Starting phenix.real_space_refine on Thu Mar 5 16:35:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r14_14230/03_2026/7r14_14230.map" } resolution = 3.4 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= 0.004 sd= 0.119 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 100 5.16 5 C 15087 2.51 5 N 3859 2.21 5 O 4603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23649 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7565 Classifications: {'peptide': 970} Link IDs: {'PTRANS': 50, 'TRANS': 919} Chain breaks: 9 Chain: "B" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7768 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 51, 'TRANS': 942} Chain breaks: 11 Chain: "C" Number of atoms: 7619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7619 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.22 Number of scatterers: 23649 At special positions: 0 Unit cell: (132.614, 133.701, 195.66, 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 100 16.00 O 4603 8.00 N 3859 7.00 C 15087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 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 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 343 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 748.0 milliseconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5498 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 46 sheets defined 23.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.646A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 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 762 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.714A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.731A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.572A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.270A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.784A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.006A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.512A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.857A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.330A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.704A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.759A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.763A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.230A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.102A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 990 removed outlier: 3.897A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1033 Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.700A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.761A 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 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.228A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.563A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.769A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.607A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1006 removed outlier: 5.096A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1033 removed outlier: 3.833A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.118A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.695A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.538A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.611A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.852A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.193A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.544A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.255A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.537A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.403A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.254A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.578A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.849A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.583A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.015A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.687A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.773A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.659A