Starting phenix.real_space_refine on Sat Jul 4 16:36:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgz_32493/07_2026/7wgz_32493.cif" } resolution = 4.5 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= 0.003 sd= 0.064 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 96 5.16 5 C 13993 2.51 5 N 3653 2.21 5 O 4178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21920 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7406 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 10 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6874 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 45, 'TRANS': 904} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7290 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 46, 'TRANS': 914} Chain breaks: 10 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 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 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 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 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.06, per 1000 atoms: 0.23 Number of scatterers: 21920 At special positions: 0 Unit cell: (130.95, 130.95, 184.95, 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 96 16.00 O 4178 8.00 N 3653 7.00 C 13993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1302 " - " ASN A1074 " " NAG A1305 " - " ASN A 282 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1074 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 898.7 milliseconds 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 26.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.835A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.705A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.187A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.882A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.009A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 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 982 removed outlier: 3.560A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.852A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.804A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.062A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.611A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 409' Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.605A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.649A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.816A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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 removed outlier: 3.558A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.800A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.249A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.281A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.696A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.933A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.482A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.617A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.228A 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 removed outlier: 3.696A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.886A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.875A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.612A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (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 removed outlier: 3.658A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.982A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.150A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 removed outlier: 3.573A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.803A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 9.371A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.859A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.005A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.283A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.946A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.411A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.360A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.868A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.601A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 