Starting phenix.real_space_refine on Fri Sep 19 01:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.map" model { file = "/net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7k_23215/09_2025/7l7k_23215.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 14136 2.51 5 N 3675 2.21 5 O 4211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.02s 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: 22124 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7370 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 5, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 6, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 7384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7384 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 7, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 170 Chain: "A" Number of atoms: 7370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7370 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 5, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 6, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 172 Time building chain proxies: 5.89, per 1000 atoms: 0.27 Number of scatterers: 22124 At special positions: 0 Unit cell: (133.56, 127.68, 173.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4211 8.00 N 3675 7.00 C 14136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 43 sheets defined 24.3% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 296 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.873A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.923A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.865A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.857A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.693A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.635A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.302A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.813A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.619A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.109A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.762A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.649A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.158A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.616A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.622A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.199A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.754A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.041A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.178A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.654A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.794A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.512A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.699A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.874A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.678A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.548A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.253A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.807A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.797A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.248A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.977A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.522A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.644A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 326 removed outlier: 6.671A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 665 through 667 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TRP B1102 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B1113 " --> pdb=" O TRP B1102 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B1106 " --> pdb=" O PHE B1109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.226A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AC1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.578A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 326 through 328 removed outlier: 4.987A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.697A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N CYS C 432 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 378 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.945A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.161A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.423A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.423A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.637A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.046A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.981A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AD6, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.740A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.028A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.586A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.184A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7164 1.35 - 1.48: 5781 1.48 - 1.60: 9523 1.60 - 1.73: 0 1.73 - 1.86: 126 Bond restraints: 22594 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.331 1.352 -0.020 1.21e-02 6.83e+03 2.80e+00 bond pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 1.808 1.856 -0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CA GLN B 804 " pdb=" C GLN B 804 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.82e+00 bond pdb=" N PRO C 272 " pdb=" CA PRO C 272 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.37e+00 bond pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.23e+00 ... (remaining 22589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 30548 2.55 - 5.10: 231 5.10 - 7.65: 12 7.65 - 10.20: 2 10.20 - 12.74: 2 Bond angle restraints: 30795 Sorted by residual: angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.71 109.64 4.07 9.50e-01 1.11e+00 1.84e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 111.62 108.98 2.64 7.90e-01 1.60e+00 1.12e+01 angle pdb=" N ILE B 805 " pdb=" CA ILE B 805 " pdb=" C ILE B 805 " ideal model delta sigma weight residual 112.12 109.47 2.65 8.40e-01 1.42e+00 9.99e+00 angle pdb=" N GLY B 404 " pdb=" CA GLY B 404 " pdb=" C GLY B 404 " ideal model delta sigma weight residual 114.66 110.98 3.68 1.24e+00 6.50e-01 8.82e+00 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" O GLY A 89 " ideal model delta sigma weight residual 122.29 119.94 2.35 8.10e-01 1.52e+00 8.44e+00 ... (remaining 30790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11829 17.81 - 35.62: 1235 35.62 - 53.43: 275 53.43 - 71.24: 62 71.24 - 89.05: 26 Dihedral angle restraints: 13427 sinusoidal: 4943 harmonic: 8484 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -30.12 -55.88 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -33.04 -52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -41.26 -44.74 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 13424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2356 0.038 - 0.076: 862 0.076 - 0.113: 318 0.113 - 0.151: 56 0.151 - 0.189: 8 Chirality restraints: 3600 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 3597 not shown) Planarity restraints: 3984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1056 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO C1057 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C1057 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1057 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1056 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B1057 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1057 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1057 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1056 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A1057 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " -0.026 5.00e-02 4.00e+02 ... (remaining 3981 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1069 2.72 - 3.26: 21376 3.26 - 3.81: 33473 3.81 - 4.35: 41055 4.35 - 4.90: 72081 Nonbonded interactions: 169054 Sorted by model distance: nonbonded pdb=" OG1 THR C1006 " pdb=" OE1 GLN A1005 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.171 3.040 nonbonded pdb=" OE1 GLN B1005 " pdb=" OG1 THR A1006 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR B1006 " pdb=" OE1 GLN C1005 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN B 978 " pdb=" OG1 THR A 547 " model vdw 2.185 3.040 ... (remaining 169049 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 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 189 or (resid 190 and (name N or name CA or name C or name O \ or name CB )) or resid 191 through 471 or resid 487 through 498 or resid 503 th \ rough 620 or resid 641 through 1146)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 189 or (resid 190 and (name N or name CA or name C or name O \ or name CB )) or resid 191 through 471 or resid 487 through 498 or resid 503 th \ rough 620 or resid 641 through 1146)) selection = (chain 'C' and (resid 27 through 66 or resid 81 through 95 or (resid 99 through \ 100 and (name N or name CA or name C or name O or name CB )) or resid 101 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 209 or resid 217 through 243 or resid 264 through 344 or (resi \ d 345 through 346 and (name N or name CA or name C or name O or name CB )) or re \ sid 347 through 1146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22629 Z= 0.157 Angle : 0.621 12.745 30865 Z= 0.349 Chirality : 0.045 0.189 3600 Planarity : 0.004 0.063 3984 Dihedral : 15.728 89.050 7826 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 7.06 % Allowed : 18.78 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.13), residues: 2835 helix: -1.33 (0.17), residues: 633 sheet: -1.89 (0.18), residues: 632 loop : -3.53 (0.12), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE B 541 TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00330 (22594) covalent geometry : angle 0.61648 (30795) SS BOND : bond 0.00494 ( 35) SS BOND : angle 1.67214 ( 70) hydrogen bonds : bond 0.12395 ( 870) hydrogen bonds : angle 6.84486 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 217 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: C 1034 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 1130 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8860 (tp) outliers start: 168 outliers final: 122 residues processed: 369 average time/residue: 0.1532 time to fit residues: 88.9979 Evaluate side-chains 274 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 