Starting phenix.real_space_refine on Thu Jun 19 05:11:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgz_32493/06_2025/7wgz_32493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgz_32493/06_2025/7wgz_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_32493/06_2025/7wgz_32493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgz_32493/06_2025/7wgz_32493.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgz_32493/06_2025/7wgz_32493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgz_32493/06_2025/7wgz_32493.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 12} 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: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 13, 'GLU:plan': 13, 'ARG:plan': 1} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 18 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 dihedrals: 12 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 14.33, per 1000 atoms: 0.65 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: 5.69 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.12 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: 9.91 Time building geometry restraints manager: 6.58 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 - 24.52: 12908 24.52 - 49.04: 454 49.04 - 73.56: 81 73.56 - 98.08: 34 98.08 - 122.61: 29 Dihedral angle restraints: 13506 sinusoidal: 5145 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=" N2 NAG C1302 " pdb=" C2 NAG C1302 " pdb=" C3 NAG C1302 " pdb=" O3 NAG C1302 " ideal model delta sinusoidal sigma weight residual 62.25 -175.14 -122.61 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 13503 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 or resid 1301 throug \ h 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 or resid 1301 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 or resid 1301 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 54.680 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 15.462 122.606 8096 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP B 886 HIS 0.006 0.001 HIS A 655 PHE 0.021 0.002 PHE A1042 TYR 0.022 0.002 TYR B1067 ARG 0.006 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 9) link_NAG-ASN : angle 2.36144 ( 27) link_BETA1-4 : bond 0.00398 ( 5) link_BETA1-4 : angle 2.08718 ( 15) hydrogen bonds : bond 0.15110 ( 923) hydrogen bonds : angle 7.31426 ( 2541) covalent geometry : bond 0.00720 (22375) covalent geometry : angle 0.70581 (30509) *********************** 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 : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8924 (t0) cc_final: 0.8673 (t70) REVERT: A 460 ASN cc_start: 0.8568 (t0) cc_final: 0.8022 (t0) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.3506 time to fit residues: 50.7706 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 : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 116 optimal weight: 0.0970 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 564 GLN C 690 GLN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.025252 restraints weight = 214475.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.026126 restraints weight = 136640.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026751 restraints weight = 98295.093| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22389 Z= 0.134 Angle : 0.576 10.194 30551 Z= 0.294 Chirality : 0.044 0.234 3647 Planarity : 0.004 0.067 3907 Dihedral : 10.781 111.224 3558 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2809 helix: 1.91 (0.20), residues: 637 sheet: 0.26 (0.21), residues: 589 loop : -1.23 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.005 0.001 HIS A 655 PHE 0.018 0.001 PHE B 823 TYR 0.014 0.001 TYR C 313 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 9) link_NAG-ASN : angle 2.96011 ( 27) link_BETA1-4 : bond 0.00527 ( 5) link_BETA1-4 : angle 2.20343 ( 15) hydrogen bonds : bond 0.05268 ( 923) hydrogen bonds : angle 5.84775 ( 2541) covalent geometry : bond 0.00265 (22375) covalent geometry : angle 0.56795 (30509) *********************** 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 