9.085A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.730A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.651A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.093A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC2, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.304A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.951A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.709A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.693A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B1088 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.801A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.718A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.518A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.885A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.994A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.743A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1086 through 1088 Processing sheet with id=AE6, first strand: chain 'C' and resid 1093 through 1097 923 hydrogen bonds defined for protein. 2541 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3550 1.31 - 1.44: 6045 1.44 - 1.56: 12660 1.56 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 22375 Sorted by residual: bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.524 -0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.518 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 22370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 29227 1.47 - 2.94: 959 2.94 - 4.41: 217 4.41 - 5.88: 88 5.88 - 7.35: 18 Bond angle restraints: 30509 Sorted by residual: angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.53 109.60 3.93 9.80e-01 1.04e+00 1.61e+01 angle pdb=" N GLN A 675 " pdb=" CA GLN A 675 " pdb=" C GLN A 675 " ideal model delta sigma weight residual 108.34 113.12 -4.78 1.31e+00 5.83e-01 1.33e+01 angle pdb=" N GLY A1059 " pdb=" CA GLY A1059 " pdb=" C GLY A1059 " ideal model delta sigma weight residual 111.19 115.38 -4.19 1.45e+00 4.76e-01 8.36e+00 angle pdb=" C SER B 810 " pdb=" N LYS B 811 " pdb=" CA LYS B 811 " ideal model delta sigma weight residual 121.80 128.67 -6.87 2.44e+00 1.68e-01 7.92e+00 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" O GLY A 416 " ideal model delta sigma weight residual 122.37 120.34 2.03 7.30e-01 1.88e+00 7.75e+00 ... (remaining 30504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12084 17.85 - 35.70: 752 35.70 - 53.55: 98 53.55 - 71.39: 25 71.39 - 89.24: 22 Dihedral angle restraints: 12981 sinusoidal: 4620 harmonic: 8361 Sorted by residual: dihedral pdb=" CA TYR B 200 " pdb=" C TYR B 200 " pdb=" N PHE B 201 " pdb=" CA PHE B 201 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLN C1106 " pdb=" C GLN C1106 " pdb=" N ARG C1107 " pdb=" CA ARG C1107 " ideal model delta harmonic sigma weight residual 180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PHE A 106 " pdb=" C PHE A 106 " pdb=" N GLY A 107 " pdb=" CA GLY A 107 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3041 0.062 - 0.123: 558 0.123 - 0.185: 43 0.185 - 0.247: 3 0.247 - 0.309: 2 Chirality restraints: 3647 Sorted by residual: chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.64e+00 ... (remaining 3644 not shown) Planarity restraints: 3916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 812 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C VAL A 952 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 952 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 953 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 763 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LEU B 763 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU B 763 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 764 " -0.013 2.00e-02 2.50e+03 ... (remaining 3913 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 1 1.99 - 2.72: 1017 2.72 - 3.44: 32066 3.44 - 4.17: 48675 4.17 - 4.90: 85369 Nonbonded interactions: 167128 Sorted by model distance: nonbonded pdb=" CA GLY A 502 " pdb=" CG GLN A 506 " model vdw 1.262 3.840 nonbonded pdb=" C GLY A 502 " pdb=" CG GLN A 506 " model vdw 1.999 3.670 nonbonded pdb=" O GLN C 935 " pdb=" OG SER C 939 " model vdw 2.122 3.040 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.166 3.120 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.182 3.040 ... (remaining 167123 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 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 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 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 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (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 \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 501 and (name N or name CA or na \ me C or name O or