Starting phenix.real_space_refine on Fri Mar 6 02:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndb_12282/03_2026/7ndb_12282.map" } resolution = 4.6 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= 0.005 sd= 0.073 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 119 5.16 5 C 17308 2.51 5 N 4458 2.21 5 O 5299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 27184 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7625 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 7909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7909 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 52, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7680 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 49, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1639 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 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: 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: "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: "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: "M" 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: "N" 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: "O" 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: "P" 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: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.98, per 1000 atoms: 0.22 Number of scatterers: 27184 At special positions: 0 Unit cell: (127.92, 127.92, 260.76, 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 119 16.00 O 5299 8.00 N 4458 7.00 C 17308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN H 102 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 54 sheets defined 25.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.762A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.737A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.598A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.119A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.702A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.369A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.507A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.585A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 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 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 removed outlier: 3.612A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 853 through 856' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.533A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.470A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.992A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.582A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.201A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 832 through 840 removed outlier: 3.551A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.192A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.889A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.058A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.640A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.545A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.900A pdb=" N GLY H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.689A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.071A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.588A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.412A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.777A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.795A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.092A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.126A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.605A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.532A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.668A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.172A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 132 through 140 removed outlier: 3.881A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.481A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.518A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.516A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.547A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.411A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.266A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.657A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.602A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.261A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.754A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.657A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 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 654 through 655 removed outlier: 6.002A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.022A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.302A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.737A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.688A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF3, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.077A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.077A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.644A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.602A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.001A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 154 through 155 1200 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 3.30 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: 8639 1.34 - 1.46: 6927 1.46 - 1.58: 12075 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 27788 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.81e+00 ... (remaining 27783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 36563 1.38 - 2.77: 1109 2.77 - 4.15: 166 4.15 - 5.53: 36 5.53 - 6.91: 8 Bond angle restraints: 37882 Sorted by residual: angle pdb=" C GLN B 52 " pdb=" N ASP B 53 " pdb=" CA ASP B 53 " ideal model delta sigma weight residual 122.32 127.44 -5.12 1.76e+00 3.23e-01 8.45e+00 angle pdb=" CA CYS A1032 " pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " ideal model delta sigma weight residual 114.40 120.35 -5.95 2.30e+00 1.89e-01 6.70e+00 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 120.32 -5.92 2.30e+00 1.89e-01 6.63e+00 angle pdb=" C ASN A 343 " pdb=" N ALA A 344 " pdb=" CA ALA A 344 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.28e+00 angle pdb=" CA CYS C1032 " pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " ideal model delta sigma weight residual 114.40 119.96 -5.56 2.30e+00 1.89e-01 5.84e+00 ... (remaining 37877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 16146 17.63 - 35.27: 707 35.27 - 52.90: 181 52.90 - 70.53: 65 70.53 - 88.17: 28 Dihedral angle restraints: 17127 sinusoidal: 7073 harmonic: 10054 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.17 79.17 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -160.92 74.92 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -157.99 71.99 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 17124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3719 0.057 - 0.115: 723 0.115 - 0.172: 68 0.172 - 0.230: 2 0.230 - 0.287: 1 Chirality restraints: 4513 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 4510 not shown) Planarity restraints: 4861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 206 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LYS A 206 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 206 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS A 207 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.24e+00 pdb=" C ASN C 122 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA C 123 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.023 2.00e-02 2.50e+03 2.17e-02 5.89e+00 pdb=" CG ASN A 234 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.025 2.00e-02 2.50e+03 ... (remaining 4858 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1031 2.72 - 3.26: 26787 3.26 - 3.81: 43946 3.81 - 4.35: 54205 4.35 - 4.90: 93226 Nonbonded interactions: 219195 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP L 171 " pdb=" OG1 THR L 173 " model vdw 2.208 3.040 nonbonded pdb=" OE1 GLU L 106 " pdb=" OH TYR L 174 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.223 3.040 nonbonded pdb=" NH1 ARG B 905 " pdb=" O GLY B1035 " model vdw 2.260 3.120 ... (remaining 219190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 87 or (resid 88 and ( \ name N or name CA or name C or name O or name CB )) or resid 89 through 95 or (r \ esid 96 through 97 and (name N or name CA or name C or name O or name CB )) or r \ esid 98 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or \ name CA or name C or name O or name CB )) or resid 126 through 131 or (resid 13 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 133 or (resi \ d 134 through 136 and (name N or name CA or name C or name O or name CB )) or re \ sid 166 through 168 or (resid 169 and (name N or name CA or name C or name O or \ name CB )) or resid 170 through 171 or (resid 172 through 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 197 or (resid 198 an \ d (name N or name CA or name C or name O or name CB )) or resid 199 through 209 \ or (resid 210 and (name N or name CA or name C or name O or name CB )) or (resid \ 215 and (name N or name CA or name C or name O or name CB )) or resid 216 throu \ gh 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or \ resid 219 through 242 or resid 265 through 308 or (resid 309 and (name N or nam \ e CA or name C