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.592A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.776A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.528A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.698A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.065A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.500A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.516A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.106A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.759A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.641A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.272A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.895A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 722 removed outlier: 5.687A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1082 781 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7430 1.34 - 1.46: 4915 1.46 - 1.58: 11696 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 24165 Sorted by residual: bond pdb=" N CYS C1126 " pdb=" CA CYS C1126 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.12e-02 7.97e+03 1.21e+01 bond pdb=" N VAL A 615 " pdb=" CA VAL A 615 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL C1133 " pdb=" CA VAL C1133 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.28e-02 6.10e+03 9.81e+00 bond pdb=" N VAL A 610 " pdb=" CA VAL A 610 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.59e+00 bond pdb=" N VAL C 642 " pdb=" CA VAL C 642 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.24e-02 6.50e+03 9.16e+00 ... (remaining 24160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 32107 1.99 - 3.98: 712 3.98 - 5.97: 46 5.97 - 7.97: 7 7.97 - 9.96: 3 Bond angle restraints: 32875 Sorted by residual: angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 111.28 104.57 6.71 1.09e+00 8.42e-01 3.79e+01 angle pdb=" CA CYS C 649 " pdb=" C CYS C 649 " pdb=" O CYS C 649 " ideal model delta sigma weight residual 122.37 118.15 4.22 1.15e+00 7.56e-01 1.35e+01 angle pdb=" CA VAL C1133 " pdb=" C VAL C1133 " pdb=" O VAL C1133 " ideal model delta sigma weight residual 121.72 118.26 3.46 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CA GLY C 648 " pdb=" C GLY C 648 " pdb=" O GLY C 648 " ideal model delta sigma weight residual 121.41 118.09 3.32 9.50e-01 1.11e+00 1.22e+01 angle pdb=" CA ASN A 616 " pdb=" C ASN A 616 " pdb=" O ASN A 616 " ideal model delta sigma weight residual 121.94 118.04 3.90 1.15e+00 7.56e-01 1.15e+01 ... (remaining 32870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 14146 23.82 - 47.64: 735 47.64 - 71.46: 104 71.46 - 95.29: 26 95.29 - 119.11: 20 Dihedral angle restraints: 15031 sinusoidal: 6495 harmonic: 8536 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -12.65 -73.35 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.59 -72.59 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.89 63.89 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 15028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3194 0.062 - 0.125: 631 0.125 - 0.187: 61 0.187 - 0.250: 5 0.250 - 0.312: 2 Chirality restraints: 3893 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE C1081 " pdb=" N ILE C1081 " pdb=" C ILE C1081 " pdb=" CB ILE C1081 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3890 not shown) Planarity restraints: 4222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO B 987 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.017 2.00e-02 2.50e+03 1.63e-02 4.67e+00 pdb=" CG PHE C 906 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 25 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 26 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " -0.028 5.00e-02 4.00e+02 ... (remaining 4219 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 460 2.68 - 3.24: 21866 3.24 - 3.79: 33475 3.79 - 4.35: 44611 4.35 - 4.90: 76644 Nonbonded interactions: 177056 Sorted by model distance: nonbonded pdb=" OD1 ASN A 122 " pdb=" N ALA A 123 " model vdw 2.127 3.120 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.198 3.120 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASN C 439 " pdb=" OG SER C 443 