name CB )) or resid 502 or (resid 503 and (name N or name CA o \ r name C or name O or name CB )) or (resid 504 through 506 and (name N or name C \ A or name C or name O or name CB )) or resid 507 or (resid 508 through 515 and ( \ name N or name CA or name C or name O or name CB )) or (resid 522 through 524 an \ d (name N or name CA or name C or name O or name CB )) or resid 525 through 528 \ or (resid 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or name \ CB )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C o \ r name O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name \ C or name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or \ name CA or name C or name O or name CB )) or resid 812 through 827 or resid 856 \ through 866 or (resid 867 through 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 987 or (res \ id 988 through 989 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 1304)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 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 n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 567 or (resid 568 and (name N or name CA or name C or name O or name C \ B )) or resid 569 through 570 or (resid 571 and (name N or name CA or name C or \ name O or name CB )) or resid 572 through 581 or (resid 582 through 583 and (nam \ e N or name CA or name C or name O or name CB )) or resid 584 through 585 or (re \ sid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 th \ rough 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 through 676 or resid 690 through 744 or (resid 745 \ and (name N or name CA or name C or name O or name CB )) or resid 746 through 8 \ 10 or (resid 811 and (name N or name CA or name C or name O or name CB )) or res \ id 812 through 827 or resid 856 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 920 or (resi \ d 921 and (name N or name CA or name C or name O or name CB )) or resid 922 thro \ ugh 939 or (resid 940 and (name N or name CA or name C or name O or name CB )) o \ r 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 resid 990 through 1072 or (resid 1 \ 073 and (name N or name CA or name C or name O or name CB )) or resid 1074 throu \ gh 1117 or (resid 1118 and (name N or name CA or name C or name O or name CB )) \ or resid 1119 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 1304)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 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 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 or (resid \ 503 and (name N or name CA or name C or name O or name CB )) or (resid 504 throu \ gh 506 and (name N or name CA or name C or name O or name CB )) or resid 507 or \ (resid 508 through 515 and (name N or name CA or name C or name O or name CB )) \ or (resid 522 through 524 and (name N or name CA or name C or name O or name CB \ )) or resid 525 through 527 or (resid 528 through 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 through 553 or (resid 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 through 567 or (resi \ d 568 and (name N or name CA or name C or name O or name CB )) or resid 569 thro \ ugh 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) o \ r resid 572 through 581 or (resid 582 through 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or \ name CA or name C or name O or name CB )) or resid 587 through 618 or (resid 61 \ 9 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 name CA or name C or name O or name \ CB )) or resid 648 through 793 or (resid 794 and (name N or name CA or name C o \ r name O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name \ C or name O or name CB )) or resid 797 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 1072 or (resid 1 \ 073 and (name N or name CA or name C or name O or name CB )) or resid 1074 throu \ gh 1117 or (resid 1118 and (name N or name CA or name C or name O or name CB )) \ or resid 1119 through 1141 or (resid 1142 and (name N or name CA or name C or na \ me O or name CB )) or resid 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 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.560 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.600 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 0.118 22389 Z= 0.361 Angle : 0.710 7.345 30551 Z= 0.362 Chirality : 0.046 0.309 3647 Planarity : 0.005 0.060 3907 Dihedral : 12.618 89.243 7571 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.16 % Favored : 94.73 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2809 helix: 0.97 (0.21), residues: 613 sheet: 0.35 (0.21), residues: 567 loop : -1.31 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.022 0.002 TYR B1067 PHE 0.021 0.002 PHE A1042 TRP 0.026 0.002 TRP B 886 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.36 (22375) covalent geometry : angle 0.70581 / 0.36 (30509) hydrogen bonds : bond 0.15110 / 9.65 ( 923) hydrogen bonds : angle 7.31426 / 5.08 ( 2541) link_BETA1-4 : bond 0.00398 / 0.19 ( 5) link_BETA1-4 : angle 2.08718 / 1.26 ( 15) link_NAG-ASN : bond 0.00409 / 0.21 ( 9) link_NAG-ASN : angle 2.36144 / 1.