74 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8686 (t0) cc_final: 0.8486 (t0) REVERT: A 902 MET cc_start: 0.9762 (mmp) cc_final: 0.9277 (mmm) REVERT: A 906 PHE cc_start: 0.9667 (m-80) cc_final: 0.9420 (m-80) REVERT: B 775 ASP cc_start: 0.9527 (m-30) cc_final: 0.9221 (p0) REVERT: B 902 MET cc_start: 0.9809 (mmm) cc_final: 0.9416 (mmm) REVERT: B 916 LEU cc_start: 0.9571 (tt) cc_final: 0.9134 (tp) REVERT: B 1041 ASP cc_start: 0.9007 (t0) cc_final: 0.8774 (t0) REVERT: C 365 TYR cc_start: 0.9478 (m-10) cc_final: 0.9020 (t80) REVERT: C 369 TYR cc_start: 0.9329 (t80) cc_final: 0.8748 (t80) REVERT: C 777 ASN cc_start: 0.9237 (m110) cc_final: 0.8935 (m110) REVERT: C 902 MET cc_start: 0.9479 (mmp) cc_final: 0.9269 (mmp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3073 time to fit residues: 39.7275 Evaluate side-chains 56 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.040140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.032742 restraints weight = 254301.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.033704 restraints weight = 124674.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034309 restraints weight = 74922.040| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22389 Z= 0.268 Angle : 0.692 12.329 30551 Z= 0.351 Chirality : 0.044 0.270 3647 Planarity : 0.005 0.069 3907 Dihedral : 9.301 110.690 3558 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2809 helix: 1.63 (0.20), residues: 623 sheet: -0.00 (0.21), residues: 568 loop : -1.31 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1102 HIS 0.010 0.002 HIS A1048 PHE 0.024 0.002 PHE B 759 TYR 0.023 0.002 TYR C 789 ARG 0.006 0.001 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 9) link_NAG-ASN : angle 2.65800 ( 27) link_BETA1-4 : bond 0.00636 ( 5) link_BETA1-4 : angle 2.08322 ( 15) hydrogen bonds : bond 0.04969 ( 923) hydrogen bonds : angle 6.25754 ( 2541) covalent geometry : bond 0.00528 (22375) covalent geometry : angle 0.68619 (30509) *********************** 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 54 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9144 (mm-30) REVERT: A 869 MET cc_start: 0.9416 (pmm) cc_final: 0.8886 (pmm) REVERT: A 902 MET cc_start: 0.9701 (mmp) cc_final: 0.9157 (mmm) REVERT: A 906 PHE cc_start: 0.9719 (m-80) cc_final: 0.9204 (m-80) REVERT: A 1029 MET cc_start: 0.9589 (tmm) cc_final: 0.9369 (tmm) REVERT: B 775 ASP cc_start: 0.9419 (m-30) cc_final: 0.9160 (p0) REVERT: B 902 MET cc_start: 0.9777 (mmm) cc_final: 0.9384 (mmm) REVERT: C 365 TYR cc_start: 0.9411 (m-10) cc_final: 0.9165 (m-10) REVERT: C 740 MET cc_start: 0.9155 (ppp) cc_final: 0.8904 (ppp) REVERT: C 777 ASN cc_start: 0.9156 (m110) cc_final: 0.8906 (m110) REVERT: C 902 MET cc_start: 0.9527 (mmp) cc_final: 0.9289 (mmp) REVERT: C 1029 MET cc_start: 0.9564 (tmm) cc_final: 0.9174 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3106 time to fit residues: 29.8534 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 : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 chunk 244 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 69 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 801 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1119 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.033519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.024191 restraints weight = 234714.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.025014 restraints weight = 146653.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.025611 restraints weight = 104690.530| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22389 Z= 0.229 Angle : 0.635 12.500 30551 Z= 0.323 Chirality : 0.044 0.246 3647 Planarity : 0.004 0.071 3907 Dihedral : 8.262 110.010 3558 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 0.04 % Allowed : 3.