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.242 3.040 ... (remaining 177051 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 26 through 121 or resid 127 or resid 169 through 172 or re \ sid 187 through 263 or resid 265 through 826 or resid 855 through 940 or resid 9 \ 44 through 1309)) selection = (chain 'B' and (resid 26 through 95 or resid 100 through 108 or resid 117 throug \ h 121 or resid 127 or resid 169 through 172 or resid 187 through 620 or resid 64 \ 1 through 826 or resid 855 through 1309)) selection = (chain 'C' and (resid 26 through 67 or resid 81 through 108 or resid 117 through \ 121 or resid 130 or resid 169 through 263 or resid 265 through 620 or resid 641 \ through 826 or resid 855 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=0.00 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: 5.750 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.410 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.005 0.053 24252 Z= 0.257 Angle : 0.671 9.957 33099 Z= 0.351 Chirality : 0.050 0.312 3893 Planarity : 0.004 0.074 4181 Dihedral : 14.655 119.108 9422 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.75 % Rotamer: Outliers : 0.08 % Allowed : 0.20 % Favored : 99.73 % 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 are not related in a simple way. whole: -1.58 (0.16), residues: 2871 helix: 1.01 (0.22), residues: 615 sheet: -1.06 (0.19), residues: 718 loop : -1.95 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1107 TYR 0.022 0.001 TYR B 369 PHE 0.038 0.002 PHE C 906 TRP 0.019 0.002 TRP C 886 HIS 0.009 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00548 (24165) covalent geometry : angle 0.65503 (32875) SS BOND : bond 0.00382 ( 37) SS BOND : angle 1.43821 ( 74) hydrogen bonds : bond 0.21168 ( 781) hydrogen bonds : angle 7.88853 ( 2121) link_BETA1-4 : bond 0.01027 ( 8) link_BETA1-4 : angle 1.74490 ( 24) link_BETA1-6 : bond 0.00310 ( 1) link_BETA1-6 : angle 2.61602 ( 3) link_NAG-ASN : bond 0.00363 ( 41) link_NAG-ASN : angle 2.10049 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7901 (mp0) cc_final: 0.7218 (mm-30) REVERT: A 448 ASN cc_start: 0.7556 (m110) cc_final: 0.7121 (m110) REVERT: A 460 ASN cc_start: 0.8989 (m-40) cc_final: 0.8629 (m-40) REVERT: B 779 GLN cc_start: 0.8067 (tt0) cc_final: 0.7738 (tt0) REVERT: C 453 TYR cc_start: 0.5916 (p90) cc_final: 0.5697 (p90) REVERT: C 823 PHE cc_start: 0.8396 (t80) cc_final: 0.7869 (t80) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1322 time to fit residues: 52.4493 Evaluate side-chains 189 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.127924 restraints weight = 30070.397| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.69 r_work: 0.3048 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24252 Z= 0.124 Angle : 0.581 9.625 33099 Z= 0.293 Chirality : 0.046 0.333 3893 Planarity : 0.004 0.065 4181 Dihedral : 9.725 105.396 4181 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.47 % Allowed : 5.23 % Favored : 94.30 % 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 are not related in a simple way. whole: -1.25 (0.16), residues: 2871 helix: 1.36 (0.22), residues: 615 sheet: -0.71 (0.19), residues: 724 loop : -1.87 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.025 0.001 TYR A 453 PHE 0.021 0.001 PHE A 238 TRP 0.015 0.001 TRP A 436 HIS 0.007 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00283 (24165) covalent geometry : angle 0.56629 (32875) SS BOND : bond 0.00347 ( 37) SS BOND : angle 1.19740 ( 74) hydrogen bonds : bond 0.05464 ( 781) hydrogen bonds : angle 5.66248 ( 2121) link_BETA1-4 : bond 0.00515 ( 8) link_BETA1-4 : angle 1.77387 ( 24) link_BETA1-6 : bond 0.00157 ( 1) link_BETA1-6 : angle 1.87902 ( 3) link_NAG-ASN : bond 0.00352 ( 41) link_NAG-ASN : angle 1.87512 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8319 (t) cc_final: 0.7978 (m) REVERT: A 406 GLU cc_start: 0.8056 (mp0) cc_final: 0.7634 (mm-30) REVERT: A 453 TYR cc_start: 0.6790 (p90) cc_final: 0.6574 (p90) REVERT: A 460 ASN cc_start: 0.9099 (m-40) cc_final: 0.8720 (m-40) REVERT: A 1002 GLN cc_start: 0.8866 (tp40) cc_final: 0.8597 (tp40) REVERT: B 779 GLN