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8924 (t0) cc_final: 0.8676 (t70) REVERT: A 460 ASN cc_start: 0.8567 (t0) cc_final: 0.8023 (t0) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1409 time to fit residues: 20.4782 Evaluate side-chains 50 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 690 GLN A 777 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 536 ASN C 564 GLN C 690 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.024685 restraints weight = 228317.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025534 restraints weight = 143076.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.026144 restraints weight = 102079.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.026585 restraints weight = 79182.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026913 restraints weight = 65322.452| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22389 Z= 0.236 Angle : 0.653 10.169 30551 Z= 0.337 Chirality : 0.045 0.313 3647 Planarity : 0.005 0.064 3907 Dihedral : 4.776 29.569 3033 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 2809 helix: 1.50 (0.20), residues: 629 sheet: 0.06 (0.21), residues: 589 loop : -1.33 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.020 0.002 TYR C 313 PHE 0.020 0.002 PHE A 377 TRP 0.011 0.001 TRP B 886 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.24 (22375) covalent geometry : angle 0.64597 / 0.34 (30509) hydrogen bonds : bond 0.05521 / 3.50 ( 923) hydrogen bonds : angle 6.29502 / 4.39 ( 2541) link_BETA1-4 : bond 0.01268 / 0.63 ( 5) link_BETA1-4 : angle 2.09992 / 1.21 ( 15) link_NAG-ASN : bond 0.00509 / 0.28 ( 9) link_NAG-ASN : angle 2.82751 / 1.61 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9774 (mmp) cc_final: 0.9321 (mmm) REVERT: B 775 ASP cc_start: 0.9443 (m-30) cc_final: 0.9147 (p0) REVERT: B 902 MET cc_start: 0.9771 (mmm) cc_final: 0.9329 (mmm) REVERT: B 916 LEU cc_start: 0.9579 (tt) cc_final: 0.9144 (tp) REVERT: B 1041 ASP cc_start: 0.9068 (t0) cc_final: 0.8821 (t0) REVERT: C 365 TYR cc_start: 0.9445 (m-10) cc_final: 0.9195 (m-80) REVERT: C 777 ASN cc_start: 0.9198 (m110) cc_final: 0.8918 (m110) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1330 time to fit residues: 14.3100 Evaluate side-chains 47 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 234 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1119 ASN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031114 restraints weight = 263935.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032045 restraints weight = 132020.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.032628 restraints weight = 79851.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033020 restraints weight = 55193.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.033275 restraints weight = 41952.590| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22389 Z= 0.333 Angle : 0.765 14.685 30551 Z= 0.395 Chirality : 0.046 0.308 3647 Planarity : 0.005 0.067 3907 Dihedral : 5.412 30.190 3033 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 2809 helix: 0.90 (0.19), residues: 639 sheet: -0.48 (0.21), residues: 528 loop : -1.50 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1019 TYR 0.027 0.003 TYR C 789 PHE 0.037 0.002 PHE C 559 TRP 0.009 0.002 TRP B1102 HIS 0.016 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.33 (22375) covalent geometry : angle 0.75986 / 0.39 (30509) hydrogen bonds : bond 0.05418 / 3.46 ( 923) hydrogen bonds : angle 6.80279 / 4.73 ( 2541) link_BETA1-4 : bond 0.01204 / 0.56 ( 5) link_BETA1-4 : angle 2.02028 / 1.14 ( 15) link_NAG-ASN : bond 0.00793 / 0.41 ( 9) link_NAG-ASN : angle 2.64377 / 1.