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2809 helix: 1.61 (0.20), residues: 638 sheet: -0.19 (0.21), residues: 546 loop : -1.37 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.008 0.002 HIS A1048 PHE 0.018 0.002 PHE A 220 TYR 0.018 0.002 TYR C 789 ARG 0.005 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 9) link_NAG-ASN : angle 2.44500 ( 27) link_BETA1-4 : bond 0.00516 ( 5) link_BETA1-4 : angle 2.16367 ( 15) hydrogen bonds : bond 0.04570 ( 923) hydrogen bonds : angle 6.19828 ( 2541) covalent geometry : bond 0.00451 (22375) covalent geometry : angle 0.62978 (30509) *********************** 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 53 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9687 (mm-30) cc_final: 0.9420 (mm-30) REVERT: A 902 MET cc_start: 0.9675 (mmp) cc_final: 0.9134 (mmm) REVERT: A 906 PHE cc_start: 0.9631 (m-80) cc_final: 0.9106 (m-80) REVERT: A 1029 MET cc_start: 0.9520 (tmm) cc_final: 0.9258 (tmm) REVERT: B 775 ASP cc_start: 0.9489 (m-30) cc_final: 0.9164 (p0) REVERT: B 902 MET cc_start: 0.9753 (mmm) cc_final: 0.9337 (mmm) REVERT: C 365 TYR cc_start: 0.9397 (m-10) cc_final: 0.9139 (m-80) REVERT: C 740 MET cc_start: 0.9222 (ppp) cc_final: 0.8936 (ppp) REVERT: C 777 ASN cc_start: 0.9138 (m110) cc_final: 0.8897 (m-40) REVERT: C 902 MET cc_start: 0.9435 (mmp) cc_final: 0.9226 (mmp) REVERT: C 1029 MET cc_start: 0.9605 (tmm) cc_final: 0.9157 (tmm) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.3244 time to fit residues: 30.2262 Evaluate side-chains 46 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 199 optimal weight: 0.0040 chunk 246 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 254 optimal weight: 2.9990 chunk 258 optimal weight: 0.0670 chunk 95 optimal weight: 6.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.024864 restraints weight = 219831.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025733 restraints weight = 136591.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026357 restraints weight = 96935.278| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22389 Z= 0.095 Angle : 0.530 10.363 30551 Z= 0.268 Chirality : 0.043 0.189 3647 Planarity : 0.004 0.076 3907 Dihedral : 7.087 105.986 3558 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2809 helix: 2.18 (0.20), residues: 645 sheet: 0.18 (0.22), residues: 538 loop : -1.27 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE C 559 TYR 0.012 0.001 TYR B1067 ARG 0.006 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 9) link_NAG-ASN : angle 2.43905 ( 27) link_BETA1-4 : bond 0.00612 ( 5) link_BETA1-4 : angle 2.10805 ( 15) hydrogen bonds : bond 0.04043 ( 923) hydrogen bonds : angle 5.50394 ( 2541) covalent geometry : bond 0.00189 (22375) covalent geometry : angle 0.52317 (30509) *********************** 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 60 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 ASP cc_start: 0.9539 (t0) cc_final: 0.9222 (p0) REVERT: A 902 MET cc_start: 0.9634 (mmp) cc_final: 0.9190 (mmm) REVERT: A 906 PHE cc_start: 0.9744 (m-80) cc_final: 0.9423 (m-80) REVERT: A 1029 MET cc_start: 0.9577 (tmm) cc_final: 0.9228 (tmm) REVERT: B 775 ASP cc_start: 0.9477 (m-30) cc_final: 0.9147 (p0) REVERT: C 365 TYR cc_start: 0.9458 (m-10) cc_final: 0.9128 (m-10) REVERT: C 740 MET cc_start: 0.9259 (ppp) cc_final: 0.8935 (ppp) REVERT: C 777 ASN cc_start: 0.9128 (m110) cc_final: 0.8858 (m-40) REVERT: C 902 MET cc_start: 0.9394 (mmp) cc_final: 0.9136 (mmp) REVERT: C 1029 MET cc_start: 0.9715 (tmm) cc_final: 0.9361 (tmm) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.3397 time to fit residues: 34.6291 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 : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 41 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 0.0870 chunk 13 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2856 r_free = 0.2856 target = 0.033421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.024152 restraints weight = 236147.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.024982 restraints weight = 146335.