149 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 122 ASN B 125 ASN B 280 ASN B 317 ASN B 536 ASN B 544 ASN B 563 GLN B 644 GLN B 658 ASN B 703 ASN B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 965 GLN B1002 GLN B1005 GLN B1010 GLN B1101 HIS C 66 HIS C 125 ASN C 211 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 536 ASN C 644 GLN C 751 ASN C 755 GLN C 901 GLN C 919 ASN C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS C1106 GLN A 61 ASN A 280 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 542 ASN A 544 ASN A 644 GLN A 755 GLN A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1010 GLN A1101 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.145885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111943 restraints weight = 38788.146| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.85 r_work: 0.3410 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 22629 Z= 0.345 Angle : 0.783 18.836 30865 Z= 0.402 Chirality : 0.052 0.201 3600 Planarity : 0.006 0.065 3984 Dihedral : 9.730 59.911 3248 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 10.17 % Allowed : 19.71 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.13), residues: 2835 helix: -0.46 (0.20), residues: 614 sheet: -1.68 (0.18), residues: 647 loop : -3.30 (0.12), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.024 0.002 TYR C1067 PHE 0.021 0.002 PHE B 541 TRP 0.030 0.003 TRP C 104 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00827 (22594) covalent geometry : angle 0.77723 (30795) SS BOND : bond 0.00627 ( 35) SS BOND : angle 2.15834 ( 70) hydrogen bonds : bond 0.07620 ( 870) hydrogen bonds : angle 5.95411 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 146 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7130 (mmm-85) REVERT: B 338 PHE cc_start: 0.5939 (m-80) cc_final: 0.5713 (m-80) REVERT: B 563 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.6190 (mm-40) REVERT: B 808 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6840 (p0) REVERT: C 611 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8411 (tp) REVERT: C 854 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.4679 (tmtt) REVERT: C 1072 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: C 1106 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: A 239 GLN cc_start: 0.6549 (tt0) cc_final: 0.6330 (tm-30) REVERT: A 269 TYR cc_start: 0.7721 (m-80) cc_final: 0.7403 (m-80) REVERT: A 430 THR cc_start: 0.3917 (OUTLIER) cc_final: 0.3296 (t) REVERT: A 1072 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8104 (pt0) outliers start: 242 outliers final: 174 residues processed: 367 average time/residue: 0.1386 time to fit residues: 83.9283 Evaluate side-chains 316 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 134 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN B 563 GLN B 658 ASN B 901 GLN B 969 ASN C 61 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.149729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123415 restraints weight = 38563.883| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.07 r_work: 0.3371 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22629 Z= 0.140 Angle : 0.598 16.122 30865 Z= 0.307 Chirality : 0.045 0.167 3600 Planarity : 0.005 0.056 3984 Dihedral : 8.356 59.683 3204 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 7.65 % Allowed : 22.18 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.14), residues: 2835 helix: 0.56 (0.21), residues: 616 sheet: -1.22 (0.19), residues: 630 loop : -2.82 (0.13), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.020 0.001 TYR C1067 PHE 0.012 0.001 PHE B 400 TRP 0.030 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00317 (22594) covalent geometry : angle 0.59418 (30795) SS BOND : bond 0.00595 ( 35) SS BOND : angle 1.61468 ( 70) hydrogen bonds : bond 0.05511 ( 870) hydrogen bonds : angle 5.35760 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 152 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ILE cc_start: 0.4080 (OUTLIER) cc_final: 0.3759 (mp) REVERT: B 269 TYR cc_start: 0.7882 (m-80) cc_final: 0.7320 (m-80) REVERT: B 425 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6513 (mt) REVERT: B 613 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: B 779 GLN cc_start: 0.7469 (tp40) cc_final: 0.7176 (tp40) REVERT: C 387 LEU cc_start: 0.8016 (mp) cc_final: 0.7660 (mt) REVERT: C 418 ILE cc_start: 0.5878 (mm) cc_final: 0.5583 (mm) REVERT: C 569 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7167 (mp) REVERT: A 269 TYR cc_start: 0.7759 (m-80) cc_final: 0.7422 (m-80) REVERT: A 613 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8016 (mt0) outliers start: 182 outliers final: 130 residues processed: 315 average time/residue: 0.1431 time to fit residues: 74.1273 Evaluate side-chains 269 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 134 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 44 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 280 optimal weight: 0.0980 chunk 249 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** A 422 ASN ** 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 = 0.4067 r_free = 0.4067 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113838 