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9421 (mm-30) REVERT: A 902 MET cc_start: 0.9737 (mmp) cc_final: 0.9240 (mmm) REVERT: A 1029 MET cc_start: 0.9592 (tmm) cc_final: 0.9350 (tmm) REVERT: B 902 MET cc_start: 0.9769 (mmm) cc_final: 0.9324 (mmm) REVERT: C 697 MET cc_start: 0.9106 (pmm) cc_final: 0.8880 (pmm) REVERT: C 740 MET cc_start: 0.9089 (ppp) cc_final: 0.8820 (ppp) REVERT: C 902 MET cc_start: 0.9595 (mmp) cc_final: 0.9345 (mmp) REVERT: C 1029 MET cc_start: 0.9617 (tmm) cc_final: 0.9148 (tmm) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.1295 time to fit residues: 11.4387 Evaluate side-chains 36 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 43 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 127 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 450 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.032664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.023576 restraints weight = 243314.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.024375 restraints weight = 152090.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.024941 restraints weight = 108419.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.025349 restraints weight = 84259.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025651 restraints weight = 69457.245| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22389 Z= 0.289 Angle : 0.700 13.534 30551 Z= 0.360 Chirality : 0.045 0.285 3647 Planarity : 0.005 0.071 3907 Dihedral : 5.360 28.984 3033 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 2809 helix: 0.97 (0.20), residues: 631 sheet: -0.60 (0.21), residues: 541 loop : -1.55 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.020 0.002 TYR C 380 PHE 0.023 0.002 PHE A 220 TRP 0.009 0.002 TRP B1102 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.29 (22375) covalent geometry : angle 0.69438 / 0.36 (30509) hydrogen bonds : bond 0.04976 / 3.15 ( 923) hydrogen bonds : angle 6.70371 / 4.65 ( 2541) link_BETA1-4 : bond 0.00565 / 0.27 ( 5) link_BETA1-4 : angle 1.99499 / 1.15 ( 15) link_NAG-ASN : bond 0.00703 / 0.36 ( 9) link_NAG-ASN : angle 2.59546 / 1.47 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9514 (mm-30) REVERT: A 902 MET cc_start: 0.9749 (mmp) cc_final: 0.9297 (mmm) REVERT: A 1029 MET cc_start: 0.9573 (tmm) cc_final: 0.9326 (tmm) REVERT: B 902 MET cc_start: 0.9771 (mmm) cc_final: 0.9338 (mmm) REVERT: C 365 TYR cc_start: 0.9378 (m-80) cc_final: 0.8862 (m-80) REVERT: C 740 MET cc_start: 0.9250 (ppp) cc_final: 0.8977 (ppp) REVERT: C 902 MET cc_start: 0.9491 (mmp) cc_final: 0.9238 (mmp) REVERT: C 1029 MET cc_start: 0.9604 (tmm) cc_final: 0.9159 (tmm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1342 time to fit residues: 11.2001 Evaluate side-chains 39 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 187 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN C 188 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.024399 restraints weight = 226475.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025240 restraints weight = 141029.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.025850 restraints weight = 100360.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.026287 restraints weight = 77625.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026606 restraints weight = 63676.179| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22389 Z= 0.105 Angle : 0.536 9.327 30551 Z= 0.275 Chirality : 0.044 0.244 3647 Planarity : 0.004 0.076 3907 Dihedral : 4.630 24.996 3033 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2809 helix: 1.84 (0.20), residues: 647 sheet: -0.19 (0.21), residues: 548 loop : -1.42 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.013 0.001 TYR C 204 PHE 0.012 0.001 PHE B 823 TRP 0.007 0.001 TRP C 104 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (22375) covalent geometry : angle 0.53154 / 0.27 (30509) hydrogen bonds : bond 0.04312 / 2.73 ( 923) hydrogen bonds : angle 5.89189 / 4.10 ( 2541) link_BETA1-4 : bond 0.00628 / 0.32 ( 5) link_BETA1-4 : angle 1.59215 / 0.93 ( 15) link_NAG-ASN : bond 0.00357 / 0.23 ( 9) link_NAG-ASN : angle 2.21966 / 1.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9733 (mm-30) cc_final: 0.9445 (mm-30) REVERT: A 774 GLN cc_start: 0.9671 (mm-40) cc_final: 0.9456 (mm-40) REVERT: A 902 MET cc_start: 0.9672 (mmp) cc_final: 0.9221 (mmm) REVERT: A 906 PHE cc_start: 0.9723 (m-80) cc_final: 0.9381 (m-80) REVERT: A 1029 MET cc_start: 0.9581 (tmm) cc_final: 0.9259 (tmm) REVERT: B 775 ASP cc_start: 0.9487 (m-30) cc_final: 0.9121 (p0) REVERT: B 916 LEU cc_start: 0.9709 (tt) cc_final: 0.9403 (tp) REVERT: C 354 ASN cc_start: 0.9748 (t0) cc_final: 0.9467 (p0) REVERT: C 365 TYR cc_start: 0.9293 (m-80) cc_final: 0.8775 (m-80) REVERT: C 697 MET cc_start: 0.8881 (pmm) cc_final: 0.8638 (pmm) REVERT: C 740 MET cc_start: 0.9237 (ppp) cc_final: 0.8930 (ppp) REVERT: C 902 MET cc_start: 0.9401 (mmp) cc_final: 0.9127 (mmp) REVERT: C 1029 MET cc_start: 0.9682 (tmm) cc_final: 0.9156 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1445 time to fit residues: 13.4555 Evaluate side-chains 45 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 142 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 126 optimal weight: 0.0010 chunk 139 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024013 restraints weight = 234538.