or name O or name CB )) or resid 310 through 323 or (resid 324 an \ d (name N or name CA or name C or name O or name CB )) or resid 325 through 332 \ or (resid 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 457 or (resid 458 and (name N or name CA or name C or name O or name \ CB )) or resid 459 through 528 or (resid 529 and (name N or name CA or name C o \ r name O or name CB )) or resid 530 through 536 or (resid 537 and (name N or nam \ e CA or name C or name O or name CB )) or resid 538 through 582 or (resid 583 an \ d (name N or name CA or name C or name O or name CB )) or resid 584 through 620 \ or resid 641 through 747 or (resid 748 and (name N or name CA or name C or name \ O or name CB )) or resid 749 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name C \ A or name C or name O or name CB )) or resid 797 through 849 or resid 852 throug \ h 853 or (resid 854 and (name N or name CA or name C or name O or name CB )) or \ resid 855 through 867 or (resid 868 and (name N or name CA or name C or name O o \ r name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or na \ me C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 987 or (resid \ 988 through 989 and (name N or name CA or name C or name O or name CB )) or resi \ d 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or \ name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 109 or (resid 110 and (name N or name CA or name C or name O or n \ ame CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 168 or (resid 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 171 or (resid 172 and (name N or name CA or name C or \ name O or name CB )) or resid 188 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 195 or (resid 196 and \ (name N or name CA or name C or name O or name CB )) or resid 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 2 \ 36 or (resid 237 and (name N or name CA or name C or name O or name CB )) or res \ id 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or \ resid 240 through 241 or (resid 242 and (name N or name CA or name C or name O \ or name CB )) or resid 265 through 280 or (resid 281 and (name N or name CA or n \ ame C or name O or name CB )) or resid 282 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 through 388 or (resid \ 389 and (name N or name CA or name C or name O or name CB )) or resid 390 throu \ gh 457 or (resid 458 and (name N or name CA or name C or name O or name CB )) or \ resid 459 through 567 or (resid 568 and (name N or name CA or name C or name O \ or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA or n \ ame C or name O or name CB )) or resid 572 through 613 or (resid 614 and (name N \ or name CA or name C or name O or name CB )) or resid 615 through 618 or (resid \ 619 and (name N or name CA or name C or name O or name CB )) or resid 620 or re \ sid 641 through 676 or resid 690 through 744 or (resid 745 and (name N or name C \ A or name C or name O or name CB )) or resid 746 through 827 or resid 849 or res \ id 852 through 853 or (resid 854 and (name N or name CA or name C or name O or n \ ame CB )) or resid 855 through 867 or (resid 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N or \ name CA or name C or name O or name CB )) or resid 941 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 989 and (name N or name CA or name C or name O or name \ CB )) or resid 990 through 1143 or (resid 1144 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 113 or resid 116 through 134 or (resid 135 through 136 and (name N or name CA or \ name C or name O or name CB )) or resid 166 through 172 or (resid 188 and (name \ N or name CA or name C or name O or name CB )) or resid 189 through 195 or (res \ id 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 215 through 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 236 or (resid 237 and (name N or name CA or \ name C or name O or name CB )) or resid 238 through 297 or (resid 298 and (name \ N or name CA or name C or name O or name CB )) or resid 299 through 308 or (res \ id 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thr \ ough 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 388 or (resid 389 and (name N or name CA or name C or name \ O or name CB )) or resid 390 through 527 or (resid 528 through 529 and (name N o \ r name CA or name C or name O or name CB )) or resid 530 through 536 or (resid 5 \ 37 and (name N or name CA or name C or name O or name CB )) or resid 538 through \ 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) or r \ esid 555 through 557 or (resid 558 and (name N or name CA or name C or name O or \ name CB )) or resid 559 through 567 or (resid 568 and (name N or name CA or nam \ e C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N o \ r name CA or name C or name O or name CB )) or resid 572 through 582 or (resid 5 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or r \ esid 615 through 618 or (resid 619 and (name N or name CA or name C or name O or \ name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N or na \ me CA or name C or name O or name CB )) or resid 648 through 795 or (resid 796 a \ nd (name N or name CA or name C or name O or name CB )) or resid 797 through 828 \ or resid 831 or resid 836 or resid 854 through 1141 or (resid 1142 and (name N \ or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 throug \ h 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147 th \ rough 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.190 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27880 Z= 0.147 Angle : 0.577 8.131 38116 Z= 0.298 Chirality : 0.045 0.287 4513 Planarity : 0.004 0.057 4823 Dihedral : 11.741 88.167 10529 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.52 % Favored : 95.33 % Rotamer: Outliers : 0.72 % Allowed : 4.55 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.78 (0.14), residues: 3404 helix: 0.89 (0.21), residues: 720 sheet: -0.35 (0.17), residues: 904 loop : -1.19 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.019 0.001 TYR A 396 PHE 0.015 0.001 PHE A 318 TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00292 (27788) covalent geometry : angle 0.56508 (37882) SS BOND : bond 0.00217 ( 42) SS BOND : angle 0.98706 ( 84) hydrogen bonds : bond 0.11489 ( 1178) hydrogen bonds : angle 7.01680 ( 3228) link_BETA1-4 : bond 0.00333 ( 11) link_BETA1-4 : angle 1.93891 ( 33) link_BETA1-6 : bond 0.00378 ( 1) link_BETA1-6 : angle 1.31793 ( 3) link_NAG-ASN : bond 0.00222 ( 38) link_NAG-ASN : angle 1.86334 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 721 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8885 (t80) cc_final: 0.8402 (t80) REVERT: A 223 LEU cc_start: 0.8585 (mp) cc_final: 0.8120 (mp) REVERT: A 229 LEU cc_start: 0.9216 (tp) cc_final: 0.8964 (tp) REVERT: A 351 TYR cc_start: 0.9353 (p90) cc_final: 0.8940 (p90) REVERT: A 365 TYR cc_start: 0.8780 (m-80) cc_final: 0.8414 (m-80) REVERT: A 374 PHE cc_start: 0.8506 (m-80) cc_final: 0.8213 (m-80) REVERT: A 394 ASN cc_start: 0.8406 (m-40) cc_final: 0.7379 (t0) REVERT: A 434 ILE cc_start: 0.7745 (mt) cc_final: 0.7456 (tt) REVERT: A 462 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8070 (pptt) REVERT: A 711 SER cc_start: 0.9145 (m) cc_final: 0.8872 (p) REVERT: A 712 ILE cc_start: 0.9493 (tt) cc_final: 0.9010 (mt) REVERT: A 773 GLU cc_start: 0.9300 (tt0) cc_final: 0.8364 (tp30) REVERT: A 789 TYR cc_start: 0.7968 (m-80) cc_final: 0.7213 (m-80) REVERT: A 805 ILE cc_start: 0.8729 (pt) cc_final: 0.8101 (pt) REVERT: A 856 ASN cc_start: 0.8909 (m-40) cc_final: 0.8485 (p0) REVERT: A 883 THR cc_start: 0.9343 (p) cc_final: 0.9100 (t) REVERT: A 888 PHE cc_start: 0.8812 (p90) cc_final: 0.8474 (p90) REVERT: A 902 MET cc_start: 0.8887 (mmm) cc_final: 0.8649 (mmm) REVERT: A 945 LEU cc_start: 0.8550 (mt) cc_final: 0.8165 (pp) REVERT: A 950 ASP cc_start: 0.9463 (t0) cc_final: 0.9191 (m-30) REVERT: A 962 LEU cc_start: 0.8718 (tp) cc_final: 0.8475 (tp) REVERT: A 964 LYS cc_start: 0.9413 (mttt) cc_final: 0.9063 (ptpt) REVERT: A 983 ARG cc_start: 0.9219 (mtp180) cc_final: 0.8903 (ptm160) REVERT: A 993 ILE cc_start: 0.9468 (mt) cc_final: 0.9163 (mt) REVERT: B 173 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8851 (tp40) REVERT: B 571 ASP cc_start: 0.8010 (t70) cc_final: 0.7475 (t0) REVERT: B 614 ASP cc_start: 0.9133 (m-30) cc_final: 0.8804 (p0) REVERT: B 693 ILE cc_start: 0.9085 (pt) cc_final: 0.8447 (mp) REVERT: B 731 MET cc_start: 0.8549 (mtp) cc_final: 0.8293 (mtp) REVERT: B 773 GLU cc_start: 0.9088 (tt0) cc_final: 0.8474 (tp30) REVERT: B 782 PHE cc_start: 0.8651 (m-80) cc_final: 0.8251 (m-10) REVERT: B 869 MET cc_start: 0.9004 (mtp) cc_final: 0.8466 (mtp) REVERT: B 870 ILE cc_start: 0.8944 (mm) cc_final: 0.8668 (mm) REVERT: B 898 PHE cc_start: 0.8290 (t80) cc_final: 0.7968 (t80) REVERT: B 954 GLN cc_start: 0.8973 (mt0) cc_final: 0.8599 (mt0) REVERT: B 983 ARG cc_start: 0.8980 (mtp180) cc_final: 0.8439 (ttm170) REVERT: B 987 PRO cc_start: 0.9239 (Cg_exo) cc_final: 0.8767 (Cg_endo) REVERT: B 1064 HIS cc_start: 0.8258 (m-70) cc_final: 0.7577 (m170) REVERT: C 61 ASN cc_start: 0.4349 (OUTLIER) cc_final: 0.4010 (t0) REVERT: C 92 PHE cc_start: 0.8959 (t80) cc_final: 0.8430 (t80) REVERT: C 104 TRP cc_start: 0.8406 (m-90) cc_final: 0.7196 (m-90) REVERT: C 194 PHE cc_start: 0.9275 (m-80) cc_final: 0.8891 (m-80) REVERT: C 201 PHE cc_start: 0.9705 (t80) cc_final: 0.9181 (t80) REVERT: C 203 ILE cc_start: 0.9125 (mt) cc_final: 0.8185 (mt) REVERT: C 204 TYR cc_start: 0.8898 (m-80) cc_final: 0.8281 (m-80) REVERT: C 229 LEU