cc_start: 0.8801 (tt0) cc_final: 0.8437 (tt0) REVERT: C 244 LEU cc_start: 0.7783 (tp) cc_final: 0.7417 (tt) REVERT: C 453 TYR cc_start: 0.6463 (p90) cc_final: 0.6262 (p90) outliers start: 12 outliers final: 9 residues processed: 214 average time/residue: 0.1272 time to fit residues: 46.1359 Evaluate side-chains 194 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 571 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS A 613 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121954 restraints weight = 30246.677| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.07 r_work: 0.2923 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24252 Z= 0.216 Angle : 0.637 9.758 33099 Z= 0.322 Chirality : 0.048 0.299 3893 Planarity : 0.004 0.062 4181 Dihedral : 8.210 93.354 4181 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.37 % Allowed : 8.47 % Favored : 90.16 % 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 are not related in a simple way. whole: -1.37 (0.16), residues: 2871 helix: 1.16 (0.22), residues: 617 sheet: -0.65 (0.19), residues: 721 loop : -1.99 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.020 0.002 TYR B1067 PHE 0.025 0.002 PHE C 906 TRP 0.016 0.002 TRP C 886 HIS 0.008 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00542 (24165) covalent geometry : angle 0.61964 (32875) SS BOND : bond 0.00426 ( 37) SS BOND : angle 1.54172 ( 74) hydrogen bonds : bond 0.06426 ( 781) hydrogen bonds : angle 5.36855 ( 2121) link_BETA1-4 : bond 0.00470 ( 8) link_BETA1-4 : angle 2.04721 ( 24) link_BETA1-6 : bond 0.00159 ( 1) link_BETA1-6 : angle 2.12124 ( 3) link_NAG-ASN : bond 0.00326 ( 41) link_NAG-ASN : angle 2.06752 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8048 (mp0) cc_final: 0.7582 (mm-30) REVERT: A 448 ASN cc_start: 0.7559 (m110) cc_final: 0.6984 (m110) REVERT: A 531 THR cc_start: 0.8844 (m) cc_final: 0.8337 (p) REVERT: A 1002 GLN cc_start: 0.8728 (tp40) cc_final: 0.8515 (tp40) REVERT: B 779 GLN cc_start: 0.8698 (tt0) cc_final: 0.8343 (tt0) REVERT: C 197 ILE cc_start: 0.8402 (pt) cc_final: 0.8147 (tt) REVERT: C 244 LEU cc_start: 0.7602 (tp) cc_final: 0.7293 (tt) REVERT: C 453 TYR cc_start: 0.6554 (p90) cc_final: 0.6322 (p90) REVERT: C 935 GLN cc_start: 0.8407 (mt0) cc_final: 0.7898 (mm-40) outliers start: 35 outliers final: 25 residues processed: 222 average time/residue: 0.1277 time to fit residues: 48.0363 Evaluate side-chains 204 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 34 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 50.0000 chunk 221 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 121 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 437 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C1058 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.161189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125093 restraints weight = 30020.604| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.26 r_work: 0.2972 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24252 Z= 0.120 Angle : 0.557 8.395 33099 Z= 0.280 Chirality : 0.045 0.301 3893 Planarity : 0.004 0.057 4181 Dihedral : 7.513 86.433 4181 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.29 % Allowed : 10.43 % Favored : 88.29 % 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 are not related in a simple way. whole: -1.14 (0.16), residues: 2871 helix: 1.44 (0.22), residues: 616 sheet: -0.55 (0.19), residues: 718 loop : -1.85 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.019 0.001 TYR A 453 PHE 0.014 0.001 PHE A 238 TRP 0.016 0.001 TRP C 886 HIS 0.006 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00282 (24165) covalent geometry : angle 0.53925 (32875) SS BOND : bond 0.00385 ( 37) SS BOND : angle 1.44465 ( 74) hydrogen bonds : bond 0.04958 ( 781) hydrogen bonds : angle 5.03561 ( 2121) link_BETA1-4 : bond 0.00511 ( 8) link_BETA1-4 : angle 1.95523 ( 24) link_BETA1-6 : bond 0.00434 ( 1) link_BETA1-6 : angle 2.09872 ( 3) link_NAG-ASN : bond 0.00344 ( 41) link_NAG-ASN : angle 1.89296 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7314 (mtt90) REVERT: A 406 GLU cc_start: 0.7975 (mp0) cc_final: 0.7625 (mm-30) REVERT: A 448 ASN cc_start: 0.7558 (m110) cc_final: 0.6953 (m110) REVERT: A 455 LEU cc_start: 0.8949 (mt) cc_final: 0.8682 (mm) REVERT: A 531 THR cc_start: 0.8827 (m) cc_final: 0.8345 (p) REVERT: B 779 GLN cc_start: 0.8753 (tt0) cc_final: 0.8409 (tt0) REVERT: C 244 LEU cc_start: 0.7545 (tp) cc_final: 0.7244 (tt) REVERT: C 453 TYR cc_start: 0.6865 (p90) cc_final: 0.6599 (p90) REVERT: C 886 TRP cc_start: 0.8691 (p90) cc_final: 0.8280 (p90) REVERT: C 935 GLN cc_start: 0.8323 (mt0) cc_final: 0.7820 (mm-40) outliers start: 33 outliers final: 18 residues processed: 215 average time/residue: 0.1327 time to fit residues: 48.1844 Evaluate side-chains 194 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 571 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 166 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124081 restraints weight = 29964.099| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.19 r_work: 0.2938 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24252 Z= 0.157 Angle : 0.584 13.039 33099 Z= 0.291 Chirality : 0.046 0.322 3893 Planarity : 0.004 0.055 4181 Dihedral : 7.108 82.128 4181 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.60 % Allowed : 11.36 % Favored : 87.04 % 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 are not related in a simple way. whole: -1.14 (0.16), residues: 2871 helix: 1.42 (0.22), residues: 617 sheet: -0.54 (0.20), residues: 715 loop : -1.85 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.017 0.001 TYR A 453 PHE 0.019 0.001 PHE C 823 TRP 0.016 0.001 TRP C 886 HIS 0.006 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00386 (24165) covalent geometry : angle 0.56671 (32875) SS BOND : bond 0.00414 ( 37) SS BOND : angle 1.50327 ( 74) hydrogen bonds : bond 0.05318 ( 781) hydrogen bonds : angle 4.95142 ( 2121) link_BETA1-4 : bond 0.00490 ( 8) link_BETA1-4 : angle 2.08421 ( 24) link_BETA1-6 : bond 0.00302 ( 1) link_BETA1-6 : angle 2.20080 ( 3) link_NAG-ASN : bond 0.00336 ( 41) link_NAG-ASN : angle 1.91155 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8581 (p90) cc_final: 0.8380 (p90) REVERT: A 406 GLU cc_start: 0.7987 (mp0) cc_final: 0.7647 (mm-30) REVERT: A 448 ASN cc_start: 0.7493 (m110) cc_final: 0.6914 (m110) REVERT: A 455 LEU cc_start: 0.8966 (mt) cc_final: 0.8682 (mm) REVERT: A 515 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7123 (p90) REVERT: A 531 THR cc_start: 0.8836 (m) cc_final: 0.8375 (p) REVERT: B 779 GLN cc_start: 0.8759 (tt0) cc_final: 0.8427 (tt0) REVERT: C 244 LEU cc_start: 0.7577 (tp) cc_final: 0.7287 (tt) REVERT: C 453 TYR cc_start: 0.6947 (p90) cc_final: 0.6705 (p90) REVERT: C 817 PHE cc_start: 0.8580 (t80) cc_final: 0.8199 (t80) REVERT: C 886 TRP cc_start: 0.8765 (p90) cc_final: 0.8290 (p90) outliers start: 41 outliers final: 29 residues processed: 218 average time/residue: 0.1302 time to fit residues: 47.7397 Evaluate side-chains 202 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 141 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1002 GLN A1054 GLN ** B 992 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 = 0.3779 r_free = 0.3779 target = 0.160312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123814 restraints weight = 30041.238| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.42 r_work: 0.2965 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24252 Z= 0.146 Angle : 0.571 10.838 33099 Z= 0.284 Chirality : 0.046 0.298 3893 Planarity : 0.004 0.055 4181 Dihedral : 6.742 78.762 4181 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 1.68 % Allowed : 12.22 % Favored : 86.10 % 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 are not related in a simple way. whole: -1.11 (0.16), residues: 2871 helix: 1.41 (0.22), residues: 616 sheet: -0.48 (0.19), residues: 716 loop : -1.83 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.025 0.001 TYR B 369 PHE 0.024 0.001 PHE C 347 TRP 0.018 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00357 (24165) covalent geometry : angle 0.55346 (32875) SS BOND : bond 0.00407 ( 37) SS BOND : angle 1.56565 ( 74) hydrogen bonds : bond 0.05121 ( 781) hydrogen bonds : angle 4.87145 ( 