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.024826 restraints weight = 146817.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.025414 restraints weight = 104905.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.025834 restraints weight = 81263.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.026149 restraints weight = 66975.413| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22389 Z= 0.201 Angle : 0.595 10.867 30551 Z= 0.304 Chirality : 0.044 0.255 3647 Planarity : 0.004 0.073 3907 Dihedral : 4.753 24.789 3033 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2809 helix: 1.77 (0.20), residues: 636 sheet: -0.33 (0.21), residues: 550 loop : -1.43 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1019 TYR 0.017 0.002 TYR C 789 PHE 0.015 0.001 PHE A 220 TRP 0.006 0.001 TRP C 104 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (22375) covalent geometry : angle 0.59013 / 0.30 (30509) hydrogen bonds : bond 0.04318 / 2.72 ( 923) hydrogen bonds : angle 6.07046 / 4.23 ( 2541) link_BETA1-4 : bond 0.00687 / 0.34 ( 5) link_BETA1-4 : angle 1.79163 / 1.03 ( 15) link_NAG-ASN : bond 0.00507 / 0.25 ( 9) link_NAG-ASN : angle 2.19440 / 1.22 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9463 (mm-30) REVERT: A 902 MET cc_start: 0.9627 (mmp) cc_final: 0.9135 (mmp) REVERT: A 906 PHE cc_start: 0.9675 (m-80) cc_final: 0.9378 (m-80) REVERT: A 1029 MET cc_start: 0.9537 (tmm) cc_final: 0.9264 (tmm) REVERT: B 697 MET cc_start: 0.9379 (ppp) cc_final: 0.9086 (ppp) REVERT: B 775 ASP cc_start: 0.9491 (m-30) cc_final: 0.9137 (p0) REVERT: B 902 MET cc_start: 0.9731 (mmm) cc_final: 0.9341 (mmm) REVERT: B 916 LEU cc_start: 0.9694 (tt) cc_final: 0.9233 (tp) REVERT: C 354 ASN cc_start: 0.9736 (t0) cc_final: 0.9486 (p0) REVERT: C 365 TYR cc_start: 0.9244 (m-80) cc_final: 0.8746 (m-80) REVERT: C 740 MET cc_start: 0.9231 (ppp) cc_final: 0.8925 (ppp) REVERT: C 902 MET cc_start: 0.9411 (mmp) cc_final: 0.9149 (mmp) REVERT: C 1029 MET cc_start: 0.9680 (tmm) cc_final: 0.9118 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1563 time to fit residues: 13.0852 Evaluate side-chains 42 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 255 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 321 GLN B 804 GLN C 321 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.024140 restraints weight = 230684.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.024965 restraints weight = 144092.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025560 restraints weight = 102627.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.025984 restraints weight = 79656.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.026302 restraints weight = 65605.795| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22389 Z= 0.165 Angle : 0.563 10.320 30551 Z= 0.288 Chirality : 0.043 0.249 3647 Planarity : 0.004 0.080 3907 Dihedral : 4.674 23.812 3033 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2809 helix: 1.83 (0.20), residues: 637 sheet: -0.28 (0.21), residues: 554 loop : -1.41 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1107 TYR 0.014 0.001 TYR C 453 PHE 0.013 0.001 PHE A 220 TRP 0.007 0.001 TRP A 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (22375) covalent geometry : angle 0.55884 / 0.29 (30509) hydrogen bonds : bond 0.04167 / 2.62 ( 923) hydrogen bonds : angle 5.94878 / 4.14 ( 2541) link_BETA1-4 : bond 0.00721 / 0.36 ( 5) link_BETA1-4 : angle 1.62567 / 0.94 ( 15) link_NAG-ASN : bond 0.00434 / 0.22 ( 9) link_NAG-ASN : angle 2.09145 / 1.