cc_start: 0.9761 (mt) cc_final: 0.9341 (mt) REVERT: C 270 LEU cc_start: 0.8112 (mt) cc_final: 0.7766 (mt) REVERT: C 351 TYR cc_start: 0.8713 (p90) cc_final: 0.8194 (p90) REVERT: C 398 ASP cc_start: 0.8116 (m-30) cc_final: 0.5838 (t0) REVERT: C 429 PHE cc_start: 0.6737 (t80) cc_final: 0.6224 (t80) REVERT: C 434 ILE cc_start: 0.9264 (mt) cc_final: 0.8911 (tp) REVERT: C 451 TYR cc_start: 0.7133 (m-80) cc_final: 0.6533 (m-80) REVERT: C 571 ASP cc_start: 0.7852 (t70) cc_final: 0.7551 (t0) REVERT: C 707 TYR cc_start: 0.6875 (t80) cc_final: 0.6416 (t80) REVERT: C 722 VAL cc_start: 0.8798 (t) cc_final: 0.8387 (p) REVERT: C 723 THR cc_start: 0.9349 (p) cc_final: 0.9139 (t) REVERT: C 740 MET cc_start: 0.9493 (ttt) cc_final: 0.8908 (tpt) REVERT: C 742 ILE cc_start: 0.9479 (mt) cc_final: 0.9240 (pt) REVERT: C 752 LEU cc_start: 0.9725 (mt) cc_final: 0.9454 (pp) REVERT: C 767 LEU cc_start: 0.8996 (mt) cc_final: 0.8451 (tp) REVERT: C 818 ILE cc_start: 0.9548 (mt) cc_final: 0.9343 (tp) REVERT: C 819 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7612 (tp30) REVERT: C 820 ASP cc_start: 0.9174 (m-30) cc_final: 0.8928 (m-30) REVERT: C 869 MET cc_start: 0.9244 (mtt) cc_final: 0.8920 (mtp) REVERT: C 881 THR cc_start: 0.9468 (m) cc_final: 0.9083 (p) REVERT: C 884 SER cc_start: 0.8751 (p) cc_final: 0.8459 (p) REVERT: C 886 TRP cc_start: 0.7788 (p90) cc_final: 0.7563 (p90) REVERT: C 915 VAL cc_start: 0.9306 (t) cc_final: 0.8803 (t) REVERT: C 926 GLN cc_start: 0.9578 (mt0) cc_final: 0.9139 (mm110) REVERT: C 934 ILE cc_start: 0.9324 (mm) cc_final: 0.9109 (mm) REVERT: C 968 SER cc_start: 0.8307 (m) cc_final: 0.7068 (t) REVERT: C 1001 LEU cc_start: 0.9370 (tp) cc_final: 0.8304 (pp) REVERT: C 1004 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9279 (tt) REVERT: C 1034 LEU cc_start: 0.9224 (mp) cc_final: 0.8495 (tt) REVERT: C 1041 ASP cc_start: 0.8913 (m-30) cc_final: 0.8662 (t0) REVERT: C 1064 HIS cc_start: 0.8568 (m-70) cc_final: 0.8081 (m-70) REVERT: C 1116 THR cc_start: 0.8595 (p) cc_final: 0.8154 (t) REVERT: C 1121 PHE cc_start: 0.8502 (p90) cc_final: 0.7640 (p90) REVERT: L 124 GLU cc_start: 0.7641 (tt0) cc_final: 0.7434 (pt0) outliers start: 21 outliers final: 3 residues processed: 736 average time/residue: 0.1868 time to fit residues: 214.3070 Evaluate side-chains 400 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 394 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 388 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 30 ASN B 239 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 965 GLN L 148 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.097050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063838 restraints weight = 112856.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066855 restraints weight = 63820.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068956 restraints weight = 42756.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070434 restraints weight = 31864.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071491 restraints weight = 25551.417| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27880 Z= 0.188 Angle : 0.642 10.790 38116 Z= 0.334 Chirality : 0.045 0.264 4513 Planarity : 0.005 0.069 4823 Dihedral : 6.574 59.627 4734 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.35 (0.14), residues: 3404 helix: 1.17 (0.19), residues: 710 sheet: -0.16 (0.16), residues: 892 loop : -0.81 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.028 0.002 TYR B 904 PHE 0.025 0.002 PHE C 759 TRP 0.015 0.002 TRP C 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00393 (27788) covalent geometry : angle 0.63156 (37882) SS BOND : bond 0.00720 ( 42) SS BOND : angle 1.55477 ( 84) hydrogen bonds : bond 0.04434 ( 1178) hydrogen bonds : angle 5.88143 ( 3228) link_BETA1-4 : bond 0.00696 ( 11) link_BETA1-4 : angle 1.46335 ( 33) link_BETA1-6 : bond 0.00293 ( 1) link_BETA1-6 : angle 1.43187 ( 3) link_NAG-ASN : bond 0.00494 ( 38) link_NAG-ASN : angle 1.66028 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 458 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8037 (m100) cc_final: 0.7541 (m100) REVERT: A 223 LEU cc_start: 0.8309 (mp) cc_final: 0.8010 (mp) REVERT: A 226 LEU cc_start: 0.9150 (mp) cc_final: 0.8662 (mp) REVERT: A 229 LEU cc_start: 0.9124 (tp) cc_final: 0.8868 (tp) REVERT: A 351 TYR cc_start: 0.9433 (p90) cc_final: 0.9090 (p90) REVERT: A 354 ASN cc_start: 0.8322 (t0) cc_final: 0.8107 (t0) REVERT: A 374 PHE cc_start: 0.8438 (m-80) cc_final: 0.8047 (m-80) REVERT: A 465 GLU cc_start: 0.5929 (tp30) cc_final: 0.5062 (mm-30) REVERT: A 611 LEU cc_start: 0.9344 (tp) cc_final: 0.9122 (tp) REVERT: A 711 SER cc_start: 0.9551 (m) cc_final: 0.9187 (p) REVERT: A 712 ILE cc_start: 0.9042 (tt) cc_final: 0.8503 (mt) REVERT: A 773 GLU cc_start: 0.9531 (tt0) cc_final: 0.8716 (tp30) REVERT: A 787 GLN cc_start: 0.9077 (mt0) cc_final: 0.8739 (mt0) REVERT: A 789 TYR cc_start: 0.7891 (m-80) cc_final: 0.7462 (m-10) REVERT: A 819 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 824 ASN cc_start: 0.8561 (m-40) cc_final: 0.7840 (p0) REVERT: A 856 ASN cc_start: 0.8915 (m-40) cc_final: 0.8684 (p0) REVERT: A 883 THR cc_start: 0.9403 (p) cc_final: 0.9070 (t) REVERT: A 900 MET cc_start: 0.9182 (mmm) cc_final: 0.8609 (mmt) REVERT: A 902 MET cc_start: 0.9054 (mmm) cc_final: 0.8738 (mmm) REVERT: A 950 ASP cc_start: 0.9141 (t0) cc_final: 0.8875 (t0) REVERT: A 962 LEU cc_start: 0.8833 (tp) cc_final: 0.8621 (tp) REVERT: A 964 LYS cc_start: 0.9355 (mttt) cc_final: 0.9004 (ptpp) REVERT: A 978 ASN cc_start: 0.9453 (m-40) cc_final: 0.8978 (t0) REVERT: A 990 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.9040 (pp20) REVERT: A 1028 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8298 (tppp) REVERT: A 1033 VAL cc_start: 0.9629 (p) cc_final: 0.9307 (m) REVERT: A 1034 LEU cc_start: 0.9460 (mp) cc_final: 0.8424 (tt) REVERT: A 1077 THR cc_start: 0.8788 (p) cc_final: 0.8345 (t) REVERT: B 596 SER cc_start: 0.8587 (m) cc_final: 0.8129 (p) REVERT: B 740 MET cc_start: 0.9411 (tpt) cc_final: 0.9086 (tpp) REVERT: B 776 LYS cc_start: 0.9505 (tttt) cc_final: 0.9221 (ptmm) REVERT: B 806 LEU cc_start: 0.8355 (tp) cc_final: 0.8010 (tt) REVERT: B 869 MET cc_start: 0.8876 (mtp) cc_final: 0.8345 (mtp) REVERT: B 898 PHE cc_start: 0.8467 (t80) cc_final: 0.8079 (t80) REVERT: B 936 ASP cc_start: 0.9281 (m-30) cc_final: 0.9077 (m-30) REVERT: B 983 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8747 (ttm170) REVERT: B 1003 SER cc_start: 0.9797 (m) cc_final: 0.9591 (p) REVERT: B 1030 SER cc_start: 0.8268 (m) cc_final: 0.7880 (p) REVERT: B 1031 GLU cc_start: 0.8079 (tt0) cc_final: 0.7667 (tt0) REVERT: B 1067 TYR cc_start: 0.7266 (t80) cc_final: 0.7037 (t80) REVERT: C 92 PHE cc_start: 0.8855 (t80) cc_final: 0.8313 (t80) REVERT: C 104 TRP cc_start: 0.8331 (m-90) cc_final: 0.7295 (m100) REVERT: C 201 PHE cc_start: 0.9591 (t80) cc_final: 0.9283 (m-80) REVERT: C 202 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8722 (mmmt) REVERT: C 269 TYR cc_start: 0.7178 (m-10) cc_final: 0.6698 (m-10) REVERT: C 353 TRP cc_start: 0.8108 (p-90) cc_final: 0.7394 (p-90) REVERT: C 414 GLN cc_start: 0.8567 (tp40) cc_final: 0.8222 (tm-30) REVERT: C 429 PHE cc_start: 0.6788 (t80) cc_final: 0.6187 (t80) REVERT: C 434 ILE cc_start: 0.9167 (mt) cc_final: 0.8836 (tp) REVERT: C 571 ASP cc_start: 0.7898 (t70) cc_final: 0.7523 (t0) REVERT: C 722 VAL cc_start: 0.8947 (t) cc_final: 0.8601 (p) REVERT: C 740 MET cc_start: 0.9448 (ttt) cc_final: 0.8989 (tpt) REVERT: C 742 ILE cc_start: 0.9286 (mt) cc_final: 0.9061 (pt) REVERT: C 776 LYS cc_start: 0.9517 (mmtt) cc_final: 0.9138 (mmmm) REVERT: C 819 GLU cc_start: 0.8635 (mt-10) cc_final: 0.6388 (mm-30) REVERT: C 869 MET cc_start: 0.8963 (mtt) cc_final: 0.8527 (mtp) REVERT: C 872 GLN cc_start: 0.9097 (mt0) cc_final: 0.8534 (mt0) REVERT: C 881 THR cc_start: 0.9264 (m) cc_final: 0.9028 (p) REVERT: C 884 SER cc_start: 0.8360 (p) cc_final: 0.7940 (p) REVERT: C 934 ILE cc_start: 0.9338 (mm) cc_final: 0.8974 (mm) REVERT: C 938 LEU cc_start: 0.9059 (mt) cc_final: 0.8443 (tt) REVERT: C 966 LEU cc_start: 0.9577 (tp) cc_final: 0.9252 (mm) REVERT: C 968 SER cc_start: 0.8938 (m) cc_final: 0.7805 (t) REVERT: C 980 ILE cc_start: 0.9318 (mm) cc_final: 0.8956 (mm) REVERT: C 1018 ILE cc_start: 0.9315 (mm) cc_final: 0.8937 (mm) REVERT: C 1041 ASP cc_start: 0.9015 (m-30) cc_final: 0.8755 (t0) REVERT: C 1064 HIS cc_start: 0.9062 (m-70) cc_final: 0.8465 (m-70) REVERT: H 73 ASP cc_start: 0.9505 (t0) cc_final: 0.9088 (t0) REVERT: L 40 LYS cc_start: 0.8571 (mppt) cc_final: 0.8127 (mppt) REVERT: L 82 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7337 (tm-30) REVERT: L 104 LYS cc_start: 0.7224 (tptt) cc_final: 0.6738 (tmtt) outliers start: 3 outliers final: 0 residues processed: 461 average time/residue: 0.1838 time to fit residues: 132.3435 Evaluate side-chains 330 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 265 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 955 ASN A1005 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN B1002 GLN C 321 GLN C 613 GLN C1011 GLN H 174 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.097615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063880 restraints weight = 112133.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066891 restraints weight = 63792.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069012 restraints weight = 42903.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070509 restraints weight = 31990.