restraints weight = 38624.352| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.77 r_work: 0.3463 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22629 Z= 0.126 Angle : 0.568 14.797 30865 Z= 0.290 Chirality : 0.044 0.174 3600 Planarity : 0.004 0.053 3984 Dihedral : 7.635 59.016 3176 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 8.11 % Allowed : 21.34 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.15), residues: 2835 helix: 1.03 (0.22), residues: 615 sheet: -0.86 (0.20), residues: 599 loop : -2.51 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.019 0.001 TYR C1067 PHE 0.015 0.001 PHE B 541 TRP 0.021 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00282 (22594) covalent geometry : angle 0.56534 (30795) SS BOND : bond 0.00379 ( 35) SS BOND : angle 1.32609 ( 70) hydrogen bonds : bond 0.05085 ( 870) hydrogen bonds : angle 5.08967 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 159 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7831 (m-80) cc_final: 0.7213 (m-80) REVERT: B 611 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 1106 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: B 1113 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: B 1130 ILE cc_start: 0.9185 (mp) cc_final: 0.8963 (mt) REVERT: C 86 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6518 (t80) REVERT: C 132 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.4792 (pm20) REVERT: C 304 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8382 (tptp) REVERT: C 387 LEU cc_start: 0.7960 (mp) cc_final: 0.7691 (mt) REVERT: C 418 ILE cc_start: 0.5707 (mm) cc_final: 0.5430 (mm) REVERT: C 569 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7111 (mp) REVERT: C 611 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8524 (tp) REVERT: C 1034 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8831 (mp) REVERT: A 175 PHE cc_start: 0.1628 (OUTLIER) cc_final: 0.0589 (m-10) REVERT: A 269 TYR cc_start: 0.7797 (m-80) cc_final: 0.7424 (m-80) REVERT: A 430 THR cc_start: 0.3669 (OUTLIER) cc_final: 0.3162 (t) REVERT: A 613 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: A 957 GLN cc_start: 0.8530 (tp40) cc_final: 0.8205 (mm110) outliers start: 193 outliers final: 135 residues processed: 330 average time/residue: 0.1462 time to fit residues: 78.9992 Evaluate side-chains 282 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 135 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 222 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 225 optimal weight: 0.3980 chunk 203 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.150677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119707 restraints weight = 38361.011| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.58 r_work: 0.3508 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22629 Z= 0.119 Angle : 0.556 13.607 30865 Z= 0.283 Chirality : 0.044 0.159 3600 Planarity : 0.004 0.053 3984 Dihedral : 7.183 59.141 3160 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.85 % Allowed : 23.24 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.15), residues: 2835 helix: 1.30 (0.22), residues: 615 sheet: -0.65 (0.20), residues: 600 loop : -2.32 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.027 0.001 TYR C1067 PHE 0.025 0.001 PHE B 238 TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00267 (22594) covalent geometry : angle 0.55403 (30795) SS BOND : bond 0.00371 ( 35) SS BOND : angle 1.21421 ( 70) hydrogen bonds : bond 0.04757 ( 870) hydrogen bonds : angle 4.91415 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 151 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ARG cc_start: 0.6045 (mtt180) cc_final: 0.5746 (mtt90) REVERT: B 110 LEU cc_start: 0.4072 (tp) cc_final: 0.3717 (tt) REVERT: B 269 TYR cc_start: 0.7804 (m-80) cc_final: 0.7225 (m-80) REVERT: B 613 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: B 1113 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: B 1130 ILE cc_start: 0.9178 (mp) cc_final: 0.8960 (mt) REVERT: C 86 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6589 (t80) REVERT: C 132 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.5238 (pm20) REVERT: C 387 LEU cc_start: 0.7909 (mp) cc_final: 0.7678 (mt) REVERT: C 418 ILE cc_start: 0.5850 (mm) cc_final: 0.5562 (mm) REVERT: C 569 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7066 (mp) REVERT: C 611 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (tp) REVERT: C 1034 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 269 TYR cc_start: 0.7760 (m-80) cc_final: 0.7407 (m-80) REVERT: A 430 THR cc_start: 0.3621 (OUTLIER) cc_final: 0.3142 (t) REVERT: A 558 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7062 (ttmt) REVERT: A 957 GLN cc_start: 0.8428 (tp40) cc_final: 0.8128 (mm110) REVERT: A 1106 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7983 (pt0) outliers start: 163 outliers final: 126 residues processed: 299 average time/residue: 0.1340 time to fit residues: 65.7109 Evaluate side-chains 273 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 137 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 187 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 263 optimal weight: 