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9415 (mm-30) REVERT: A 902 MET cc_start: 0.9619 (mmp) cc_final: 0.9192 (mmm) REVERT: A 906 PHE cc_start: 0.9674 (m-80) cc_final: 0.9348 (m-80) REVERT: A 1029 MET cc_start: 0.9555 (tmm) cc_final: 0.9262 (tmm) REVERT: B 697 MET cc_start: 0.9415 (ppp) cc_final: 0.9084 (ppp) REVERT: B 775 ASP cc_start: 0.9502 (m-30) cc_final: 0.9122 (p0) REVERT: B 902 MET cc_start: 0.9727 (mmm) cc_final: 0.9335 (mmm) REVERT: B 916 LEU cc_start: 0.9697 (tt) cc_final: 0.9239 (tp) REVERT: C 354 ASN cc_start: 0.9720 (t0) cc_final: 0.9453 (p0) REVERT: C 365 TYR cc_start: 0.9246 (m-80) cc_final: 0.8785 (m-80) REVERT: C 740 MET cc_start: 0.9248 (ppp) cc_final: 0.8950 (ppp) REVERT: C 902 MET cc_start: 0.9417 (mmp) cc_final: 0.9121 (mmp) REVERT: C 1029 MET cc_start: 0.9717 (tmm) cc_final: 0.9119 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1429 time to fit residues: 12.5411 Evaluate side-chains 45 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 26 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.033375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.024117 restraints weight = 231359.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.024933 restraints weight = 145635.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025512 restraints weight = 104175.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.025935 restraints weight = 81063.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.026234 restraints weight = 66782.486| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22389 Z= 0.175 Angle : 0.572 10.396 30551 Z= 0.292 Chirality : 0.043 0.252 3647 Planarity : 0.004 0.073 3907 Dihedral : 4.663 23.433 3033 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2809 helix: 1.80 (0.20), residues: 638 sheet: -0.32 (0.22), residues: 538 loop : -1.39 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.016 0.002 TYR C 453 PHE 0.013 0.001 PHE A 220 TRP 0.008 0.001 TRP A 886 HIS 0.006 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (22375) covalent geometry : angle 0.56834 / 0.29 (30509) hydrogen bonds : bond 0.04058 / 2.56 ( 923) hydrogen bonds : angle 5.94811 / 4.14 ( 2541) link_BETA1-4 : bond 0.00689 / 0.34 ( 5) link_BETA1-4 : angle 1.62668 / 0.95 ( 15) link_NAG-ASN : bond 0.00463 / 0.24 ( 9) link_NAG-ASN : angle 2.06930 / 1.14 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9696 (mm-30) cc_final: 0.9412 (mm-30) REVERT: A 902 MET cc_start: 0.9645 (mmp) cc_final: 0.9022 (mmp) REVERT: A 906 PHE cc_start: 0.9703 (m-80) cc_final: 0.9111 (m-80) REVERT: A 1029 MET cc_start: 0.9613 (tmm) cc_final: 0.9309 (tmm) REVERT: B 697 MET cc_start: 0.9417 (ppp) cc_final: 0.9061 (ppp) REVERT: B 775 ASP cc_start: 0.9518 (m-30) cc_final: 0.9162 (p0) REVERT: B 902 MET cc_start: 0.9766 (mmm) cc_final: 0.9351 (mmm) REVERT: B 916 LEU cc_start: 0.9712 (tt) cc_final: 0.9268 (tp) REVERT: C 354 ASN cc_start: 0.9713 (t0) cc_final: 0.9436 (p0) REVERT: C 365 TYR cc_start: 0.9263 (m-80) cc_final: 0.8818 (m-80) REVERT: C 740 MET cc_start: 0.9262 (ppp) cc_final: 0.8957 (ppp) REVERT: C 902 MET cc_start: 0.9428 (mmp) cc_final: 0.9155 (mmp) REVERT: C 1029 MET cc_start: 0.9735 (tmm) cc_final: 0.9142 (tmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1407 time to fit residues: 11.8501 Evaluate side-chains 42 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 200 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 251 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 0.0870 chunk 191 optimal weight: 10.0000 overall best weight: 3.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.024247 restraints weight = 230216.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.025084 restraints weight = 143904.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.025688 restraints weight = 102533.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.026121 restraints weight = 79280.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.026443 restraints weight = 65059.759| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22389 Z= 0.146 Angle : 0.544 9.585 30551 Z= 0.278 Chirality : 0.043 0.248 3647 Planarity : 0.004 0.074 3907 Dihedral : 4.551 22.834 3033 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2809 helix: 1.95 (0.20), residues: 644 sheet: -0.23 (0.22), residues: 555 loop : -1.36 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 346 TYR 0.014 0.001 TYR A 265 PHE 0.011 0.001 PHE A 220 TRP 0.012 0.001 TRP C 353 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (22375) covalent geometry : angle 0.53977 / 0.28 (30509) hydrogen bonds : bond 0.03925 / 2.46 ( 923) hydrogen bonds : angle 5.80525 / 4.05 ( 2541) link_BETA1-4 : bond 0.00677 / 0.34 ( 5) link_BETA1-4 : angle 1.52432 / 0.89 ( 15) link_NAG-ASN : bond 0.00396 / 0.21 ( 9) link_NAG-ASN : angle 2.00238 / 1.