2121) link_BETA1-4 : bond 0.00522 ( 8) link_BETA1-4 : angle 2.11273 ( 24) link_BETA1-6 : bond 0.00355 ( 1) link_BETA1-6 : angle 2.33707 ( 3) link_NAG-ASN : bond 0.00319 ( 41) link_NAG-ASN : angle 1.84989 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8042 (mp0) cc_final: 0.7645 (mm-30) REVERT: A 448 ASN cc_start: 0.7484 (m110) cc_final: 0.6840 (m110) REVERT: A 455 LEU cc_start: 0.8924 (mt) cc_final: 0.8618 (mm) REVERT: A 515 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7083 (p90) REVERT: A 531 THR cc_start: 0.8803 (m) cc_final: 0.8356 (p) REVERT: B 779 GLN cc_start: 0.8695 (tt0) cc_final: 0.8350 (tt0) REVERT: C 244 LEU cc_start: 0.7528 (tp) cc_final: 0.7265 (tt) REVERT: C 592 PHE cc_start: 0.8681 (p90) cc_final: 0.8479 (p90) REVERT: C 886 TRP cc_start: 0.8893 (p90) cc_final: 0.8307 (p90) REVERT: C 1029 MET cc_start: 0.9137 (tpp) cc_final: 0.8754 (ttm) outliers start: 43 outliers final: 33 residues processed: 216 average time/residue: 0.1219 time to fit residues: 45.1123 Evaluate side-chains 204 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 258 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 0.0010 chunk 186 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.161067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124590 restraints weight = 29870.677| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.53 r_work: 0.2992 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24252 Z= 0.116 Angle : 0.547 11.083 33099 Z= 0.272 Chirality : 0.045 0.317 3893 Planarity : 0.004 0.054 4181 Dihedral : 6.263 74.461 4181 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 1.72 % Allowed : 12.77 % Favored : 85.51 % 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 are not related in a simple way. whole: -0.99 (0.16), residues: 2871 helix: 1.51 (0.22), residues: 617 sheet: -0.39 (0.20), residues: 702 loop : -1.76 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1107 TYR 0.027 0.001 TYR C 453 PHE 0.014 0.001 PHE C 823 TRP 0.018 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00275 (24165) covalent geometry : angle 0.53054 (32875) SS BOND : bond 0.00413 ( 37) SS BOND : angle 1.39239 ( 74) hydrogen bonds : bond 0.04593 ( 781) hydrogen bonds : angle 4.71612 ( 2121) link_BETA1-4 : bond 0.00537 ( 8) link_BETA1-4 : angle 2.13230 ( 24) link_BETA1-6 : bond 0.00406 ( 1) link_BETA1-6 : angle 2.44675 ( 3) link_NAG-ASN : bond 0.00337 ( 41) link_NAG-ASN : angle 1.79617 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7990 (mp0) cc_final: 0.7726 (mm-30) REVERT: A 448 ASN cc_start: 0.7487 (m110) cc_final: 0.6851 (m110) REVERT: A 455 LEU cc_start: 0.8891 (mt) cc_final: 0.8640 (mm) REVERT: A 515 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7057 (p90) REVERT: A 531 THR cc_start: 0.8820 (m) cc_final: 0.8367 (p) REVERT: B 779 GLN cc_start: 0.8637 (tt0) cc_final: 0.8296 (tt0) REVERT: C 244 LEU cc_start: 0.7508 (tp) cc_final: 0.7262 (tt) REVERT: C 592 PHE cc_start: 0.8644 (p90) cc_final: 0.8419 (p90) REVERT: C 774 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8570 (mm-40) REVERT: C 814 LYS cc_start: 0.8408 (mtmm) cc_final: 0.8156 (mttm) REVERT: C 886 TRP cc_start: 0.8822 (p90) cc_final: 0.8252 (p90) REVERT: C 1029 MET cc_start: 0.9063 (tpp) cc_final: 0.8723 (ttm) outliers start: 44 outliers final: 38 residues processed: 219 average time/residue: 0.1264 time to fit residues: 46.9871 Evaluate side-chains 216 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 66 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 171 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126577 restraints weight = 29885.975| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.91 r_work: 0.2962 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24252 Z= 0.125 Angle : 0.555 11.563 33099 Z= 0.274 Chirality : 0.045 0.314 3893 Planarity : 0.004 0.054 4181 Dihedral : 6.073 71.598 4181 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 1.76 % Allowed : 13.00 % Favored : 85.24 % 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 are not related in a simple way. whole: -0.94 (0.16), residues: 2871 helix: 1.52 (0.22), residues: 618 sheet: -0.34 (0.20), residues: 694 loop : -1.72 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1107 TYR 0.021 0.001 TYR B 369 PHE 0.014 0.001 PHE B 86 TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00298 (24165) covalent geometry : angle 0.53811 (32875) SS BOND : bond 0.00423 ( 37) SS BOND : angle 1.43262 ( 74) hydrogen bonds : bond 0.04675 ( 781) hydrogen bonds : angle 4.68094 ( 2121) link_BETA1-4 : bond 0.00509 ( 8) link_BETA1-4 : angle 2.14491 ( 24) link_BETA1-6 : bond 0.00392 ( 1) link_BETA1-6 : angle 2.66298 ( 3) link_NAG-ASN : bond 0.00331 ( 41) link_NAG-ASN : angle 1.79975 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.7416 (m110) cc_final: 0.6967 (m110) REVERT: A 455 LEU cc_start: 0.8919 (mt) cc_final: 0.8648 (mm) REVERT: A 515 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7126 (p90) REVERT: A 531 THR cc_start: 0.8793 (m) cc_final: 0.8375 (p) REVERT: B 203 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 779 GLN cc_start: 0.8698 (tt0) cc_final: 0.8379 (tt0) REVERT: C 244 LEU cc_start: 0.7558 (tp) cc_final: 0.7311 (tt) REVERT: C 592 PHE cc_start: 0.8695 (p90) cc_final: 0.8475 (p90) REVERT: C 774 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8589 (mm-40) REVERT: C 814 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8160 (mttm) REVERT: C 886 TRP cc_start: 0.8876 (p90) cc_final: 0.8356 (p90) REVERT: C 1029 MET cc_start: 0.9074 (tpp) cc_final: 0.8723 (ttm) outliers start: 45 outliers final: 41 residues processed: 215 average time/residue: 0.1283 time to fit residues: 46.5532 Evaluate side-chains 214 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 935 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 150 optimal weight: 0.2980 chunk 284 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 267 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 226 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.162133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127693 restraints weight = 29907.387| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.88 r_work: 0.2989 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24252 Z= 0.112 Angle : 0.547 11.577 33099 Z= 0.271 Chirality : 0.045 0.298 3893 Planarity : 0.004 0.054 4181 Dihedral : 5.878 68.313 4181 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 1.84 % Allowed : 13.08 % Favored : 85.08 % 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 are not related in a simple way. whole: -0.89 (0.16), residues: 2871 helix: 1.58 (0.22), residues: 618 sheet: -0.29 (0.20), residues: 697 loop : -1.70 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1107 TYR 0.021 0.001 TYR B 369 PHE 0.040 0.001 PHE C 817 TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00265 (24165) covalent geometry : angle 0.53085 (32875) SS BOND : bond 0.00403 ( 37) SS BOND : angle 1.34360 ( 74) hydrogen bonds : bond 0.04461 ( 781) hydrogen bonds : angle 4.62407 ( 2121) link_BETA1-4 : bond 0.00495 ( 8) link_BETA1-4 : angle 2.12694 ( 24) link_BETA1-6 : bond 0.00409 ( 1) link_BETA1-6 : angle 2.83063 ( 3) link_NAG-ASN : bond 0.00317 ( 41) link_NAG-ASN : angle 1.73235 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 448 ASN cc_start: 0.7424 (m110) cc_final: 0.6904 (m110) REVERT: A 455 LEU cc_start: 0.8913 (mt) cc_final: 0.8655 (mm) REVERT: A 515 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7088 (p90) REVERT: A 531 THR cc_start: 0.8787 (m) cc_final: 0.8356 (p) REVERT: B 203 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 779 GLN cc_start: 0.8706 (tt0) cc_final: 0.8389 (tt0) REVERT: C 244 LEU cc_start: 0.7547 (tp) cc_final: 0.7295 (tt) REVERT: C 592 PHE cc_start: 0.8681 (p90) cc_final: 0.8472 (p90) REVERT: C 774 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8559 (mm-40) REVERT: C 814 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8177 (mttm) REVERT: C 817 PHE cc_start: 0.8018 (t80) cc_final: 0.7744 (t80) REVERT: C 886 TRP cc_start: 0.8883 (p90) cc_final: 0.8361 (p90) REVERT: C 1029 MET cc_start: 0.9037 (tpp) cc_final: 0.8721 (ttm) outliers start: 47 outliers final: 42 residues processed: 220 average time/residue: 0.1276 time to fit residues: 47.7460 Evaluate side-chains 