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.071356 restraints weight = 25692.207| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27880 Z= 0.133 Angle : 0.585 10.003 38116 Z= 0.302 Chirality : 0.045 0.185 4513 Planarity : 0.005 0.076 4823 Dihedral : 6.001 58.471 4734 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.09 (0.14), residues: 3404 helix: 1.22 (0.19), residues: 727 sheet: 0.07 (0.16), residues: 898 loop : -0.63 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 408 TYR 0.028 0.001 TYR A 741 PHE 0.022 0.001 PHE A 970 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (27788) covalent geometry : angle 0.57343 (37882) SS BOND : bond 0.00202 ( 42) SS BOND : angle 1.80149 ( 84) hydrogen bonds : bond 0.04047 ( 1178) hydrogen bonds : angle 5.58057 ( 3228) link_BETA1-4 : bond 0.00432 ( 11) link_BETA1-4 : angle 1.41234 ( 33) link_BETA1-6 : bond 0.00512 ( 1) link_BETA1-6 : angle 1.18384 ( 3) link_NAG-ASN : bond 0.00223 ( 38) link_NAG-ASN : angle 1.49402 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 420 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8515 (mm) cc_final: 0.7679 (mm) REVERT: A 104 TRP cc_start: 0.7776 (m100) cc_final: 0.7462 (m100) REVERT: A 223 LEU cc_start: 0.8425 (mp) cc_final: 0.7938 (mp) REVERT: A 229 LEU cc_start: 0.9173 (tp) cc_final: 0.8961 (tp) REVERT: A 241 LEU cc_start: 0.8700 (mt) cc_final: 0.8358 (mt) REVERT: A 351 TYR cc_start: 0.9497 (p90) cc_final: 0.9074 (p90) REVERT: A 354 ASN cc_start: 0.8415 (t0) cc_final: 0.8183 (t0) REVERT: A 365 TYR cc_start: 0.8906 (m-80) cc_final: 0.8634 (m-80) REVERT: A 462 LYS cc_start: 0.8579 (mttp) cc_final: 0.8329 (mttp) REVERT: A 465 GLU cc_start: 0.5987 (tp30) cc_final: 0.5180 (mm-30) REVERT: A 517 LEU cc_start: 0.8329 (mt) cc_final: 0.6597 (mp) REVERT: A 611 LEU cc_start: 0.9534 (tp) cc_final: 0.9308 (tp) REVERT: A 711 SER cc_start: 0.9546 (m) cc_final: 0.9264 (p) REVERT: A 773 GLU cc_start: 0.9134 (tt0) cc_final: 0.8663 (tp30) REVERT: A 787 GLN cc_start: 0.9143 (mt0) cc_final: 0.8706 (mt0) REVERT: A 789 TYR cc_start: 0.7697 (m-80) cc_final: 0.7425 (m-10) REVERT: A 820 ASP cc_start: 0.8969 (m-30) cc_final: 0.8748 (m-30) REVERT: A 856 ASN cc_start: 0.9089 (m-40) cc_final: 0.8833 (p0) REVERT: A 883 THR cc_start: 0.9367 (p) cc_final: 0.9086 (t) REVERT: A 900 MET cc_start: 0.9122 (mmm) cc_final: 0.8452 (mmt) REVERT: A 950 ASP cc_start: 0.9123 (t0) cc_final: 0.8869 (t0) REVERT: A 964 LYS cc_start: 0.9327 (mttt) cc_final: 0.8938 (ptpp) REVERT: A 973 ILE cc_start: 0.9349 (pt) cc_final: 0.9038 (pt) REVERT: A 1029 MET cc_start: 0.9194 (tmm) cc_final: 0.8873 (tmm) REVERT: A 1034 LEU cc_start: 0.9436 (mp) cc_final: 0.8847 (mt) REVERT: B 241 LEU cc_start: 0.9632 (tp) cc_final: 0.9239 (mm) REVERT: B 301 CYS cc_start: 0.7608 (m) cc_final: 0.7324 (m) REVERT: B 740 MET cc_start: 0.9441 (tpt) cc_final: 0.9087 (tpp) REVERT: B 759 PHE cc_start: 0.7736 (m-80) cc_final: 0.7179 (m-80) REVERT: B 789 TYR cc_start: 0.8181 (m-80) cc_final: 0.7828 (m-10) REVERT: B 819 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8601 (mm-30) REVERT: B 869 MET cc_start: 0.8855 (mtp) cc_final: 0.8494 (mtp) REVERT: B 898 PHE cc_start: 0.8407 (t80) cc_final: 0.7977 (t80) REVERT: B 936 ASP cc_start: 0.9254 (m-30) cc_final: 0.9041 (m-30) REVERT: B 983 ARG cc_start: 0.9090 (mtp180) cc_final: 0.8605 (ttm170) REVERT: B 1018 ILE cc_start: 0.9437 (mm) cc_final: 0.9068 (mm) REVERT: B 1030 SER cc_start: 0.8329 (m) cc_final: 0.7970 (p) REVERT: B 1031 GLU cc_start: 0.8139 (tt0) cc_final: 0.7842 (mt-10) REVERT: C 92 PHE cc_start: 0.8801 (t80) cc_final: 0.8340 (t80) REVERT: C 104 TRP cc_start: 0.8362 (m-90) cc_final: 0.7065 (m100) REVERT: C 201 PHE cc_start: 0.9604 (t80) cc_final: 0.9329 (m-80) REVERT: C 238 PHE cc_start: 0.8985 (p90) cc_final: 0.8074 (p90) REVERT: C 269 TYR cc_start: 0.7024 (m-10) cc_final: 0.6602 (m-10) REVERT: C 279 TYR cc_start: 0.6417 (m-10) cc_final: 0.5829 (m-80) REVERT: C 402 ILE cc_start: 0.9652 (pt) cc_final: 0.9342 (tt) REVERT: C 408 ARG cc_start: 0.9557 (mmp80) cc_final: 0.9330 (mmp80) REVERT: C 414 GLN cc_start: 0.8762 (tp40) cc_final: 0.8386 (tm-30) REVERT: C 429 PHE cc_start: 0.6796 (t80) cc_final: 0.6353 (t80) REVERT: C 434 ILE cc_start: 0.9291 (mt) cc_final: 0.8902 (tp) REVERT: C 571 ASP cc_start: 0.7977 (t70) cc_final: 0.7524 (t0) REVERT: C 650 LEU cc_start: 0.9037 (mt) cc_final: 0.8833 (mt) REVERT: C 725 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 740 MET cc_start: 0.9477 (ttt) cc_final: 0.9041 (tpt) REVERT: C 776 LYS cc_start: 0.9511 (mmtt) cc_final: 0.9171 (mmmm) REVERT: C 819 GLU cc_start: 0.8589 (mt-10) cc_final: 0.6751 (mm-30) REVERT: C 869 MET cc_start: 0.9019 (mtt) cc_final: 0.8441 (mtp) REVERT: C 872 GLN cc_start: 0.9072 (mt0) cc_final: 0.8522 (mt0) REVERT: C 881 THR cc_start: 0.9253 (m) cc_final: 0.9017 (p) REVERT: C 884 SER cc_start: 0.9010 (p) cc_final: 0.8706 (p) REVERT: C 900 MET cc_start: 0.8692 (mmp) cc_final: 0.8404 (mmm) REVERT: C 950 ASP cc_start: 0.8958 (t70) cc_final: 0.8696 (t0) REVERT: C 966 LEU cc_start: 0.9568 (tp) cc_final: 0.9196 (mm) REVERT: C 968 SER cc_start: 0.8615 (m) cc_final: 0.7668 (t) REVERT: C 1001 LEU cc_start: 0.9280 (pp) cc_final: 0.9013 (pp) REVERT: C 1018 ILE cc_start: 0.9350 (mm) cc_final: 0.8987 (tt) REVERT: C 1041 ASP cc_start: 0.9018 (m-30) cc_final: 0.8645 (t0) REVERT: C 1064 HIS cc_start: 0.8891 (m-70) cc_final: 0.8259 (m-70) REVERT: H 74 MET cc_start: 0.8103 (ppp) cc_final: 0.7732 (mpp) REVERT: H 81 MET cc_start: 0.8294 (tpt) cc_final: 0.7753 (tpp) REVERT: L 82 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7525 (tm-30) REVERT: L 104 LYS cc_start: 0.7268 (tptt) cc_final: 0.6810 (tmtt) outliers start: 3 outliers final: 3 residues processed: 423 average time/residue: 0.1753 time to fit residues: 118.0810 Evaluate side-chains 312 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 309 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 0.0270 chunk 38 optimal weight: 9.9990 chunk 329 optimal weight: 50.0000 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 310 optimal weight: 7.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 784 GLN B1005 GLN B1108 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.096567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063038 restraints weight = 112538.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065992 restraints weight = 64361.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068061 restraints weight = 43511.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069517 restraints weight = 32516.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070588 restraints weight = 26151.243| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27880 Z= 0.138 Angle : 0.577 9.771 38116 Z= 0.298 Chirality : 0.044 0.208 4513 Planarity : 0.004 0.064 4823 Dihedral : 5.619 57.517 4734 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3404 helix: 1.22 (0.19), residues: 732 sheet: 0.16 (0.17), residues: 880 loop : -0.57 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 567 TYR 0.033 0.001 TYR A 741 PHE 0.019 0.001 PHE B 275 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00297 (27788) covalent geometry : angle 0.56801 (37882) SS BOND : bond 0.00198 ( 42) SS BOND : angle 1.36634 ( 84) hydrogen bonds : bond 0.03989 ( 1178) hydrogen bonds : angle 5.52549 ( 3228) link_BETA1-4 : bond 0.00308 ( 11) link_BETA1-4 : angle 1.47341 ( 33) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.38749 ( 3) link_NAG-ASN : bond 0.00312 ( 38) link_NAG-ASN : angle 1.48194 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 400 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8882 (t80) cc_final: 0.8617 (t80) REVERT: A 223 LEU cc_start: 0.8450 (mp) cc_final: 0.7999 (mp) REVERT: A 229 LEU cc_start: 0.9303 (tp) cc_final: 0.9057 (tp) REVERT: A 241 LEU cc_start: 0.8740 (mt) cc_final: 0.8397 (mt) REVERT: A 351 TYR cc_start: 0.9539 (p90) cc_final: 0.9026 (p90) REVERT: A 354 ASN cc_start: 0.8383 (t0) cc_final: 0.8155 (t0) REVERT: A 365 TYR cc_start: 0.8920 (m-80) cc_final: 0.8642 (m-80) REVERT: A 552 LEU cc_start: 0.9541 (mt) cc_final: 0.9338 (mt) REVERT: A 611 LEU cc_start: 0.9542 (tp) cc_final: 0.9317 (tp) REVERT: A 711 SER cc_start: 0.9560 (m) cc_final: 0.9324 (p) REVERT: A 773 GLU cc_start: 0.9114 (tt0) cc_final: 0.8603 (tp30) REVERT: A 820 ASP cc_start: 0.8960 (m-30) cc_final: 0.8730 (m-30) REVERT: A 824 ASN cc_start: 0.8635 (m-40) cc_final: 0.8426 (m-40) REVERT: A 856 ASN cc_start: 0.9160 (m-40) cc_final: 0.8745 (p0) REVERT: A 869 MET cc_start: 0.8684 (mtm) cc_final: 0.8357 (ptp) REVERT: A 883 THR cc_start: 0.9353 (p) cc_final: 0.9117 (t) REVERT: A 900 MET cc_start: 0.9202 (mmm) cc_final: 0.8680 (mmt) REVERT: A 950 ASP cc_start: 0.9067 (t0) cc_final: 0.8845 (t0) REVERT: A 964 LYS cc_start: 0.9355 (mttt) cc_final: 0.9118 (mttt) REVERT: A 990 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9164 (pp20) REVERT: A 1002 GLN cc_start: 0.9201 (tt0) cc_final: 0.8758 (tm-30) REVERT: A 1028 LYS cc_start: 0.8470 (mmtp) cc_final: 0.7861 (mmtp) REVERT: A 1029 MET cc_start: 0.9268 (tmm) cc_final: 0.8977 (tmm) REVERT: A 1034 LEU cc_start: 0.9369 (mp) cc_final: 0.8876 (mt) REVERT: B 241 LEU cc_start: 0.9608 (tp) cc_final: 0.9253 (mm) REVERT: B 740 MET cc_start: 0.9451 (tpt) cc_final: 0.9110 (tpp) REVERT: B 819 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8499 (mm-30) REVERT: B 869 MET cc_start: 0.8769 (mtp) cc_final: 0.8460 (mtp) REVERT: B 898 PHE cc_start: 0.8558 (t80) cc_final: 0.8103 (t80) REVERT: B 936 ASP cc_start: 0.9261 (m-30) cc_final: 0.9050 (m-30) REVERT: B 983 ARG cc_start: 0.9202 (mtp180) cc_final: 0.8752 (ttm170) REVERT: B 1030 SER cc_start: 