Starting phenix.real_space_refine on Mon Mar 18 19:33:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_32493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_32493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_32493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_32493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgz_32493/03_2024/7wgz_32493.pdb" } 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 Residue "C GLU 654": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.74, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 8.84 Conformation dependent library (CDL) restraints added in 4.3 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: 3.02 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: 8.53 Time building geometry restraints manager: 9.56 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: 99.97 - 106.78: 615 106.78 - 113.59: 12571 113.59 - 120.40: 7927 120.40 - 127.22: 9215 127.22 - 134.03: 181 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 2.440 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.166 2.520 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.182 2.440 ... (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 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: 0.730 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: 4.560 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 57.310 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.130 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.310 ------------------------------------------------------------------------------- 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 22375 Z= 0.486 Angle : 0.706 7.345 30509 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 2.778 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: 0.4144 time to fit residues: 61.5905 Evaluate side-chains 50 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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: 5.9990 chunk 217 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 536 ASN C 564 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22375 Z= 0.244 Angle : 0.618 10.054 30509 Z= 0.314 Chirality : 0.044 0.246 3647 Planarity : 0.004 0.069 3907 Dihedral : 10.908 109.058 3558 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.34 (0.15), residues: 2809 helix: 1.83 (0.20), residues: 631 sheet: 0.11 (0.21), residues: 588 loop : -1.27 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.006 0.002 HIS A 655 PHE 0.020 0.001 PHE A 377 TYR 0.017 0.002 TYR C 313 ARG 0.004 0.001 ARG B 765 *********************** 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 66 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8808 (t0) cc_final: 0.8527 (t70) REVERT: A 460 ASN cc_start: 0.8633 (t0) cc_final: 0.8330 (t0) REVERT: A 869 MET cc_start: 0.8918 (ptp) cc_final: 0.8655 (ptp) REVERT: A 900 MET cc_start: 0.8534 (mmp) cc_final: 0.8142 (mmt) REVERT: B 902 MET cc_start: 0.8517 (mmm) cc_final: 0.8177 (mmm) REVERT: B 916 LEU cc_start: 0.8951 (tt) cc_final: 0.8682 (tp) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.3265 time to fit residues: 37.1689 Evaluate side-chains 49 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 261 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 258 optimal weight: 40.0000 chunk 89 optimal weight: 30.0000 chunk 209 optimal weight: 10.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22375 Z= 0.306 Angle : 0.653 12.099 30509 Z= 0.331 Chirality : 0.044 0.267 3647 Planarity : 0.004 0.067 3907 Dihedral : 9.291 111.255 3558 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: -0.56 (0.15), residues: 2809 helix: 1.70 (0.20), residues: 635 sheet: -0.15 (0.21), residues: 554 loop : -1.36 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1102 HIS 0.010 0.002 HIS A1048 PHE 0.027 0.002 PHE B 759 TYR 0.021 0.002 TYR C 789 ARG 0.004 0.001 ARG B1019 *********************** 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 51 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8861 (t0) cc_final: 0.8572 (t70) REVERT: A 460 ASN cc_start: 0.8585 (t0) cc_final: 0.8260 (t0) REVERT: B 902 MET cc_start: 0.8375 (mmm) cc_final: 0.7927 (mmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3084 time to fit residues: 28.5294 Evaluate side-chains 42 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 801 