216 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 245 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 262 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.161121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124500 restraints weight = 29976.138| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.67 r_work: 0.3020 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24252 Z= 0.136 Angle : 0.562 11.777 33099 Z= 0.279 Chirality : 0.045 0.303 3893 Planarity : 0.004 0.055 4181 Dihedral : 5.746 63.242 4181 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 1.84 % Allowed : 13.24 % Favored : 84.93 % 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 are not related in a simple way. whole: -0.87 (0.16), residues: 2871 helix: 1.56 (0.22), residues: 619 sheet: -0.23 (0.20), residues: 694 loop : -1.71 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1107 TYR 0.019 0.001 TYR B 369 PHE 0.046 0.001 PHE C 817 TRP 0.019 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00331 (24165) covalent geometry : angle 0.54502 (32875) SS BOND : bond 0.00422 ( 37) SS BOND : angle 1.44312 ( 74) hydrogen bonds : bond 0.04834 ( 781) hydrogen bonds : angle 4.63551 ( 2121) link_BETA1-4 : bond 0.00457 ( 8) link_BETA1-4 : angle 2.16725 ( 24) link_BETA1-6 : bond 0.00341 ( 1) link_BETA1-6 : angle 3.13855 ( 3) link_NAG-ASN : bond 0.00318 ( 41) link_NAG-ASN : angle 1.78575 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8464 (p90) cc_final: 0.8248 (p90) REVERT: A 406 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 448 ASN cc_start: 0.7481 (m110) cc_final: 0.6910 (m110) REVERT: A 455 LEU cc_start: 0.8873 (mt) cc_final: 0.8575 (mm) REVERT: A 515 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6995 (p90) REVERT: A 531 THR cc_start: 0.8825 (m) cc_final: 0.8358 (p) REVERT: B 779 GLN cc_start: 0.8665 (tt0) cc_final: 0.8320 (tt0) REVERT: C 244 LEU cc_start: 0.7556 (tp) cc_final: 0.7317 (tt) REVERT: C 347 PHE cc_start: 0.7106 (m-80) cc_final: 0.6775 (m-80) REVERT: C 592 PHE cc_start: 0.8628 (p90) cc_final: 0.8407 (p90) REVERT: C 774 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8590 (mm-40) REVERT: C 814 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8066 (mttm) REVERT: C 886 TRP cc_start: 0.8883 (p90) cc_final: 0.8403 (p90) REVERT: C 1029 MET cc_start: 0.9145 (tpp) cc_final: 0.8808 (ttm) outliers start: 47 outliers final: 43 residues processed: 215 average time/residue: 0.1244 time to fit residues: 45.5113 Evaluate side-chains 216 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 205 optimal weight: 4.9990 chunk 272 optimal weight: 0.5980 chunk 275 optimal weight: 0.0000 chunk 16 optimal weight: 0.0000 chunk 273 optimal weight: 0.5980 chunk 157 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 292 optimal weight: 0.6980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128548 restraints weight = 29826.197| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.77 r_work: 0.2979 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24252 Z= 0.104 Angle : 0.541 11.482 33099 Z= 0.268 Chirality : 0.045 0.298 3893 Planarity : 0.004 0.054 4181 Dihedral : 5.575 59.540 4181 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 1.76 % Allowed : 13.43 % Favored : 84.81 % 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 are not related in a simple way. whole: -0.77 (0.16), residues: 2871 helix: 1.71 (0.23), residues: 617 sheet: -0.20 (0.20), residues: 689 loop : -1.65 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.021 0.001 TYR B 369 PHE 0.045 0.001 PHE C 817 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00238 (24165) covalent geometry : angle 0.52517 (32875) SS BOND : bond 0.00425 ( 37) SS BOND : angle 1.32172 ( 74) hydrogen bonds : bond 0.04316 ( 781) hydrogen bonds : angle 4.54334 ( 2121) link_BETA1-4 : bond 0.00505 ( 8) link_BETA1-4 : angle 2.10270 ( 24) link_BETA1-6 : bond 0.00358 ( 1) link_BETA1-6 : angle 3.24410 ( 3) link_NAG-ASN : bond 0.00329 ( 41) link_NAG-ASN : angle 1.72066 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4765.75 seconds wall clock time: 82 minutes 31.35 seconds (4951.35 seconds total)