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9674 (mm-30) cc_final: 0.9361 (mm-30) REVERT: A 902 MET cc_start: 0.9619 (mmp) cc_final: 0.8981 (mmp) REVERT: A 906 PHE cc_start: 0.9668 (m-80) cc_final: 0.9088 (m-80) REVERT: A 1029 MET cc_start: 0.9584 (tmm) cc_final: 0.9268 (tmm) REVERT: B 697 MET cc_start: 0.9420 (ppp) cc_final: 0.9065 (ppp) REVERT: B 775 ASP cc_start: 0.9461 (m-30) cc_final: 0.9105 (p0) REVERT: B 916 LEU cc_start: 0.9700 (tt) cc_final: 0.9410 (tp) REVERT: C 354 ASN cc_start: 0.9735 (t0) cc_final: 0.9464 (p0) REVERT: C 365 TYR cc_start: 0.9230 (m-80) cc_final: 0.8799 (m-80) REVERT: C 731 MET cc_start: 0.9283 (tpt) cc_final: 0.9010 (tpt) REVERT: C 740 MET cc_start: 0.9185 (ppp) cc_final: 0.8950 (ppp) REVERT: C 902 MET cc_start: 0.9407 (mmp) cc_final: 0.9140 (mmp) REVERT: C 1029 MET cc_start: 0.9723 (tmm) cc_final: 0.9110 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1436 time to fit residues: 13.1787 Evaluate side-chains 45 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 204 optimal weight: 0.3980 chunk 206 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.024493 restraints weight = 228051.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025337 restraints weight = 141905.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.025947 restraints weight = 100806.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.026387 restraints weight = 77904.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.026704 restraints weight = 63814.323| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22389 Z= 0.114 Angle : 0.522 8.306 30551 Z= 0.267 Chirality : 0.043 0.242 3647 Planarity : 0.004 0.074 3907 Dihedral : 4.361 22.460 3033 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2809 helix: 2.07 (0.20), residues: 649 sheet: -0.09 (0.22), residues: 549 loop : -1.32 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 509 TYR 0.014 0.001 TYR A 265 PHE 0.009 0.001 PHE C 43 TRP 0.007 0.001 TRP A 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (22375) covalent geometry : angle 0.51832 / 0.27 (30509) hydrogen bonds : bond 0.03763 / 2.36 ( 923) hydrogen bonds : angle 5.62466 / 3.92 ( 2541) link_BETA1-4 : bond 0.00700 / 0.35 ( 5) link_BETA1-4 : angle 1.46466 / 0.86 ( 15) link_NAG-ASN : bond 0.00307 / 0.17 ( 9) link_NAG-ASN : angle 1.91381 / 1.06 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9616 (mmp) cc_final: 0.8980 (mmp) REVERT: A 906 PHE cc_start: 0.9663 (m-80) cc_final: 0.9062 (m-80) REVERT: A 1029 MET cc_start: 0.9578 (tmm) cc_final: 0.9253 (tmm) REVERT: B 697 MET cc_start: 0.9369 (ppp) cc_final: 0.8999 (ppp) REVERT: B 775 ASP cc_start: 0.9413 (m-30) cc_final: 0.9093 (p0) REVERT: B 916 LEU cc_start: 0.9711 (tt) cc_final: 0.9363 (tp) REVERT: C 354 ASN cc_start: 0.9708 (t0) cc_final: 0.9435 (p0) REVERT: C 365 TYR cc_start: 0.9216 (m-80) cc_final: 0.8781 (m-80) REVERT: C 740 MET cc_start: 0.9137 (ppp) cc_final: 0.8920 (ppp) REVERT: C 902 MET cc_start: 0.9390 (mmp) cc_final: 0.9118 (mmp) REVERT: C 1029 MET cc_start: 0.9731 (tmm) cc_final: 0.9154 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1605 time to fit residues: 13.6525 Evaluate side-chains 44 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 277 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 251 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.024793 restraints weight = 221914.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025654 restraints weight = 138313.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026276 restraints weight = 98498.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.026725 restraints weight = 76100.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027054 restraints weight = 62366.307| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22389 Z= 0.093 Angle : 0.503 8.901 30551 Z= 0.257 Chirality : 0.043 0.237 3647 Planarity : 0.004 0.075 3907 Dihedral : 4.123 21.964 3033 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2809 helix: 2.26 (0.20), residues: 644 sheet: 0.07 (0.22), residues: 531 loop : -1.22 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.013 0.001 TYR A 265 PHE 0.019 0.001 PHE A 347 TRP 0.006 0.001 TRP A 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (22375) covalent geometry : angle 0.49966 / 0.26 (30509) hydrogen bonds : bond 0.03551 / 2.21 ( 923) hydrogen bonds : angle 5.37644 / 3.76 ( 2541) link_BETA1-4 : bond 0.00684 / 0.34 ( 5) link_BETA1-4 : angle 1.41002 / 0.83 ( 15) link_NAG-ASN : bond 0.00292 / 0.18 ( 9) link_NAG-ASN : angle 1.77321 / 0.98 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.97 seconds wall clock time: 44 minutes 44.94 seconds (2684.94 seconds total)