919 (tmm) cc_final: 0.5654 (tmm) REVERT: A 188 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: A 477 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 495 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.4170 (t70) REVERT: A 546 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 623 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8091 (tt0) REVERT: A 649 MET cc_start: 0.6414 (tpp) cc_final: 0.5379 (tpp) REVERT: A 754 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7860 (t-90) REVERT: A 927 ASN cc_start: 0.7708 (t0) cc_final: 0.6582 (p0) REVERT: B 649 MET cc_start: 0.8063 (ptt) cc_final: 0.7288 (ptt) REVERT: B 901 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 927 ASN cc_start: 0.8545 (t0) cc_final: 0.8294 (t0) REVERT: C 537 ASN cc_start: 0.8393 (p0) cc_final: 0.8040 (p0) REVERT: C 564 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7097 (pp20) REVERT: C 649 MET cc_start: 0.8170 (ttp) cc_final: 0.7907 (mtp) REVERT: C 811 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (pptt) REVERT: C 941 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5210 (ptp-170) REVERT: E 8 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7760 (mt-10) REVERT: E 20 ASN cc_start: 0.8492 (p0) cc_final: 0.8096 (p0) REVERT: E 104 PHE cc_start: 0.8417 (m-80) cc_final: 0.8050 (m-80) REVERT: E 118 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7476 (m-70) REVERT: F 218 ARG cc_start: 0.8408 (tpp-160) cc_final: 0.7667 (tpp80) REVERT: F 247 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: F 284 MET cc_start: 0.5494 (ppp) cc_final: 0.5034 (ppp) REVERT: F 319 ASP cc_start: 0.8206 (p0) cc_final: 0.7857 (p0) outliers start: 106 outliers final: 81 residues processed: 290 average time/residue: 0.1339 time to fit residues: 64.2611 Evaluate side-chains 296 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 207 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 932 GLN Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 941 ARG Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 984 PHE Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 269 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 217 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 964 GLN F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.094525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080429 restraints weight = 92542.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.081327 restraints weight = 64890.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081472 restraints weight = 49345.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081740 restraints weight = 49217.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081863 restraints weight = 43971.416| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 22772 Z= 0.137 Angle : 0.625 8.912 30953 Z= 0.323 Chirality : 0.043 0.173 3256 Planarity : 0.004 0.082 4018 Dihedral : 6.398 83.808 3096 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 3.67 % Allowed : 21.66 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.81 (0.15), residues: 2886 helix: 1.40 (0.23), residues: 549 sheet: -1.20 (0.29), residues: 297 loop : -1.03 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 647 TYR 0.022 0.002 TYR D 141 PHE 0.026 0.002 PHE A 984 TRP 0.064 0.001 TRP F 310 HIS 0.011 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00318 (22679) covalent geometry : angle 0.62408 (30771) SS BOND : bond 0.00262 ( 91) SS BOND : angle 0.77977 ( 182) hydrogen bonds : bond 0.03212 ( 633) hydrogen bonds : angle 4.90260 ( 1839) Misc. bond : bond 0.15765 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5893 (tmm) cc_final: 0.5634 (tmm) REVERT: A 546 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 623 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8005 (tt0) REVERT: A 649 MET cc_start: 0.6297 (tpp) cc_final: 0.5227 (tpp) REVERT: A 754 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7799 (t-90) REVERT: A 927 ASN cc_start: 0.7662 (t0) cc_final: 0.6647 (p0) REVERT: B 649 MET cc_start: 0.8023 (ptt) cc_final: 0.7336 (ptt) REVERT: B 659 MET cc_start: 0.8620 (tmm) cc_final: 0.8324 (tmm) REVERT: B 927 ASN cc_start: 0.8514 (t0) cc_final: 0.8228 (t0) REVERT: C 537 ASN cc_start: 0.8261 (p0) cc_final: 0.7880 (p0) REVERT: C 564 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7006 (pp20) REVERT: C 649 MET cc_start: 0.8095 (ttp) cc_final: 0.7832 (mtp) REVERT: E 20 ASN cc_start: 0.8536 (p0) cc_final: 0.8104 (p0) REVERT: E 100 ASP cc_start: 0.9127 (t70) cc_final: 0.8565 (t70) REVERT: E 102 GLU cc_start: 0.7396 (mp0) cc_final: 0.7063 (mp0) REVERT: E 104 PHE cc_start: 0.8397 (m-80) cc_final: 0.8058 (m-80) REVERT: E 118 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7391 (m-70) REVERT: F 218 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7871 (tpp-160) REVERT: F 247 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: F 284 MET cc_start: 0.4916 (ppp) cc_final: 0.4667 (ppp) REVERT: F 319 ASP cc_start: 0.8022 (p0) cc_final: 0.7552 (p0) outliers start: 87 outliers final: 68 residues processed: 285 average time/residue: 0.1280 time to fit residues: 59.9044 Evaluate side-chains 282 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 984 PHE Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 239 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 932 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.093378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.079245 restraints weight = 92776.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080060 restraints weight = 65439.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.080884 restraints weight = 48749.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081025 restraints weight = 44707.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081126 restraints weight = 40576.369| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 22772 Z= 0.181 Angle : 0.645 9.387 30953 Z= 0.336 Chirality : 0.043 0.178 3256 Planarity : 0.004 0.069 4018 Dihedral : 6.402 83.728 3094 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 3.92 % Allowed : 21.49 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.87 (0.15), residues: 2886 helix: 1.35 (0.23), residues: 544 sheet: -1.24 (0.29), residues: 296 loop : -1.07 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 647 TYR 0.022 0.002 TYR F 330 PHE 0.031 0.002 PHE A 984 TRP 0.051 0.002 TRP F 310 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00414 (22679) covalent geometry : angle 0.64266 (30771) SS BOND : bond 0.00341 ( 91) SS BOND : angle 0.94481 ( 182) hydrogen bonds : bond 0.03340 ( 633) hydrogen bonds : angle 4.98623 ( 1839) Misc. bond : bond 0.21185 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.71 seconds wall clock time: 54 minutes 15.42 seconds (3255.42 seconds total)