0.0980 chunk 188 optimal weight: 0.5980 chunk 275 optimal weight: 1.9990 chunk 190 optimal weight: 0.0570 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 542 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 439 ASN A 506 GLN A1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118006 restraints weight = 38758.825| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.92 r_work: 0.3491 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22629 Z= 0.108 Angle : 0.535 12.584 30865 Z= 0.272 Chirality : 0.043 0.152 3600 Planarity : 0.004 0.053 3984 Dihedral : 6.672 58.658 3140 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.47 % Allowed : 23.87 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 2835 helix: 1.53 (0.22), residues: 615 sheet: -0.43 (0.21), residues: 599 loop : -2.17 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.028 0.001 TYR C1067 PHE 0.024 0.001 PHE B 238 TRP 0.018 0.001 TRP C 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (22594) covalent geometry : angle 0.53350 (30795) SS BOND : bond 0.00323 ( 35) SS BOND : angle 1.08669 ( 70) hydrogen bonds : bond 0.04471 ( 870) hydrogen bonds : angle 4.76247 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 157 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ARG cc_start: 0.5984 (mtt180) cc_final: 0.5769 (mtt90) REVERT: B 110 LEU cc_start: 0.3969 (tp) cc_final: 0.3613 (tt) REVERT: B 132 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3775 (pm20) REVERT: B 269 TYR cc_start: 0.7871 (m-80) cc_final: 0.7330 (m-80) REVERT: B 613 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: B 1113 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: B 1130 ILE cc_start: 0.9164 (mp) cc_final: 0.8960 (mt) REVERT: C 86 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6615 (t80) REVERT: C 132 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5245 (pm20) REVERT: C 387 LEU cc_start: 0.7838 (mp) cc_final: 0.7613 (mt) REVERT: C 418 ILE cc_start: 0.5815 (mm) cc_final: 0.5520 (mm) REVERT: C 569 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6932 (mp) REVERT: C 611 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8526 (tp) REVERT: C 1034 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 92 PHE cc_start: 0.7255 (t80) cc_final: 0.7030 (t80) REVERT: A 175 PHE cc_start: 0.1920 (OUTLIER) cc_final: 0.0648 (m-10) REVERT: A 269 TYR cc_start: 0.7887 (m-80) cc_final: 0.7502 (m-80) REVERT: A 430 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3093 (t) REVERT: A 957 GLN cc_start: 0.8434 (tp40) cc_final: 0.8150 (mm110) outliers start: 154 outliers final: 117 residues processed: 293 average time/residue: 0.1370 time to fit residues: 65.9500 Evaluate side-chains 269 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 142 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 185 optimal weight: 0.4980 chunk 258 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 160 optimal weight: 0.1980 chunk 198 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 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 = 0.4068 r_free = 0.4068 target = 0.149803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123831 restraints weight = 38512.144| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.11 r_work: 0.3362 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22629 Z= 0.181 Angle : 0.595 15.058 30865 Z= 0.302 Chirality : 0.045 0.160 3600 Planarity : 0.004 0.056 3984 Dihedral : 6.796 59.044 3134 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.89 % Allowed : 23.66 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.15), residues: 2835 helix: 1.26 (0.22), residues: 616 sheet: -0.44 (0.21), residues: 601 loop : -2.19 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.029 0.001 TYR C1067 PHE 0.024 0.001 PHE B 238 TRP 0.019 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00433 (22594) covalent geometry : angle 0.59229 (30795) SS BOND : bond 0.00408 ( 35) SS BOND : angle 1.41043 ( 70) hydrogen bonds : bond 0.05421 ( 870) hydrogen bonds : angle 4.94163 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 137 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.3863 (tp) cc_final: 0.3537 (tt) REVERT: B 132 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3815 (pm20) REVERT: B 269 TYR cc_start: 0.7906 (m-80) cc_final: 0.7414 (m-80) REVERT: B 613 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: B 1113 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: C 86 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6651 (t80) REVERT: C 132 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.4901 (pm20) REVERT: C 235 ILE cc_start: 0.4208 (mt) cc_final: 0.4003 (mp) REVERT: C 387 LEU cc_start: 0.7885 (mp) cc_final: 0.7649 (mt) REVERT: C 418 ILE cc_start: 0.5842 (mm) cc_final: 0.5545 (mm) REVERT: C 569 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7006 (mp) REVERT: C 611 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8482 (tp) REVERT: C 854 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.4694 (tmtt) REVERT: C 1034 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 175 PHE cc_start: 0.1962 (OUTLIER) cc_final: 0.0782 (m-10) REVERT: A 269 TYR cc_start: 0.7912 (m-80) cc_final: 0.7512 (m-80) REVERT: A 430 THR cc_start: 0.3612 (OUTLIER) cc_final: 0.3055 (t) REVERT: A 558 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6995 (ttmt) REVERT: A 957 GLN cc_start: 0.8496 (tp40) cc_final: 0.8211 (mm110) outliers start: 164 outliers final: 133 residues processed: 287 average time/residue: 0.1322 time to fit residues: 62.5713 Evaluate side-chains 273 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 128 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 80 optimal weight: 4.9990 chunk 153 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 201 optimal weight: 0.0770 chunk 160 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 542 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A1106 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 = 0.4085 r_free = 0.4085 target = 0.151143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118142 restraints weight = 38449.675| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.81 r_work: 0.3475 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22629 Z= 0.111 Angle : 0.536 13.305 30865 Z= 0.273 Chirality : 0.043 0.153 3600 Planarity : 0.004 0.056 3984 Dihedral : 6.507 59.976 3134 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.51 % Allowed : 24.45 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.15), residues: 2835 helix: 1.54 (0.22), residues: 615 sheet: -0.25 (0.21), residues: 602 loop : -2.03 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.024 0.001 TYR C1067 PHE 0.026 0.001 PHE B 238 TRP 0.025 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00248 (22594) covalent geometry : angle 0.53405 (30795) SS BOND : bond 0.00323 ( 35) SS BOND : angle 1.20094 ( 70) hydrogen bonds : bond 0.04555 ( 870) hydrogen bonds : angle 4.73714 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 145 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.3916 (tp) cc_final: 0.3607 (tt) REVERT: B 132 GLU cc_start: 0.4395 (OUTLIER) cc_final: 0.3736 (pm20) REVERT: B 269 TYR cc_start: 0.7871 (m-80) cc_final: 0.7319 (m-80) REVERT: B 613 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: B 779 GLN cc_start: 0.7252 (tp40) cc_final: 0.6974 (tp40) REVERT: B 1113 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: B 1130 ILE cc_start: 0.9159 (mp) cc_final: 0.8940 (mt) REVERT: C 86 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6644 (t80) REVERT: C 132 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.5241 (pm20) REVERT: C 387 LEU cc_start: 0.7758 (mp) cc_final: 0.7533 (mt) REVERT: C 611 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 854 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.4575 (tmtt) REVERT: C 1034 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 175 PHE cc_start: 0.1904 (OUTLIER) cc_final: 0.0604 (m-10) REVERT: A 269 TYR cc_start: 0.7941 (m-80) cc_final: 0.7545 (m-80) REVERT: A 430 THR cc_start: 0.3665 (OUTLIER) cc_final: 0.3166 (t) REVERT: A 558 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6928 (ttmt) REVERT: A 957 GLN cc_start: 0.8506 (tp40) cc_final: 0.8219 (mm110) outliers start: 155 outliers final: 121 residues processed: 284 average time/residue: 0.1342 time to fit residues: 62.9272 Evaluate side-chains 269 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 137 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 78 optimal weight: 5.9990 chunk 240 optimal weight: 0.2980 chunk 177 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 542 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 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 = 0.4067 r_free = 0.4067 target = 0.149675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.113728 restraints weight = 38439.897| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.83 r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22629 Z= 0.188 Angle : 0.604 15.426 30865 Z= 0.306 Chirality : 0.045 0.174 3600 Planarity : 0.004 0.057 3984 Dihedral : 6.673 59.965 3130 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.60 % Allowed : 24.45 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 2835 helix: 1.30 (0.22), residues: 616 sheet: -0.35 (0.21), residues: 599 loop : -2.10 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.027 0.001 TYR C1067 PHE 0.025 0.002 PHE B 238 TRP 0.036 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00450 (22594) covalent geometry : angle 0.60052 (30795) SS BOND : bond 0.00412 ( 35) SS BOND : angle 1.47813 ( 70) hydrogen bonds : bond 0.05466 ( 870) hydrogen bonds : angle 4.92379 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 138 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.3616 (tp) cc_final: 0.3365 (tt) REVERT: B 132 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3539 (pm20) REVERT: B 235 ILE cc_start: 0.4238 (OUTLIER) cc_final: 0.3972 (mp) REVERT: B 269 TYR cc_start: 0.7905 (m-80) cc_final: 0.7332 (m-80) REVERT: B 543 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5116 (t80) REVERT: B 613 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: B 1106 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: B 1113 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: B 1130 ILE cc_start: 0.9182 (mp) cc_final: 0.8938 (mt) REVERT: C 86 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6549 (t80) REVERT: C 132 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4873 (pm20) REVERT: C 387 LEU cc_start: 0.7811 (mp) cc_final: 0.7572 (mt) REVERT: C 611 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (tp) REVERT: C 854 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4568 (tmtt) REVERT: C 1034 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8856 (mp) REVERT: A 175 PHE cc_start: 0.2043 (OUTLIER) cc_final: 0.0702 (m-10) REVERT: A 269 TYR cc_start: 0.7969 (m-80) cc_final: 0.7520 (m-80) REVERT: A 430 THR cc_start: 0.3536 (OUTLIER) cc_final: 0.2964 (t) REVERT: A 558 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6976 (ttmt) REVERT: A 613 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: A 957 GLN cc_start: 0.8569 (tp40) cc_final: 0.8280 (mm110) outliers start: 157 outliers final: 129 residues processed: 278 average time/residue: 0.1368 time to fit residues: 63.1130 Evaluate side-chains 277 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 133 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 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 = 0.4077 r_free = 0.4077 target = 0.150474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125546 restraints weight = 38595.060| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.03 r_work: 0.3375 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22629 Z= 0.149 Angle : 0.581 15.031 30865 Z= 0.293 Chirality : 0.045 0.166 3600 Planarity : 0.004 0.073 3984 Dihedral : 6.626 59.931 3130 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.09 % Allowed : 25.00 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 2835 helix: 1.33 (0.22), residues: 616 sheet: -0.26 (0.21), residues: 595 loop : -2.08 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.026 0.001 TYR C1067 PHE 0.027 0.001 PHE B 238 TRP 0.034 0.002 TRP C 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00349 (22594) covalent geometry : angle 0.57766 (30795) SS BOND : bond 0.00376 ( 35) SS BOND : angle 1.35577 ( 70) hydrogen bonds : bond 0.05169 ( 870) hydrogen bonds : angle 4.87046 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 136 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.3620 (tp) cc_final: 0.3385 (tt) REVERT: B 132 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.3540 (pm20) REVERT: B 235 ILE cc_start: 0.4308 (OUTLIER) cc_final: 0.4028 (mp) REVERT: B 269 TYR cc_start: 0.7854 (m-80) cc_final: 0.7340 (m-80) REVERT: B 543 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5154 (t80) REVERT: B 613 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: B 1106 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: B 1113 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: B 1130 ILE cc_start: 0.9155 (mp) cc_final: 0.8904 (mt) REVERT: C 86 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6634 (t80) REVERT: C 132 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.5205 (pm20) REVERT: C 387 LEU cc_start: 0.7837 (mp) cc_final: 0.7600 (mt) REVERT: C 611 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8495 (tp) REVERT: C 854 LYS cc_start: 0.5573 (OUTLIER) cc_final: 0.4664 (tmtt) REVERT: C 1034 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 175 PHE cc_start: 0.2126 (OUTLIER) cc_final: 0.0732 (m-10) REVERT: A 269 TYR cc_start: 0.7934 (m-80) cc_final: 0.7542 (m-80) REVERT: A 430 THR cc_start: 0.3642 (OUTLIER) cc_final: 0.3121 (t) REVERT: A 558 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6955 (ttmt) REVERT: A 613 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: A 957 GLN cc_start: 0.8427 (tp40) cc_final: 0.8146 (mm110) outliers start: 145 outliers final: 128 residues processed: 268 average time/residue: 0.1403 time to fit residues: 61.9253 Evaluate side-chains 274 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 131 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 284 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 0.0470 chunk 83 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 544 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A1106 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 = 0.4099 r_free = 0.4099 target = 0.152098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115988 restraints weight = 38609.893| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.81 r_work: 0.3495 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22629 Z= 0.106 Angle : 0.540 12.899 30865 Z= 0.275 Chirality : 0.043 0.153 3600 Planarity : 0.004 0.072 3984 Dihedral : 6.361 59.879 3129 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.34 % Allowed : 25.84 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2835 helix: 1.62 (0.22), residues: 615 sheet: -0.10 (0.21), residues: 594 loop : -1.88 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.023 0.001 TYR C1067 PHE 0.028 0.001 PHE B 238 TRP 0.028 0.002 TRP C 104 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00229 (22594) covalent geometry : angle 0.53848 (30795) SS BOND : bond 0.00319 ( 35) SS BOND : angle 1.08283 ( 70) hydrogen bonds : bond 0.04406 ( 870) hydrogen bonds : angle 4.66441 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.79 seconds wall clock time: 109 minutes 36.95 seconds (6576.95 seconds total)