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.025576 restraints weight = 103719.363| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2725 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= 0.198 Angle : 0.592 10.077 30551 Z= 0.299 Chirality : 0.043 0.241 3647 Planarity : 0.004 0.072 3907 Dihedral : 7.128 107.815 3558 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2809 helix: 2.11 (0.20), residues: 643 sheet: -0.08 (0.21), residues: 557 loop : -1.30 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1102 HIS 0.008 0.002 HIS B1048 PHE 0.015 0.001 PHE A 220 TYR 0.017 0.002 TYR C 789 ARG 0.005 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 9) link_NAG-ASN : angle 2.28955 ( 27) link_BETA1-4 : bond 0.00476 ( 5) link_BETA1-4 : angle 2.03486 ( 15) hydrogen bonds : bond 0.04068 ( 923) hydrogen bonds : angle 5.76860 ( 2541) covalent geometry : bond 0.00394 (22375) covalent geometry : angle 0.58692 (30509) *********************** 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 49 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9555 (pmm) cc_final: 0.9128 (pmm) REVERT: A 902 MET cc_start: 0.9654 (mmp) cc_final: 0.9138 (mmp) REVERT: A 906 PHE cc_start: 0.9750 (m-80) cc_final: 0.9440 (m-80) REVERT: A 1029 MET cc_start: 0.9601 (tmm) cc_final: 0.9303 (tmm) REVERT: B 775 ASP cc_start: 0.9534 (m-30) cc_final: 0.9211 (p0) REVERT: C 365 TYR cc_start: 0.9463 (m-10) cc_final: 0.9124 (m-80) REVERT: C 740 MET cc_start: 0.9267 (ppp) cc_final: 0.8951 (ppp) REVERT: C 777 ASN cc_start: 0.9216 (m110) cc_final: 0.8950 (m-40) REVERT: C 902 MET cc_start: 0.9444 (mmp) cc_final: 0.8773 (mmm) REVERT: C 1029 MET cc_start: 0.9755 (tmm) cc_final: 0.9365 (tmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3992 time to fit residues: 34.6389 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 : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 41 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 132 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 450 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.024435 restraints weight = 231568.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.025286 restraints weight = 142709.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025891 restraints weight = 100804.329| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22389 Z= 0.128 Angle : 0.525 10.276 30551 Z= 0.266 Chirality : 0.042 0.216 3647 Planarity : 0.004 0.075 3907 Dihedral : 6.812 107.282 3558 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2809 helix: 2.23 (0.20), residues: 651 sheet: -0.00 (0.22), residues: 558 loop : -1.27 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.005 0.001 HIS B1048 PHE 0.010 0.001 PHE A 220 TYR 0.011 0.001 TYR C 789 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 9) link_NAG-ASN : angle 2.14258 ( 27) link_BETA1-4 : bond 0.00479 ( 5) link_BETA1-4 : angle 2.05284 ( 15) hydrogen bonds : bond 0.03829 ( 923) hydrogen bonds : angle 5.55125 ( 2541) covalent geometry : bond 0.00257 (22375) covalent geometry : angle 0.51994 (30509) *********************** 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 54 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9525 (pmm) cc_final: 0.9125 (pmm) REVERT: A 902 MET cc_start: 0.9650 (mmp) cc_final: 0.9116 (mmp) REVERT: A 906 PHE cc_start: 0.9764 (m-80) cc_final: 0.9431 (m-80) REVERT: A 1029 MET cc_start: 0.9609 (tmm) cc_final: 0.9285 (tmm) REVERT: B 775 ASP cc_start: 0.9501 (m-30) cc_final: 0.9163 (p0) REVERT: C 354 ASN cc_start: 0.9745 (t0) cc_final: 0.9434 (p0) REVERT: C 365 TYR cc_start: 0.9478 (m-10) cc_final: 0.9118 (m-80) REVERT: C 740 MET cc_start: 0.9285 (ppp) cc_final: 0.8967 (ppp) REVERT: C 777 ASN cc_start: 0.9199 (m110) cc_final: 0.8918 (m-40) REVERT: C 902 MET cc_start: 0.9448 (mmp) cc_final: 0.8757 (mmm) REVERT: C 1029 MET cc_start: 0.9751 (tmm) cc_final: 0.9342 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3579 time to fit residues: 33.1518 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 : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 285 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 253 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2868 r_free = 0.2868 target = 0.033688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.024271 restraints weight = 228199.