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22375 Z= 0.250 Angle : 0.592 11.266 30509 Z= 0.301 Chirality : 0.043 0.240 3647 Planarity : 0.004 0.075 3907 Dihedral : 8.086 111.280 3558 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.68 % 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: -0.47 (0.15), residues: 2809 helix: 1.96 (0.20), residues: 636 sheet: -0.17 (0.21), residues: 554 loop : -1.36 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.007 0.002 HIS A1048 PHE 0.015 0.001 PHE A 220 TYR 0.014 0.001 TYR C 789 ARG 0.008 0.000 ARG A1019 *********************** 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 56 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8573 (t0) cc_final: 0.8256 (t0) REVERT: A 869 MET cc_start: 0.8944 (ptp) cc_final: 0.8591 (ptp) REVERT: B 902 MET cc_start: 0.8325 (mmm) cc_final: 0.7989 (mmm) REVERT: B 916 LEU cc_start: 0.9156 (tt) cc_final: 0.8770 (tp) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.3302 time to fit residues: 31.8278 Evaluate side-chains 43 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 4.9990 chunk 157 optimal weight: 0.0050 chunk 4 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 249 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C1083 HIS ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22375 Z= 0.132 Angle : 0.505 10.311 30509 Z= 0.256 Chirality : 0.042 0.203 3647 Planarity : 0.004 0.071 3907 Dihedral : 7.187 110.409 3558 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % 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: -0.11 (0.16), residues: 2809 helix: 2.54 (0.20), residues: 632 sheet: 0.14 (0.22), residues: 533 loop : -1.28 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS A 655 PHE 0.013 0.001 PHE C 374 TYR 0.011 0.001 TYR A 265 ARG 0.003 0.000 ARG B1019 *********************** 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 59 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8594 (t0) cc_final: 0.8210 (t0) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.3055 time to fit residues: 32.0537 Evaluate side-chains 38 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 162 optimal weight: 0.1980 chunk 68 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22375 Z= 0.169 Angle : 0.518 10.193 30509 Z= 0.263 Chirality : 0.042 0.244 3647 Planarity : 0.004 0.072 3907 Dihedral : 6.971 111.303 3558 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -0.07 (0.16), residues: 2809 helix: 2.56 (0.20), residues: 636 sheet: 0.03 (0.22), residues: 558 loop : -1.22 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 PHE 0.025 0.001 PHE A 347 TYR 0.012 0.001 TYR C 789 ARG 0.007 0.000 ARG A 509 *********************** 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 53 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8556 (t0) cc_final: 0.8198 (t0) REVERT: B 902 MET cc_start: 0.8071 (mmm) cc_final: 0.7787 (mmm) REVERT: C 697 MET cc_start: 0.8405 (pmm) cc_final: 0.8109 (pmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3258 time to fit residues: 30.7570 Evaluate side-chains 39 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 158 optimal weight: 0.3980 chunk 202 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 50.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22375 Z= 0.224 Angle : 0.552 10.252 30509 Z= 0.283 Chirality : 0.042 0.233 3647 Planarity : 0.004 0.069 3907 Dihedral : 7.020 112.948 3558 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.16), residues: 2809 helix: 2.37 (0.20), residues: 642 sheet: -0.04 (0.22), residues: 551 loop : -1.24 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.007 0.002 HIS A1048 PHE 0.017 0.001 PHE A 347 TYR 0.015 0.001 TYR C 789 ARG 0.003 0.000 ARG C 357 *********************** 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 49 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8552 (t0) cc_final: 0.8228 (t0) REVERT: A 869 MET cc_start: 0.9175 (ptp) cc_final: 0.8671 (ptp) REVERT: B 902 MET cc_start: 0.8191 (mmm) cc_final: 0.7805 (mmm) REVERT: C 365 TYR cc_start: 0.8974 (m-80) cc_final: 0.8653 (m-10) REVERT: C 697 MET cc_start: 0.8475 (pmm) cc_final: 0.8231 (pmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3258 time to fit residues: 28.2734 Evaluate side-chains 40 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22375 Z= 0.147 Angle : 0.497 10.630 30509 Z= 0.254 Chirality : 0.042 0.245 3647 