0.8528 (m) cc_final: 0.8197 (p) REVERT: B 1031 GLU cc_start: 0.8180 (tt0) cc_final: 0.7885 (mt-10) REVERT: C 92 PHE cc_start: 0.8800 (t80) cc_final: 0.8387 (t80) REVERT: C 104 TRP cc_start: 0.8283 (m-90) cc_final: 0.6797 (m100) REVERT: C 202 LYS cc_start: 0.9692 (mmpt) cc_final: 0.9475 (mmmt) REVERT: C 204 TYR cc_start: 0.8871 (m-80) cc_final: 0.8502 (m-80) REVERT: C 238 PHE cc_start: 0.9055 (p90) cc_final: 0.8241 (p90) REVERT: C 269 TYR cc_start: 0.7122 (m-10) cc_final: 0.6719 (m-10) REVERT: C 279 TYR cc_start: 0.6547 (m-10) cc_final: 0.5729 (m-80) REVERT: C 414 GLN cc_start: 0.8788 (tp40) cc_final: 0.8452 (tm-30) REVERT: C 429 PHE cc_start: 0.6627 (t80) cc_final: 0.6180 (t80) REVERT: C 434 ILE cc_start: 0.9238 (mt) cc_final: 0.8873 (tp) REVERT: C 571 ASP cc_start: 0.8022 (t70) cc_final: 0.7578 (t0) REVERT: C 650 LEU cc_start: 0.9059 (mt) cc_final: 0.8855 (mt) REVERT: C 725 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 740 MET cc_start: 0.9484 (ttt) cc_final: 0.9025 (tpt) REVERT: C 776 LYS cc_start: 0.9507 (mmtt) cc_final: 0.9151 (mmmm) REVERT: C 869 MET cc_start: 0.8986 (mtt) cc_final: 0.8401 (mtp) REVERT: C 872 GLN cc_start: 0.9100 (mt0) cc_final: 0.8547 (mt0) REVERT: C 954 GLN cc_start: 0.9281 (mt0) cc_final: 0.8889 (tp40) REVERT: C 968 SER cc_start: 0.8635 (m) cc_final: 0.7589 (t) REVERT: C 1001 LEU cc_start: 0.9228 (pp) cc_final: 0.8948 (pp) REVERT: C 1017 GLU cc_start: 0.8693 (pp20) cc_final: 0.8328 (pp20) REVERT: C 1018 ILE cc_start: 0.9352 (mm) cc_final: 0.8688 (mm) REVERT: C 1041 ASP cc_start: 0.8944 (m-30) cc_final: 0.8625 (t0) REVERT: C 1064 HIS cc_start: 0.8918 (m-70) cc_final: 0.8489 (m-70) REVERT: H 73 ASP cc_start: 0.9237 (t0) cc_final: 0.9021 (t0) REVERT: H 74 MET cc_start: 0.8425 (ppp) cc_final: 0.8224 (mpp) REVERT: H 81 MET cc_start: 0.9039 (tpt) cc_final: 0.8621 (tpt) REVERT: H 219 LYS cc_start: 0.8051 (tmmt) cc_final: 0.7823 (ttpt) REVERT: L 104 LYS cc_start: 0.7414 (tptt) cc_final: 0.6730 (tttt) outliers start: 3 outliers final: 0 residues processed: 403 average time/residue: 0.1786 time to fit residues: 113.2389 Evaluate side-chains 292 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 203 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 762 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.095923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062392 restraints weight = 113264.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065223 restraints weight = 65206.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067213 restraints weight = 44138.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068648 restraints weight = 33167.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069692 restraints weight = 26819.052| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27880 Z= 0.148 Angle : 0.582 11.959 38116 Z= 0.302 Chirality : 0.044 0.188 4513 Planarity : 0.005 0.209 4823 Dihedral : 5.373 55.460 4734 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.07 (0.14), residues: 3404 helix: 1.11 (0.19), residues: 738 sheet: 0.06 (0.17), residues: 881 loop : -0.55 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.030 0.001 TYR B 904 PHE 0.040 0.002 PHE C 898 TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (27788) covalent geometry : angle 0.57464 (37882) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.17172 ( 84) hydrogen bonds : bond 0.03934 ( 1178) hydrogen bonds : angle 5.55988 ( 3228) link_BETA1-4 : bond 0.00424 ( 11) link_BETA1-4 : angle 1.49620 ( 33) link_BETA1-6 : bond 0.00146 ( 1) link_BETA1-6 : angle 1.39690 ( 3) link_NAG-ASN : bond 0.00232 ( 38) link_NAG-ASN : angle 1.37876 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8316 (m100) cc_final: 0.8012 (m100) REVERT: A 201 PHE cc_start: 0.8835 (t80) cc_final: 0.8613 (t80) REVERT: A 223 LEU cc_start: 0.8498 (mp) cc_final: 0.8103 (mp) REVERT: A 241 LEU cc_start: 0.8678 (mt) cc_final: 0.8310 (mt) REVERT: A 351 TYR cc_start: 0.9546 (p90) cc_final: 0.8968 (p90) REVERT: A 354 ASN cc_start: 0.8408 (t0) cc_final: 0.8179 (t0) REVERT: A 365 TYR cc_start: 0.8958 (m-80) cc_final: 0.8665 (m-80) REVERT: A 711 SER cc_start: 0.9607 (m) cc_final: 0.9397 (p) REVERT: A 773 GLU cc_start: 0.9108 (tt0) cc_final: 0.8556 (tp30) REVERT: A 820 ASP cc_start: 0.8959 (m-30) cc_final: 0.8742 (m-30) REVERT: A 824 ASN cc_start: 0.8660 (m-40) cc_final: 0.8440 (m-40) REVERT: A 856 ASN cc_start: 0.9130 (m-40) cc_final: 0.8717 (p0) REVERT: A 883 THR cc_start: 0.9394 (p) cc_final: 0.9179 (t) REVERT: A 900 MET cc_start: 0.9038 (mmm) cc_final: 0.8479 (mmt) REVERT: A 950 ASP cc_start: 0.9074 (t0) cc_final: 0.8830 (t0) REVERT: A 964 LYS cc_start: 0.9365 (mttt) cc_final: 0.9121 (mttt) REVERT: A 1002 GLN cc_start: 0.9255 (tt0) cc_final: 0.8776 (tm-30) REVERT: A 1029 MET cc_start: 0.9197 (tmm) cc_final: 0.8981 (tmm) REVERT: A 1034 LEU cc_start: 0.9349 (mp) cc_final: 0.8902 (mt) REVERT: A 1036 GLN cc_start: 0.8391 (tt0) cc_final: 0.7527 (tt0) REVERT: A 1041 ASP cc_start: 0.8402 (t70) cc_final: 0.8183 (t70) REVERT: B 241 LEU cc_start: 0.9535 (tp) cc_final: 0.9102 (pp) REVERT: B 740 MET cc_start: 0.9458 (tpt) cc_final: 0.9140 (tpp) REVERT: B 789 TYR cc_start: 0.8416 (m-10) cc_final: 0.7909 (m-10) REVERT: B 819 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8425 (mm-30) REVERT: B 869 MET cc_start: 0.8727 (mtp) cc_final: 0.8270 (mtp) REVERT: B 898 PHE cc_start: 0.8560 (t80) cc_final: 0.8099 (t80) REVERT: B 983 ARG cc_start: 0.9158 (mtp180) cc_final: 0.8673 (ttm170) REVERT: C 92 PHE cc_start: 0.8786 (t80) cc_final: 0.8515 (t80) REVERT: C 238 PHE cc_start: 0.9134 (p90) cc_final: 0.8477 (p90) REVERT: C 269 TYR cc_start: 0.7250 (m-10) cc_final: 0.6827 (m-10) REVERT: C 279 TYR cc_start: 0.6603 (m-10) cc_final: 0.6156 (m-10) REVERT: C 429 PHE cc_start: 0.6658 (t80) cc_final: 0.6380 (t80) REVERT: C 434 ILE cc_start: 0.9235 (mt) cc_final: 0.8882 (tp) REVERT: C 725 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 740 MET cc_start: 0.9458 (ttt) cc_final: 0.8965 (tpt) REVERT: C 776 LYS cc_start: 0.9498 (mmtt) cc_final: 0.9159 (mmmm) REVERT: C 869 MET cc_start: 0.8993 (mtt) cc_final: 0.8392 (mtp) REVERT: C 872 GLN cc_start: 0.9133 (mt0) cc_final: 0.8594 (mt0) REVERT: C 881 THR cc_start: 0.9288 (m) cc_final: 0.9062 (p) REVERT: C 884 SER cc_start: 0.8911 (p) cc_final: 0.8614 (p) REVERT: C 900 MET cc_start: 0.8752 (mmp) cc_final: 0.8441 (mmm) REVERT: C 954 GLN cc_start: 0.9243 (mt0) cc_final: 0.8875 (tp40) REVERT: C 966 LEU cc_start: 0.9541 (tp) cc_final: 0.9168 (mm) REVERT: C 968 SER cc_start: 0.8742 (m) cc_final: 0.7741 (t) REVERT: C 1001 LEU cc_start: 0.9135 (pp) cc_final: 0.8848 (pp) REVERT: C 1017 GLU cc_start: 0.8689 (pp20) cc_final: 0.8325 (pp20) REVERT: C 1018 ILE cc_start: 0.9364 (mm) cc_final: 0.8753 (mm) REVERT: C 1034 LEU cc_start: 0.9288 (mp) cc_final: 0.8179 (tt) REVERT: C 1041 ASP cc_start: 0.8896 (m-30) cc_final: 0.8585 (t0) REVERT: C 1064 HIS cc_start: 0.8980 (m-70) cc_final: 0.8545 (m-70) REVERT: H 74 MET cc_start: 0.8776 (ppp) cc_final: 0.8468 (mpp) REVERT: H 81 MET cc_start: 0.9057 (tpt) cc_final: 0.8670 (tpt) REVERT: H 219 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7570 (ttpt) REVERT: L 104 LYS cc_start: 0.7378 (tptt) cc_final: 0.6683 (tttt) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1782 time to fit residues: 108.3887 Evaluate side-chains 288 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 233 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 450 ASN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 52 GLN C 388 ASN C 703 ASN L 190 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.092751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058828 restraints weight = 117103.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061502 restraints weight = 67908.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063452 restraints weight = 46510.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064799 restraints weight = 35056.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065738 restraints weight = 28537.090| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27880 Z= 0.253 Angle : 0.666 8.130 38116 Z= 0.350 Chirality : 0.046 0.231 4513 Planarity : 0.005 0.113 4823 Dihedral : 5.496 48.945 4734 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.37 (0.14), residues: 3404 helix: 0.62 (0.19), residues: 741 sheet: -0.04 (0.17), residues: 868 loop : -0.66 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 567 TYR 0.027 0.002 TYR A 741 PHE 0.022 0.002 PHE C1062 TRP 0.013 0.002 TRP C 353 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00513 (27788) covalent geometry : angle 0.65817 (37882) SS BOND : bond 0.00312 ( 42) SS BOND : angle 1.17173 ( 84) hydrogen bonds : bond 0.04395 ( 1178) hydrogen bonds : angle 5.88621 ( 3228) link_BETA1-4 : bond 0.00309 ( 11) link_BETA1-4 : angle 1.60824 ( 33) link_BETA1-6 : bond 0.00142 ( 1) link_BETA1-6 : angle 1.39487 ( 3) link_NAG-ASN : bond 0.00585 ( 38) link_NAG-ASN : angle 1.64623 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8349 (m100) cc_final: 0.8108 (m100) REVERT: A 241 LEU cc_start: 0.8810 (mt) cc_final: 0.8425 (mt) REVERT: A 350 VAL cc_start: 0.8952 (p) cc_final: 0.8632 (p) REVERT: A 351 TYR cc_start: 0.9516 (p90) cc_final: 0.8973 (p90) REVERT: A 365 TYR cc_start: 0.8940 (m-80) cc_final: 0.8706 (m-80) REVERT: A 380 TYR cc_start: 0.8904 (m-80) cc_final: 0.8612 (m-80) REVERT: A 403 ARG cc_start: 0.9347 (ptt90) cc_final: 0.9097 (ptp-110) REVERT: A 456 PHE cc_start: 0.9535 (m-10) cc_final: 0.9201 (m-80) REVERT: A 465 GLU cc_start: 0.7500 (tp30) cc_final: 0.6946 (tp30) REVERT: A 773 GLU cc_start: 0.9058 (tt0) cc_final: 0.8532 (tp30) REVERT: A 820 ASP cc_start: 0.8964 (m-30) cc_final: 0.8751 (m-30) REVERT: A 856 ASN cc_start: 0.9185 (m-40) cc_final: 0.8457 (p0) REVERT: A 869 MET cc_start: 0.8860 (mtp) cc_final: 0.8650 (mtp) REVERT: A 950 ASP cc_start: 0.9090 (t0) cc_final: 0.8863 (t0) REVERT: A 978 ASN cc_start: 0.9640 (m-40) cc_final: 0.9239 (t0) REVERT: A 990 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9160 (pp20) REVERT: A 1002 GLN cc_start: 0.9271 (tt0) cc_final: 0.8772 (tm-30) REVERT: A 1029 MET cc_start: 0.9281 (tmm) cc_final: 0.9031 (tmm) REVERT: A 1034 LEU cc_start: 0.9352 (mp) cc_final: 0.8928 (mt) REVERT: A 1040 VAL cc_start: 0.9473 (t) cc_final: 0.9112 (t) REVERT: A 1067 TYR cc_start: 0.8771 (t80) cc_final: 0.8536 (t80) REVERT: B 118 LEU cc_start: 0.9697 (tt) cc_final: 0.9475 (mt) REVERT: B 241 LEU cc_start: 0.9513 (tp) cc_final: 0.9184 (pp) REVERT: B 740 MET cc_start: 0.9459 (tpt) cc_final: 0.9207 (tpp) REVERT: B 898 PHE cc_start: 0.8522 (t80) cc_final: 0.8216 (t80) REVERT: B 936 ASP cc_start: 0.9267 (m-30) cc_final: 0.9058 (m-30) REVERT: B 983 ARG cc_start: 0.9151 (mtp180) cc_final: 0.8526 (ttm170) REVERT: C 92 PHE cc_start: 0.8766 (t80) cc_final: 0.8496 (t80) REVERT: C 104 TRP cc_start: 0.8332 (m-90) cc_final: 0.7272 (m-90) REVERT: C 201 PHE cc_start: 0.8192 (m-80) cc_final: 0.7985 (m-80) REVERT: C 229 LEU cc_start: 0.9743 (mt) cc_final: 0.9506 (tp) REVERT: C 238 PHE cc_start: 0.9284 (p90) cc_final: 0.8573 (p90) REVERT: C 269 TYR cc_start: 0.7078 (m-10) cc_final: 0.6460 (m-10) REVERT: C 279 TYR cc_start: 0.6617 (m-10) cc_final: 0.6197 (m-10) REVERT: C 434 ILE cc_start: 0.9258 (mt) cc_final: 0.8937 (tp) REVERT: C 697 MET cc_start: 0.7120 (ppp) cc_final: 0.6917 (ppp) REVERT: C 726 ILE cc_start: 0.8761 (tt) cc_final: 0.8540 (tp) REVERT: C 740 MET cc_start: 0.9474 (ttt) cc_final: 0.9020 (tpt) REVERT: C 759 PHE cc_start: 0.8631 (m-80) cc_final: 0.8386 (m-80) REVERT: C 776 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9161 (mmmm) REVERT: C 872 GLN cc_start: 0.9181 (mt0) cc_final: 0.8688 (mt0) REVERT: C 884 SER cc_start: 0.8999 (p) cc_final: 0.8791 (p) REVERT: C 886 TRP cc_start: 0.8732 (p90) cc_final: 0.8166 (p90) REVERT: C 954 GLN cc_start: 0.9256 (mt0) cc_final: 0.8944 (tp40) REVERT: C 966 LEU cc_start: 0.9607 (tp) cc_final: 0.9156 (mm) REVERT: C 980 ILE cc_start: 0.9413 (mm) cc_final: 0.9185 (mm) REVERT: C 1001 LEU cc_start: 0.9161 (pp) cc_final: 0.8873 (pp) REVERT: C 1018 ILE cc_start: 0.9200 (mm) cc_final: 0.8934 (tt) REVERT: C 1050 MET cc_start: 0.7635 (ptp) cc_final: 0.7275 (ptp) REVERT: C 1064 HIS cc_start: 0.9144 (m-70) cc_final: 0.8640 (m90) REVERT: H 73 ASP cc_start: 0.9233 (t0) cc_final: 0.9022 (t0) REVERT: H 74 MET cc_start: 0.8726 (ppp) cc_final: 0.8262 (mpp) REVERT: H 81 MET cc_start: 0.9191 (tpt) cc_final: 0.8942 (tpt) REVERT: L 104 LYS cc_start: 0.7599 (tptt) cc_final: 0.6941 (tmtt) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.1790 time to fit residues: 98.5592 Evaluate side-chains 266 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 30 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 234 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 285 optimal weight: 0.0980 chunk 334 optimal weight: 40.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 66 HIS B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.094943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061466 restraints weight = 110983.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064369 restraints weight = 63190.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066366 restraints weight = 42478.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067775 restraints weight = 31788.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068788 restraints weight = 25650.075| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27880 Z= 0.128 Angle : 0.585 7.963 38116 Z= 0.301 Chirality : 0.045 0.200 4513 Planarity : 0.005 0.087 4823 Dihedral : 5.137 49.286 4734 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.16 (0.14), residues: 3404 helix: 0.94 (0.19), residues: 741 sheet: 0.01 (0.17), residues: 875 loop : -0.55 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 567 TYR 0.027 0.001 TYR A 741 PHE 0.027 0.001 PHE B 906 TRP 0.021 0.001 TRP A 64 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00277 (27788) covalent geometry : angle 0.57748 (37882) SS BOND : bond 0.00216 ( 42) SS BOND : angle 1.21650 ( 84) hydrogen bonds : bond 0.03901 ( 1178) hydrogen bonds : angle 5.60794 ( 3228) link_BETA1-4 : bond 0.00299 ( 11) link_BETA1-4 : angle 1.39302 ( 33) link_BETA1-6 : bond 0.00047 ( 1) link_BETA1-6 : angle 1.40747 ( 3) link_NAG-ASN : bond 0.00187 ( 38) link_NAG-ASN : angle 1.38035 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8126 (m100) cc_final: 0.7899 (m100) REVERT: A 223 LEU cc_start: 0.8796 (mp) cc_final: 0.8448 (mp) REVERT: A 229 LEU cc_start: 0.9313 (tp) cc_final: 0.8920 (tp) REVERT: A 241 LEU cc_start: 0.8678 (mt) cc_final: 0.8335 (mt) REVERT: A 350 VAL cc_start: 0.8925 (p) cc_final: 0.8673 (p) REVERT: A 351 TYR cc_start: 0.9514 (p90) cc_final: 0.8954 (p90) REVERT: A 354 ASN cc_start: 0.8401 (t0) cc_final: 0.8154 (t0) REVERT: A 365 TYR cc_start: 0.8881 (m-80) cc_final: 0.8626 (m-80) REVERT: A 456 PHE cc_start: 0.9519 (m-10) cc_final: 0.9124 (m-80) REVERT: A 505 TYR cc_start: 0.9442 (m-80) cc_final: 0.9192 (m-80) REVERT: A 697 MET cc_start: 0.6432 (ppp) cc_final: 0.5930 (ppp) REVERT: A 711 SER cc_start: 0.9686 (m) cc_final: 0.9455 (p) REVERT: A 740 MET cc_start: 0.8958 (tmm) cc_final: 0.8730 (tmm) REVERT: A 767 LEU cc_start: 0.9582 (mt) cc_final: 0.9173 (pp) REVERT: A 773 GLU cc_start: 0.9098 (tt0) cc_final: 0.8542 (tp30) REVERT: A 820 ASP cc_start: 0.8927 (m-30) cc_final: 0.8717 (m-30) REVERT: A 824 ASN cc_start: 0.8710 (m-40) cc_final: 0.8485 (m-40) REVERT: A 856 ASN cc_start: 0.9037 (m-40) cc_final: 0.8360 (p0) REVERT: A 869 MET cc_start: 0.8945 (mtp) cc_final: 0.8682 (mtp) REVERT: A 883 THR cc_start: 0.9403 (p) cc_final: 0.9185 (t) REVERT: A 900 MET cc_start: 0.9170 (mmm) cc_final: 0.8794 (mmt) REVERT: A 978 ASN cc_start: 0.9429 (m-40) cc_final: 0.8989 (t0) REVERT: A 1002 GLN cc_start: 0.9229 (tt0) cc_final: 0.8765 (tm-30) REVERT: A 1029 MET cc_start: 0.9323 (tmm) cc_final: 0.9066 (tmm) REVERT: A 1034 LEU cc_start: 0.9076 (mp) cc_final: 0.8876 (mp) REVERT: A 1036 GLN cc_start: 0.7789 (tt0) cc_final: 0.7439 (tt0) REVERT: A 1067 TYR cc_start: 0.8490 (t80) cc_final: 0.8274 (t80) REVERT: A 1106 GLN cc_start: 0.8238 (mp-120) cc_final: 0.8013 (mp10) REVERT: B 92 PHE cc_start: 0.8938 (t80) cc_final: 0.8530 (t80) REVERT: B 118 LEU cc_start: 0.9683 (tt) cc_final: 0.9478 (mt) REVERT: B 241 LEU cc_start: 0.9462 (tp) cc_final: 0.9130 (pp) REVERT: B 265 TYR cc_start: 0.9003 (p90) cc_final: 0.8744 (p90) REVERT: B 540 ASN cc_start: 0.9333 (p0) cc_final: 0.9062 (t0) REVERT: B 720 ILE cc_start: 0.9312 (mm) cc_final: 0.8890 (pt) REVERT: B 740 MET cc_start: 0.9451 (tpt) cc_final: 0.9184 (tpp) REVERT: B 758 SER cc_start: 0.9367 (t) cc_final: 0.8969 (t) REVERT: B 789 TYR cc_start: 0.8294 (m-10) cc_final: 0.7722 (m-10) REVERT: B 869 MET cc_start: 0.8954 (mtm) cc_final: 0.8708 (ptp) REVERT: B 898 PHE cc_start: 0.8618 (t80) cc_final: 0.8118 (t80) REVERT: B 900 MET cc_start: 0.8835 (ttm) cc_final: 0.8606 (tpp) REVERT: B 1000 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8273 (mtt180) REVERT: C 90 VAL cc_start: 0.8514 (t) cc_final: 0.8310 (t) REVERT: C 92 PHE cc_start: 0.8713 (t80) cc_final: 0.8450 (t80) REVERT: C 104 TRP cc_start: 0.8271 (m-90) cc_final: 0.7211 (m-90) REVERT: C 238 PHE cc_start: 0.9182 (p90) cc_final: 0.8452 (p90) REVERT: C 269 TYR cc_start: 0.7353 (m-10) cc_final: 0.6749 (m-10) REVERT: C 279 TYR cc_start: 0.6477 (m-10) cc_final: 0.5998 (m-10) REVERT: C 434 ILE cc_start: 0.9366 (mt) cc_final: 0.8997 (tp) REVERT: C 650 LEU cc_start: 0.9076 (mt) cc_final: 0.8847 (mt) REVERT: C 697 MET cc_start: 0.6526 (ppp) cc_final: 0.6306 (ppp) REVERT: C 740 MET cc_start: 0.9464 (ttt) cc_final: 0.8980 (tpt) REVERT: C 763 LEU cc_start: 0.8543 (pp) cc_final: 0.8081 (pp) REVERT: C 767 LEU cc_start: 0.8964 (mm) cc_final: 0.8096 (tp) REVERT: C 774 GLN cc_start: 0.9628 (mm-40) cc_final: 0.9410 (mm-40) REVERT: C 776 LYS cc_start: 0.9511 (mmtt) cc_final: 0.9181 (mmmm) REVERT: C 869 MET cc_start: 0.8868 (mtt) cc_final: 0.8564 (mtp) REVERT: C 872 GLN cc_start: 0.9089 (mt0) cc_final: 0.8298 (mm-40) REVERT: C 886 TRP cc_start: 0.8628 (p90) cc_final: 0.8212 (p90) REVERT: C 900 MET cc_start: 0.9192 (mmp) cc_final: 0.8876 (mmm) REVERT: C 902 MET cc_start: 0.9077 (mpp) cc_final: 0.8785 (mmm) REVERT: C 954 GLN cc_start: 0.9245 (mt0) cc_final: 0.8903 (tp40) REVERT: C 966 LEU cc_start: 0.9573 (tp) cc_final: 0.9088 (mm) REVERT: C 980 ILE cc_start: 0.9413 (mm) cc_final: 0.8972 (mm) REVERT: C 1001 LEU cc_start: 0.9248 (pp) cc_final: 0.8934 (pp) REVERT: C 1018 ILE cc_start: 0.9126 (mm) cc_final: 0.8792 (tt) REVERT: C 1064 HIS cc_start: 0.9135 (m-70) cc_final: 0.8756 (m90) REVERT: H 73 ASP cc_start: 0.9246 (t0) cc_final: 0.9015 (t0) REVERT: H 74 MET cc_start: 0.8704 (ppp) cc_final: 0.8275 (mpp) REVERT: H 81 MET cc_start: 0.8182 (tpt) cc_final: 0.7881 (tpt) REVERT: L 4 MET cc_start: 0.7623 (mtp) cc_final: 0.7251 (ttm) REVERT: L 104 LYS cc_start: 0.7487 (tptt) cc_final: 0.6779 (tmtt) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1747 time to fit residues: 102.2623 Evaluate side-chains 279 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 155 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 239 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 296 optimal weight: 0.0980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN L 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062070 restraints weight = 113807.