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.025115 restraints weight = 142296.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025715 restraints weight = 101147.120| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22389 Z= 0.138 Angle : 0.533 10.275 30551 Z= 0.269 Chirality : 0.042 0.220 3647 Planarity : 0.004 0.073 3907 Dihedral : 6.756 108.577 3558 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2809 helix: 2.25 (0.20), residues: 649 sheet: 0.01 (0.22), residues: 542 loop : -1.25 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.005 0.001 HIS B1048 PHE 0.010 0.001 PHE A 220 TYR 0.015 0.001 TYR A 265 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 2.09261 ( 27) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 2.01258 ( 15) hydrogen bonds : bond 0.03785 ( 923) hydrogen bonds : angle 5.52994 ( 2541) covalent geometry : bond 0.00277 (22375) covalent geometry : angle 0.52737 (30509) *********************** 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 51 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9508 (pmm) cc_final: 0.9105 (pmm) REVERT: A 902 MET cc_start: 0.9659 (mmp) cc_final: 0.9002 (mmp) REVERT: A 906 PHE cc_start: 0.9740 (m-80) cc_final: 0.9133 (m-80) REVERT: A 1029 MET cc_start: 0.9632 (tmm) cc_final: 0.9302 (tmm) REVERT: B 775 ASP cc_start: 0.9504 (m-30) cc_final: 0.9184 (p0) REVERT: C 354 ASN cc_start: 0.9737 (t0) cc_final: 0.9427 (p0) REVERT: C 365 TYR cc_start: 0.9459 (m-10) cc_final: 0.9099 (m-80) REVERT: C 731 MET cc_start: 0.9063 (tpp) cc_final: 0.8425 (tmm) REVERT: C 740 MET cc_start: 0.9280 (ppp) cc_final: 0.8971 (ppp) REVERT: C 777 ASN cc_start: 0.9203 (m110) cc_final: 0.8939 (m-40) REVERT: C 902 MET cc_start: 0.9445 (mmp) cc_final: 0.8771 (mmm) REVERT: C 1029 MET cc_start: 0.9759 (tmm) cc_final: 0.9344 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3468 time to fit residues: 31.1472 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 : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 66 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 120 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1064 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.024737 restraints weight = 221487.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025592 restraints weight = 138783.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026212 restraints weight = 98907.986| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22389 Z= 0.089 Angle : 0.495 10.800 30551 Z= 0.251 Chirality : 0.042 0.194 3647 Planarity : 0.004 0.077 3907 Dihedral : 6.295 108.016 3558 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2809 helix: 2.48 (0.21), residues: 645 sheet: 0.12 (0.22), residues: 553 loop : -1.19 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.003 0.001 HIS B1048 PHE 0.013 0.001 PHE A 347 TYR 0.013 0.001 TYR A 265 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 9) link_NAG-ASN : angle 2.10430 ( 27) link_BETA1-4 : bond 0.00534 ( 5) link_BETA1-4 : angle 1.95939 ( 15) hydrogen bonds : bond 0.03545 ( 923) hydrogen bonds : angle 5.25140 ( 2541) covalent geometry : bond 0.00180 (22375) covalent geometry : angle 0.48964 (30509) *********************** 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 57 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 3.423 Fit side-chains revert: symmetry clash REVERT: A 869 MET cc_start: 0.9427 (pmm) cc_final: 0.8953 (pmm) REVERT: A 902 MET cc_start: 0.9647 (mmp) cc_final: 0.9096 (mmp) REVERT: A 906 PHE cc_start: 0.9753 (m-80) cc_final: 0.9403 (m-80) REVERT: A 1029 MET cc_start: 0.9615 (tmm) cc_final: 0.9293 (tmm) REVERT: B 775 ASP cc_start: 0.9472 (m-30) cc_final: 0.9179 (p0) REVERT: B 869 MET cc_start: 0.9672 (mtm) cc_final: 0.9433 (ptp) REVERT: B 1004 LEU cc_start: 0.9794 (mt) cc_final: 0.9570 (mt) REVERT: C 354 ASN cc_start: 0.9717 (t0) cc_final: 0.9361 (p0) REVERT: C 365 TYR cc_start: 0.9435 (m-10) cc_final: 0.9087 (m-80) REVERT: C 513 LEU cc_start: 0.9706 (mp) cc_final: 0.9463 (pp) REVERT: C 740 MET cc_start: 0.9197 (ppp) cc_final: 0.8914 (ppp) REVERT: C 777 ASN cc_start: 0.9210 (m110) cc_final: 0.8929 (m-40) REVERT: C 902 MET cc_start: 0.9400 (mmp) cc_final: 0.8703 (mmm) REVERT: C 1029 MET cc_start: 0.9756 (tmm) cc_final: 0.9338 (tmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4943 time to fit residues: 45.8773 Evaluate side-chains 48 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 6.