Planarity : 0.004 0.073 3907 Dihedral : 6.706 112.537 3558 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.16), residues: 2809 helix: 2.44 (0.20), residues: 650 sheet: 0.06 (0.22), residues: 554 loop : -1.23 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS A1048 PHE 0.012 0.001 PHE A 347 TYR 0.015 0.001 TYR A 265 ARG 0.002 0.000 ARG A1039 *********************** 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 fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8545 (t0) cc_final: 0.8205 (t0) REVERT: A 869 MET cc_start: 0.9125 (ptp) cc_final: 0.8542 (ptp) REVERT: B 902 MET cc_start: 0.8121 (mmm) cc_final: 0.7769 (mmm) REVERT: C 365 TYR cc_start: 0.8973 (m-80) cc_final: 0.8644 (m-10) REVERT: C 513 LEU cc_start: 0.9564 (mp) cc_final: 0.9346 (pp) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.3102 time to fit residues: 28.7185 Evaluate side-chains 43 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22375 Z= 0.211 Angle : 0.541 10.657 30509 Z= 0.276 Chirality : 0.042 0.219 3647 Planarity : 0.004 0.069 3907 Dihedral : 6.805 113.072 3558 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.16), residues: 2809 helix: 2.42 (0.20), residues: 639 sheet: -0.02 (0.21), residues: 551 loop : -1.21 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.006 0.001 HIS A1048 PHE 0.018 0.001 PHE A 906 TYR 0.013 0.001 TYR C 789 ARG 0.002 0.000 ARG C 357 *********************** 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 47 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.521 Fit side-chains revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8402 (t0) cc_final: 0.8075 (t0) REVERT: A 869 MET cc_start: 0.9137 (ptp) cc_final: 0.8730 (ptp) REVERT: B 902 MET cc_start: 0.8157 (mmm) cc_final: 0.7788 (mmm) REVERT: C 365 TYR cc_start: 0.9008 (m-80) cc_final: 0.8687 (m-10) REVERT: C 697 MET cc_start: 0.8501 (pmm) cc_final: 0.8190 (pmm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3182 time to fit residues: 27.3810 Evaluate side-chains 41 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 50.0000 chunk 189 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22375 Z= 0.139 Angle : 0.497 11.084 30509 Z= 0.254 Chirality : 0.042 0.189 3647 Planarity : 0.004 0.072 3907 Dihedral : 6.467 112.648 3558 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % 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: -0.03 (0.16), residues: 2809 helix: 2.54 (0.20), residues: 646 sheet: 0.08 (0.21), residues: 558 loop : -1.19 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 PHE 0.024 0.001 PHE A 906 TYR 0.014 0.001 TYR A 265 ARG 0.002 0.000 ARG A1039 ********************** 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 49 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.535 Fit side-chains revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8436 (t0) cc_final: 0.8138 (t0) REVERT: A 869 MET cc_start: 0.9111 (ptp) cc_final: 0.8773 (ptp) REVERT: C 365 TYR cc_start: 0.8929 (m-80) cc_final: 0.8631 (m-80) REVERT: C 513 LEU cc_start: 0.9564 (mp) cc_final: 0.9343 (pp) REVERT: C 697 MET cc_start: 0.8357 (pmm) cc_final: 0.8052 (pmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3151 time to fit residues: 27.9341 Evaluate side-chains 41 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 30.0000 chunk 180 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 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 = 0.3022 r_free = 0.3022 target = 0.040755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033330 restraints weight = 253667.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034296 restraints weight = 124633.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034910 restraints weight = 74065.589| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22375 Z= 0.194 Angle : 0.526 11.316 30509 Z= 0.269 Chirality : 0.042 0.189 3647 Planarity : 0.004 0.069 3907 Dihedral : 6.467 113.023 3558 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % 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: -0.10 (0.16), residues: 2809 helix: 2.44 (0.20), residues: 647 sheet: -0.04 (0.21), residues: 567 loop : -1.20 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 PHE 0.015 0.001 PHE B 201 TYR 0.013 0.001 TYR A 265 ARG 0.003 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.45 seconds wall clock time: 53 minutes 19.87 seconds (3199.87 seconds total)