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064975 restraints weight = 64538.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067058 restraints weight = 43483.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068442 restraints weight = 32414.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069520 restraints weight = 26104.719| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27880 Z= 0.113 Angle : 0.574 11.589 38116 Z= 0.294 Chirality : 0.045 0.242 4513 Planarity : 0.004 0.074 4823 Dihedral : 4.871 50.253 4734 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.12 (0.14), residues: 3404 helix: 0.98 (0.19), residues: 745 sheet: 0.03 (0.17), residues: 876 loop : -0.53 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 567 TYR 0.022 0.001 TYR A 741 PHE 0.038 0.001 PHE B 906 TRP 0.016 0.001 TRP A 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00246 (27788) covalent geometry : angle 0.56574 (37882) SS BOND : bond 0.00218 ( 42) SS BOND : angle 1.41926 ( 84) hydrogen bonds : bond 0.03759 ( 1178) hydrogen bonds : angle 5.48703 ( 3228) link_BETA1-4 : bond 0.00314 ( 11) link_BETA1-4 : angle 1.36661 ( 33) link_BETA1-6 : bond 0.00138 ( 1) link_BETA1-6 : angle 1.39181 ( 3) link_NAG-ASN : bond 0.00175 ( 38) link_NAG-ASN : angle 1.35251 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8090 (m100) cc_final: 0.7848 (m100) REVERT: A 223 LEU cc_start: 0.8858 (mp) cc_final: 0.8509 (mp) REVERT: A 350 VAL cc_start: 0.9207 (p) cc_final: 0.8847 (p) REVERT: A 351 TYR cc_start: 0.9385 (p90) cc_final: 0.8905 (p90) REVERT: A 365 TYR cc_start: 0.8869 (m-80) cc_final: 0.8619 (m-80) REVERT: A 456 PHE cc_start: 0.9527 (m-10) cc_final: 0.9112 (m-80) REVERT: A 462 LYS cc_start: 0.8133 (tmmt) cc_final: 0.7868 (tmtt) REVERT: A 505 TYR cc_start: 0.9439 (m-80) cc_final: 0.9178 (m-80) REVERT: A 697 MET cc_start: 0.6905 (ppp) cc_final: 0.6259 (ppp) REVERT: A 767 LEU cc_start: 0.9540 (mt) cc_final: 0.9151 (pp) REVERT: A 773 GLU cc_start: 0.9000 (tt0) cc_final: 0.8491 (tp30) REVERT: A 820 ASP cc_start: 0.8909 (m-30) cc_final: 0.8675 (m-30) REVERT: A 824 ASN cc_start: 0.8676 (m-40) cc_final: 0.8439 (m-40) REVERT: A 856 ASN cc_start: 0.8881 (m-40) cc_final: 0.8241 (p0) REVERT: A 869 MET cc_start: 0.8903 (mtp) cc_final: 0.8671 (mtp) REVERT: A 883 THR cc_start: 0.9382 (p) cc_final: 0.9158 (t) REVERT: A 900 MET cc_start: 0.9143 (mmm) cc_final: 0.8718 (mmt) REVERT: A 902 MET cc_start: 0.9066 (mmm) cc_final: 0.8661 (mmm) REVERT: A 966 LEU cc_start: 0.9386 (mt) cc_final: 0.8958 (mp) REVERT: A 1002 GLN cc_start: 0.9226 (tt0) cc_final: 0.8766 (tm-30) REVERT: A 1040 VAL cc_start: 0.9445 (t) cc_final: 0.9159 (p) REVERT: B 92 PHE cc_start: 0.8873 (t80) cc_final: 0.8536 (t80) REVERT: B 241 LEU cc_start: 0.9466 (tp) cc_final: 0.9070 (pp) REVERT: B 265 TYR cc_start: 0.9002 (p90) cc_final: 0.8748 (p90) REVERT: B 540 ASN cc_start: 0.9350 (p0) cc_final: 0.9105 (t0) REVERT: B 720 ILE cc_start: 0.9345 (mm) cc_final: 0.8870 (pt) REVERT: B 740 MET cc_start: 0.9458 (tpt) cc_final: 0.9196 (tpp) REVERT: B 869 MET cc_start: 0.8934 (mtm) cc_final: 0.8459 (mtm) REVERT: B 898 PHE cc_start: 0.8543 (t80) cc_final: 0.8152 (t80) REVERT: B 906 PHE cc_start: 0.8490 (m-10) cc_final: 0.7941 (m-10) REVERT: B 936 ASP cc_start: 0.9269 (m-30) cc_final: 0.9053 (m-30) REVERT: B 983 ARG cc_start: 0.9016 (mtp180) cc_final: 0.8786 (ttp80) REVERT: B 1000 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8166 (mtt180) REVERT: B 1030 SER cc_start: 0.8770 (m) cc_final: 0.8162 (p) REVERT: B 1064 HIS cc_start: 0.8623 (m-70) cc_final: 0.8006 (m90) REVERT: C 92 PHE cc_start: 0.8615 (t80) cc_final: 0.8379 (t80) REVERT: C 104 TRP cc_start: 0.8299 (m-90) cc_final: 0.7035 (m-90) REVERT: C 238 PHE cc_start: 0.9125 (p90) cc_final: 0.8398 (p90) REVERT: C 269 TYR cc_start: 0.7449 (m-10) cc_final: 0.6876 (m-10) REVERT: C 279 TYR cc_start: 0.6396 (m-10) cc_final: 0.5912 (m-10) REVERT: C 396 TYR cc_start: 0.7974 (m-80) cc_final: 0.7615 (m-10) REVERT: C 398 ASP cc_start: 0.8428 (m-30) cc_final: 0.6728 (t70) REVERT: C 429 PHE cc_start: 0.7599 (t80) cc_final: 0.7382 (t80) REVERT: C 434 ILE cc_start: 0.9362 (mt) cc_final: 0.8986 (tp) REVERT: C 650 LEU cc_start: 0.9084 (mt) cc_final: 0.8851 (mt) REVERT: C 731 MET cc_start: 0.8652 (mtp) cc_final: 0.7840 (mtp) REVERT: C 740 MET cc_start: 0.9467 (ttt) cc_final: 0.8982 (tpt) REVERT: C 763 LEU cc_start: 0.8500 (pp) cc_final: 0.8032 (pp) REVERT: C 767 LEU cc_start: 0.8969 (mm) cc_final: 0.8084 (tp) REVERT: C 776 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9258 (mmmm) REVERT: C 819 GLU cc_start: 0.7927 (mt-10) cc_final: 0.6088 (tp30) REVERT: C 869 MET cc_start: 0.8869 (mtt) cc_final: 0.8525 (mtp) REVERT: C 872 GLN cc_start: 0.9075 (mt0) cc_final: 0.8265 (mm-40) REVERT: C 874 THR cc_start: 0.9549 (p) cc_final: 0.9344 (p) REVERT: C 886 TRP cc_start: 0.8625 (p90) cc_final: 0.8211 (p90) REVERT: C 902 MET cc_start: 0.9190 (mpp) cc_final: 0.8930 (mmm) REVERT: C 950 ASP cc_start: 0.9046 (t70) cc_final: 0.8830 (t0) REVERT: C 966 LEU cc_start: 0.9549 (tp) cc_final: 0.9049 (mm) REVERT: C 980 ILE cc_start: 0.9395 (mm) cc_final: 0.8750 (mm) REVERT: C 983 ARG cc_start: 0.8739 (ptp-170) cc_final: 0.8187 (ptt180) REVERT: C 1001 LEU cc_start: 0.9253 (pp) cc_final: 0.8950 (pp) REVERT: C 1017 GLU cc_start: 0.8685 (pp20) cc_final: 0.8391 (pp20) REVERT: C 1018 ILE cc_start: 0.9155 (mm) cc_final: 0.8213 (mm) REVERT: C 1064 HIS cc_start: 0.9104 (m-70) cc_final: 0.8477 (m-70) REVERT: H 63 LYS cc_start: 0.5767 (pttm) cc_final: 0.5529 (pttm) REVERT: H 74 MET cc_start: 0.8758 (ppp) cc_final: 0.8484 (mpp) REVERT: H 81 MET cc_start: 0.8327 (tpt) cc_final: 0.8004 (tpt) REVERT: L 4 MET cc_start: 0.7349 (mtp) cc_final: 0.6853 (ttm) REVERT: L 104 LYS cc_start: 0.7432 (tptt) cc_final: 0.6831 (tmtt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1789 time to fit residues: 102.7200 Evaluate side-chains 279 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 253 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 96 optimal weight: 0.0070 chunk 42 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062182 restraints weight = 113841.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065123 restraints weight = 64805.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067143 restraints weight = 43453.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068624 restraints weight = 32334.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069603 restraints weight = 25922.051| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27880 Z= 0.121 Angle : 0.580 8.041 38116 Z= 0.299 Chirality : 0.045 0.231 4513 Planarity : 0.005 0.094 4823 Dihedral : 4.779 50.299 4734 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.11 (0.14), residues: 3404 helix: 0.91 (0.19), residues: 750 sheet: 0.08 (0.17), residues: 870 loop : -0.52 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 78 TYR 0.030 0.001 TYR C 904 PHE 0.049 0.001 PHE B 906 TRP 0.012 0.001 TRP A 353 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00266 (27788) covalent geometry : angle 0.57159 (37882) SS BOND : bond 0.00218 ( 42) SS BOND : angle 1.43915 ( 84) hydrogen bonds : bond 0.03747 ( 1178) hydrogen bonds : angle 5.48500 ( 3228) link_BETA1-4 : bond 0.00311 ( 11) link_BETA1-4 : angle 1.37142 ( 33) link_BETA1-6 : bond 0.00161 ( 1) link_BETA1-6 : angle 1.37764 ( 3) link_NAG-ASN : bond 0.00165 ( 38) link_NAG-ASN : angle 1.32290 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8190 (m-80) cc_final: 0.7492 (m-80) REVERT: A 223 LEU cc_start: 0.8885 (mp) cc_final: 0.8524 (mp) REVERT: A 229 LEU cc_start: 0.9348 (tp) cc_final: 0.9119 (tp) REVERT: A 350 VAL cc_start: 0.9073 (p) cc_final: 0.8815 (p) REVERT: A 351 TYR cc_start: 0.9505 (p90) cc_final: 0.8894 (p90) REVERT: A 365 TYR cc_start: 0.8893 (m-80) cc_final: 0.8638 (m-80) REVERT: A 456 PHE cc_start: 0.9529 (m-10) cc_final: 0.9111 (m-80) REVERT: A 462 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7879 (tmtt) REVERT: A 486 PHE cc_start: 0.7689 (t80) cc_final: 0.7457 (t80) REVERT: A 505 TYR cc_start: 0.9462 (m-80) cc_final: 0.9198 (m-80) REVERT: A 697 MET cc_start: 0.6949 (ppp) cc_final: 0.6540 (ppp) REVERT: A 712 ILE cc_start: 0.9385 (tt) cc_final: 0.9055 (mt) REVERT: A 773 GLU cc_start: 0.9150 (tt0) cc_final: 0.8555 (tp30) REVERT: A 820 ASP cc_start: 0.8893 (m-30) cc_final: 0.8669 (m-30) REVERT: A 856 ASN cc_start: 0.8880 (m-40) cc_final: 0.8334 (p0) REVERT: A 869 MET cc_start: 0.8853 (mtp) cc_final: 0.8634 (mtp) REVERT: A 1002 GLN cc_start: 0.9113 (tt0) cc_final: 0.8740 (tm-30) REVERT: A 1067 TYR cc_start: 0.8514 (t80) cc_final: 0.8093 (t80) REVERT: B 241 LEU cc_start: 0.9462 (tp) cc_final: 0.9104 (pp) REVERT: B 540 ASN cc_start: 0.9389 (p0) cc_final: 0.9141 (t0) REVERT: B 740 MET cc_start: 0.9475 (tpt) cc_final: 0.9221 (tpp) REVERT: B 753 LEU cc_start: 0.9600 (tp) cc_final: 0.9389 (tt) REVERT: B 789 TYR cc_start: 0.8371 (m-10) cc_final: 0.8030 (m-10) REVERT: B 869 MET cc_start: 0.8937 (mtm) cc_final: 0.8501 (mtp) REVERT: B 898 PHE cc_start: 0.8553 (t80) cc_final: 0.8109 (t80) REVERT: B 900 MET cc_start: 0.8336 (tpp) cc_final: 0.8092 (tpp) REVERT: B 906 PHE cc_start: 0.8611 (m-10) cc_final: 0.8368 (m-10) REVERT: B 936 ASP cc_start: 0.9282 (m-30) cc_final: 0.9078 (m-30) REVERT: B 983 ARG cc_start: 0.8962 (mtp180) cc_final: 0.8686 (ttp80) REVERT: B 1002 GLN cc_start: 0.9152 (mp10) cc_final: 0.8863 (mp10) REVERT: B 1030 SER cc_start: 0.8839 (m) cc_final: 0.8574 (p) REVERT: C 92 PHE cc_start: 0.8718 (t80) cc_final: 0.8422 (t80) REVERT: C 104 TRP cc_start: 0.8305 (m-90) cc_final: 0.7087 (m-90) REVERT: C 201 PHE cc_start: 0.8958 (m-80) cc_final: 0.8713 (m-80) REVERT: C 238 PHE cc_start: 0.9153 (p90) cc_final: 0.8394 (p90) REVERT: C 269 TYR cc_start: 0.7372 (m-10) cc_final: 0.6800 (m-10) REVERT: C 279 TYR cc_start: 0.6425 (m-10) cc_final: 0.5953 (m-10) REVERT: C 398 ASP cc_start: 0.8446 (m-30) cc_final: 0.6782 (t70) REVERT: C 429 PHE cc_start: 0.7631 (t80) cc_final: 0.7412 (t80) REVERT: C 434 ILE cc_start: 0.9364 (mt) cc_final: 0.8992 (tp) REVERT: C 650 LEU cc_start: 0.9086 (mt) cc_final: 0.8851 (mt) REVERT: C 697 MET cc_start: 0.6741 (ppp) cc_final: 0.6423 (ppp) REVERT: C 731 MET cc_start: 0.8636 (mtp) cc_final: 0.7911 (mtp) REVERT: C 740 MET cc_start: 0.9466 (ttt) cc_final: 0.8989 (tpt) REVERT: C 763 LEU cc_start: 0.8457 (pp) cc_final: 0.8013 (pp) REVERT: C 767 LEU cc_start: 0.8931 (mm) cc_final: 0.8029 (tp) REVERT: C 773 GLU cc_start: 0.9082 (pt0) cc_final: 0.8750 (pp20) REVERT: C 776 LYS cc_start: 0.9537 (mmtt) cc_final: 0.9257 (mmmm) REVERT: C 872 GLN cc_start: 0.9078 (mt0) cc_final: 0.8403 (mm-40) REVERT: C 886 TRP cc_start: 0.8586 (p90) cc_final: 0.8183 (p90) REVERT: C 950 ASP cc_start: 0.9036 (t70) cc_final: 0.8813 (t0) REVERT: C 966 LEU cc_start: 0.9557 (tp) cc_final: 0.9072 (mm) REVERT: C 979 ASP cc_start: 0.9711 (m-30) cc_final: 0.9395 (m-30) REVERT: C 980 ILE cc_start: 0.9373 (mm) cc_final: 0.8622 (mm) REVERT: C 983 ARG cc_start: 0.8723 (ptp-170) cc_final: 0.8199 (ptt180) REVERT: C 1001 LEU cc_start: 0.9268 (pp) cc_final: 0.8956 (pp) REVERT: C 1017 GLU cc_start: 0.8673 (pp20) cc_final: 0.8379 (pp20) REVERT: C 1018 ILE cc_start: 0.9184 (mm) cc_final: 0.8232 (mm) REVERT: C 1064 HIS cc_start: 0.9137 (m-70) cc_final: 0.8496 (m-70) REVERT: H 74 MET cc_start: 0.8781 (ppp) cc_final: 0.8545 (mpp) REVERT: H 81 MET cc_start: 0.8356 (tpt) cc_final: 0.8031 (tpt) REVERT: L 104 LYS cc_start: 0.7414 (tptt) cc_final: 0.6783 (tmtt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1721 time to fit residues: 98.5688 Evaluate side-chains 273 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 12 optimal weight: 0.0670 chunk 304 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1083 HIS B 30 ASN B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.094935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061335 restraints weight = 112524.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064182 restraints weight = 64409.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066244 restraints weight = 43558.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067612 restraints weight = 32446.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068562 restraints weight = 26203.622| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27880 Z= 0.130 Angle : 0.584 9.791 38116 Z= 0.300 Chirality : 0.045 0.394 4513 Planarity : 0.004 0.076 4823 Dihedral : 4.721 49.900 4734 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.10 (0.14), residues: 3404 helix: 0.96 (0.20), residues: 740 sheet: 0.11 (0.17), residues: 868 loop : -0.53 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 567 TYR 0.027 0.001 TYR A 741 PHE 0.035 0.001 PHE B 906 TRP 0.022 0.001 TRP A 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00281 (27788) covalent geometry : angle 0.57621 (37882) SS BOND : bond 0.00225 ( 42) SS BOND : angle 1.31976 ( 84) hydrogen bonds : bond 0.03773 ( 1178) hydrogen bonds : angle 5.55335 ( 3228) link_BETA1-4 : bond 0.00336 ( 11) link_BETA1-4 : angle 1.37769 ( 33) link_BETA1-6 : bond 0.00322 ( 1) link_BETA1-6 : angle 1.39280 ( 3) link_NAG-ASN : bond 0.00157 ( 38) link_NAG-ASN : angle 1.31295 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8269 (m100) cc_final: 0.8023 (m100) REVERT: A 223 LEU cc_start: 0.8892 (mp) cc_final: 0.8540 (mp) REVERT: A 229 LEU cc_start: 0.9126 (tp) cc_final: 0.8915 (tp) REVERT: A 350 VAL cc_start: 0.9242 (p) cc_final: 0.8893 (p) REVERT: A 351 TYR cc_start: 0.9399 (p90) cc_final: 0.8760 (p90) REVERT: A 365 TYR cc_start: 0.8975 (m-80) cc_final: 0.8736 (m-80) REVERT: A 456 PHE cc_start: 0.9550 (m-10) cc_final: 0.9114 (m-80) REVERT: A 462 LYS cc_start: 0.8170 (tmmt) cc_final: 0.7890 (tmtt) REVERT: A 486 PHE cc_start: 0.7700 (t80) cc_final: 0.7465 (t80) REVERT: A 505 TYR cc_start: 0.9413 (m-80) cc_final: 0.9153 (m-80) REVERT: A 697 MET cc_start: 0.7045 (ppp) cc_final: 0.6668 (ppp) REVERT: A 767 LEU cc_start: 0.9549 (mt) cc_final: 0.9147 (pp) REVERT: A 773 GLU cc_start: 0.9099 (tt0) cc_final: 0.8497 (tp30) REVERT: A 820 ASP cc_start: 0.8900 (m-30) cc_final: 0.8672 (m-30) REVERT: A 856 ASN cc_start: 0.8915 (m-40) cc_final: 0.8366 (p0) REVERT: A 902 MET cc_start: 0.9045 (mmm) cc_final: 0.8674 (mmm) REVERT: A 950 ASP cc_start: 0.9137 (m-30) cc_final: 0.8925 (m-30) REVERT: A 1002 GLN cc_start: 0.9178 (tt0) cc_final: 0.8738 (tm-30) REVERT: A 1029 MET cc_start: 0.9360 (tmm) cc_final: 0.9117 (tmm) REVERT: A 1040 VAL cc_start: 0.9493 (t) cc_final: 0.9235 (t) REVERT: B 241 LEU cc_start: 0.9466 (tp) cc_final: 0.9109 (pp) REVERT: B 740 MET cc_start: 0.9515 (tpt) cc_final: 0.9282 (tpp) REVERT: B 753 LEU cc_start: 0.9618 (tp) cc_final: 0.9407 (tt) REVERT: B 789 TYR cc_start: 0.8392 (m-10) cc_final: 0.8070 (m-10) REVERT: B 819 GLU cc_start: 0.8800 (pt0) cc_final: 0.8311 (mt-10) REVERT: B 820 ASP cc_start: 0.8809 (m-30) cc_final: 0.8542 (m-30) REVERT: B 869 MET cc_start: 0.8946 (mtm) cc_final: 0.8520 (mtp) REVERT: B 898 PHE cc_start: 0.8504 (t80) cc_final: 0.8095 (t80) REVERT: B 900 MET cc_start: 0.8308 (tpp) cc_final: 0.8051 (tpp) REVERT: B 906 PHE cc_start: 0.8694 (m-10) cc_final: 0.8411 (m-10) REVERT: B 936 ASP cc_start: 0.9246 (m-30) cc_final: 0.9038 (m-30) REVERT: B 983 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8695 (ttp80) REVERT: B 1002 GLN cc_start: 0.9142 (mp10) cc_final: 0.8807 (mp10) REVERT: B 1030 SER cc_start: 0.8866 (m) cc_final: 0.8461 (p) REVERT: C 86 PHE cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: C 92 PHE cc_start: 0.8628 (t80) cc_final: 0.8385 (t80) REVERT: C 104 TRP cc_start: 0.8407 (m-90) cc_final: 0.7220 (m-90) REVERT: C 195 LYS cc_start: 0.9532 (pttm) cc_final: 0.9200 (pttm) REVERT: C 238 PHE cc_start: 0.9158 (p90) cc_final: 0.8453 (p90) REVERT: C 279 TYR cc_start: 0.6451 (m-10) cc_final: 0.5979 (m-10) REVERT: C 398 ASP cc_start: 0.8343 (m-30) cc_final: 0.6530 (t70) REVERT: C 429 PHE cc_start: 0.7627 (t80) cc_final: 0.7409 (t80) REVERT: C 434 ILE cc_start: 0.9367 (mt) cc_final: 0.9000 (tp) REVERT: C 650 LEU cc_start: 0.9097 (mt) cc_final: 0.8782 (mt) REVERT: C 697 MET cc_start: 0.6289 (ppp) cc_final: 0.5890 (ppp) REVERT: C 740 MET cc_start: 0.9456 (ttt) cc_final: 0.8966 (tpt) REVERT: C 776 LYS cc_start: 0.9532 (mmtt) cc_final: 0.9253 (mmmm) REVERT: C 872 GLN cc_start: 0.9096 (mt0) cc_final: 0.8427 (mm-40) REVERT: C 886 TRP cc_start: 0.8647 (p90) cc_final: 0.8241 (p90) REVERT: C 950 ASP cc_start: 0.9028 (t70) cc_final: 0.8819 (t0) REVERT: C 1001 LEU cc_start: 0.9264 (pp) cc_final: 0.8970 (pp) REVERT: C 1017 GLU cc_start: 0.8677 (pp20) cc_final: 0.8357 (pp20) REVERT: C 1018 ILE cc_start: 0.9181 (mm) cc_final: 0.8266 (mm) REVERT: C 1064 HIS cc_start: 0.9154 (m-70) cc_final: 0.8499 (m-70) REVERT: H 74 MET cc_start: 0.8780 (ppp) cc_final: 0.8538 (mpp) REVERT: H 80 TYR cc_start: 0.9711 (m-80) cc_final: 0.9487 (m-80) REVERT: H 81 MET cc_start: 0.8342 (tpt) cc_final: 0.7980 (tpt) REVERT: L 104 LYS cc_start: 0.7473 (tptt) cc_final: 0.6854 (tmtt) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1810 time to fit residues: 101.3363 Evaluate side-chains 274 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 218 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 276 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 450 ASN B 536 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1005 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 703 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.092509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058592 restraints weight = 115033.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061330 restraints weight = 66442.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063231 restraints weight = 45232.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064518 restraints weight = 34231.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065436 restraints weight = 27854.698| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27880 Z= 0.215 Angle : 0.646 7.962 38116 Z= 0.338 Chirality : 0.046 0.295 4513 Planarity : 0.005 0.087 4823 Dihedral : 5.073 47.492 4734 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.37 (0.14), residues: 3404 helix: 0.57 (0.19), residues: 752 sheet: -0.07 (0.17), residues: 866 loop : -0.63 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 346 TYR 0.033 0.002 TYR A 873 PHE 0.041 0.002 PHE B 906 TRP 0.025 0.002 TRP A 104 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00447 (27788) covalent geometry : angle 0.63833 (37882) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.23601 ( 84) hydrogen bonds : bond 0.04210 ( 1178) hydrogen bonds : angle 5.85426 ( 3228) link_BETA1-4 : bond 0.00285 ( 11) link_BETA1-4 : angle 1.49326 ( 33) link_BETA1-6 : bond 0.00247 ( 1) link_BETA1-6 : angle 1.39803 ( 3) link_NAG-ASN : bond 0.00316 ( 38) link_NAG-ASN : angle 1.45724 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5510.36 seconds wall clock time: 95 minutes 48.99 seconds (5748.99 seconds total)