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 200 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 321 GLN B1106 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.024174 restraints weight = 232940.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.025001 restraints weight = 145829.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.025589 restraints weight = 104026.973| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22389 Z= 0.212 Angle : 0.593 10.695 30551 Z= 0.301 Chirality : 0.042 0.236 3647 Planarity : 0.004 0.071 3907 Dihedral : 6.643 109.578 3558 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2809 helix: 2.17 (0.20), residues: 649 sheet: -0.03 (0.22), residues: 553 loop : -1.27 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.008 0.002 HIS B1048 PHE 0.017 0.002 PHE A 347 TYR 0.029 0.002 TYR B 904 ARG 0.013 0.001 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 9) link_NAG-ASN : angle 2.06730 ( 27) link_BETA1-4 : bond 0.00379 ( 5) link_BETA1-4 : angle 2.01369 ( 15) hydrogen bonds : bond 0.03850 ( 923) hydrogen bonds : angle 5.63135 ( 2541) covalent geometry : bond 0.00419 (22375) covalent geometry : angle 0.58844 (30509) ********************** 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 50 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9677 (mmp) cc_final: 0.9038 (mmp) REVERT: A 906 PHE cc_start: 0.9747 (m-80) cc_final: 0.9127 (m-80) REVERT: A 1029 MET cc_start: 0.9643 (tmm) cc_final: 0.9354 (tmm) REVERT: B 775 ASP cc_start: 0.9486 (m-30) cc_final: 0.9204 (p0) REVERT: B 1004 LEU cc_start: 0.9785 (mt) cc_final: 0.9562 (mt) REVERT: C 354 ASN cc_start: 0.9723 (t0) cc_final: 0.9392 (p0) REVERT: C 365 TYR cc_start: 0.9462 (m-10) cc_final: 0.9103 (m-80) REVERT: C 740 MET cc_start: 0.9278 (ppp) cc_final: 0.9004 (ppp) REVERT: C 777 ASN cc_start: 0.9244 (m110) cc_final: 0.8980 (m-40) REVERT: C 869 MET cc_start: 0.9464 (ptp) cc_final: 0.9248 (ptp) REVERT: C 902 MET cc_start: 0.9504 (mmp) cc_final: 0.9301 (mmp) REVERT: C 1029 MET cc_start: 0.9749 (tmm) cc_final: 0.9343 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3041 time to fit residues: 27.3843 Evaluate side-chains 43 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 280 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 206 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 228 optimal weight: 8.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 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 = 0.2874 r_free = 0.2874 target = 0.033931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.024565 restraints weight = 228913.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025409 restraints weight = 142601.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.026023 restraints weight = 101316.278| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 22389 Z= 0.123 Angle : 0.519 11.066 30551 Z= 0.263 Chirality : 0.042 0.199 3647 Planarity : 0.004 0.074 3907 Dihedral : 6.388 108.931 3558 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2809 helix: 2.34 (0.20), residues: 650 sheet: 0.06 (0.22), residues: 549 loop : -1.23 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.004 0.001 HIS B1048 PHE 0.013 0.001 PHE A 347 TYR 0.022 0.001 TYR B 904 ARG 0.010 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 9) link_NAG-ASN : angle 2.04289 ( 27) link_BETA1-4 : bond 0.00399 ( 5) link_BETA1-4 : angle 1.96943 ( 15) hydrogen bonds : bond 0.03657 ( 923) hydrogen bonds : angle 5.44214 ( 2541) covalent geometry : bond 0.00247 (22375) covalent geometry : angle 0.51425 (30509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.93 seconds wall clock time: 95 minutes 29.68 seconds (5729.68 seconds total)