Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 22:18:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2023/7wz2_32902.pdb" } resolution = 2.7 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= 0.001 sd= 0.020 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 114 5.16 5 C 16226 2.51 5 N 4222 2.21 5 O 4928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 25490 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.81, per 1000 atoms: 0.50 Number of scatterers: 25490 At special positions: 0 Unit cell: (158.536, 150.024, 165.984, 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 114 16.00 O 4928 8.00 N 4222 7.00 C 16226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 331 " " NAG A1312 " - " ASN A1134 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 331 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 331 " " NAG E1304 " - " ASN E 343 " " NAG E1305 " - " ASN E 616 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1134 " " NAG E1309 " - " ASN E1098 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E 709 " Time building additional restraints: 10.14 Conformation dependent library (CDL) restraints added in 3.5 seconds 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6030 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 51 sheets defined 20.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.697A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.660A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.926A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.637A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.162A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.995A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.685A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.141A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.169A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.650A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.728A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.523A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.930A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.526A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.219A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.863A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 3.664A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.576A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 405 through 410 removed outlier: 3.575A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.558A pdb=" N LEU E 754 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.669A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.167A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 964 removed outlier: 3.751A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 967 No H-bonds generated for 'chain 'E' and resid 965 through 967' Processing helix chain 'E' and resid 976 through 981 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.958A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.867A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.810A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.785A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.523A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 319 removed outlier: 7.202A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.548A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.799A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.152A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.539A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.719A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.935A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.283A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.045A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.549A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 5.246A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.906A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.733A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.684A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AC8, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.120A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 210 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 152 through 156 removed outlier: 4.021A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.520A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.365A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 378 through 380 removed outlier: 3.710A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.120A pdb=" N PHE C 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.019A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD7, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.986A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.986A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.164A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.901A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.003A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.776A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.772A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 117 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE E 128 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AE7, first strand: chain 'E' and resid 311 through 316 removed outlier: 6.872A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 325 through 326 removed outlier: 6.915A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.997A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 376 through 380 Processing sheet with id=AF2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.199A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 711 through 728 removed outlier: 7.108A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 711 through 728 removed outlier: 7.108A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'E' and resid 1081 through 1082 833 hydrogen bonds defined for protein. 2301 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: 10.06 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6138 1.33 - 1.45: 5623 1.45 - 1.57: 14173 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 26078 Sorted by residual: bond pdb=" CA ASN E 331 " pdb=" C ASN E 331 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.25e-02 6.40e+03 4.36e+01 bond pdb=" CA ASN E 61 " pdb=" C ASN E 61 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.11e-02 8.12e+03 3.98e+01 bond pdb=" CA ASN E1074 " pdb=" C ASN E1074 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.24e-02 6.50e+03 2.44e+01 bond pdb=" N ASN E 709 " pdb=" CA ASN E 709 " ideal model delta sigma weight residual 1.456 1.405 0.052 1.31e-02 5.83e+03 1.56e+01 bond pdb=" CA GLN A 607 " pdb=" C GLN A 607 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.22e-02 6.72e+03 1.23e+01 ... (remaining 26073 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 759 107.06 - 113.79: 14483 113.79 - 120.52: 9498 120.52 - 127.25: 10551 127.25 - 133.98: 233 Bond angle restraints: 35524 Sorted by residual: angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.50 132.01 -11.51 1.34e+00 5.57e-01 7.38e+01 angle pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 113.19 121.65 -8.46 1.19e+00 7.06e-01 5.05e+01 angle pdb=" N LEU A 368 " pdb=" CA LEU A 368 " pdb=" C LEU A 368 " ideal model delta sigma weight residual 114.75 108.26 6.49 1.26e+00 6.30e-01 2.65e+01 angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.71 108.82 4.89 9.50e-01 1.11e+00 2.65e+01 angle pdb=" O PRO A 330 " pdb=" C PRO A 330 " pdb=" N ASN A 331 " ideal model delta sigma weight residual 122.64 115.75 6.89 1.35e+00 5.49e-01 2.61e+01 ... (remaining 35519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14420 17.57 - 35.13: 625 35.13 - 52.70: 139 52.70 - 70.26: 33 70.26 - 87.83: 8 Dihedral angle restraints: 15225 sinusoidal: 5838 harmonic: 9387 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -144.30 58.30 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 136.85 -43.85 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 15222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 4125 0.244 - 0.488: 7 0.488 - 0.732: 0 0.732 - 0.976: 0 0.976 - 1.220: 1 Chirality restraints: 4133 Sorted by residual: chirality pdb=" C1 NAG E1303 " pdb=" ND2 ASN E 331 " pdb=" C2 NAG E1303 " pdb=" O5 NAG E1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.72e+01 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1 NAG E1305 " pdb=" ND2 ASN E 616 " pdb=" C2 NAG E1305 " pdb=" O5 NAG E1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4130 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1310 " 0.308 2.00e-02 2.50e+03 2.61e-01 8.51e+02 pdb=" C7 NAG E1310 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E1310 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG E1310 " -0.452 2.00e-02 2.50e+03 pdb=" O7 NAG E1310 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " -0.297 2.00e-02 2.50e+03 2.54e-01 8.07e+02 pdb=" C7 NAG C1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1303 " -0.283 2.00e-02 2.50e+03 2.42e-01 7.34e+02 pdb=" C7 NAG E1303 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG E1303 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG E1303 " 0.424 2.00e-02 2.50e+03 pdb=" O7 NAG E1303 " -0.042 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4214 2.77 - 3.30: 23988 3.30 - 3.83: 42665 3.83 - 4.37: 49335 4.37 - 4.90: 85550 Nonbonded interactions: 205752 Sorted by model distance: nonbonded pdb=" OD1 ASN E 122 " pdb=" OG1 THR E 124 " model vdw 2.236 2.440 nonbonded pdb=" OD2 ASP A 737 " pdb=" OG1 THR A 739 " model vdw 2.238 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.253 2.440 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.263 2.440 ... (remaining 205747 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 14 through 1147 or resid 1301 through 1311)) selection = chain 'C' selection = chain 'E' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 13.960 Check model and map are aligned: 0.430 Set scattering table: 0.220 Process input model: 66.120 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.120 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 26078 Z= 0.230 Angle : 0.702 11.512 35524 Z= 0.445 Chirality : 0.048 1.220 4133 Planarity : 0.014 0.261 4570 Dihedral : 10.223 87.827 9072 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 5.57 % 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: -3.27 (0.13), residues: 3204 helix: 0.60 (0.20), residues: 633 sheet: -2.40 (0.18), residues: 610 loop : -3.24 (0.11), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 748 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 34 residues processed: 854 average time/residue: 1.0545 time to fit residues: 1077.7182 Evaluate side-chains 608 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 574 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 1.0770 time to fit residues: 12.7844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 164 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 251 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 121 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 196 ASN A 218 GLN A 360 ASN A 394 ASN A 414 GLN A 439 ASN A 493 GLN A 498 GLN A 519 HIS A 540 ASN A 606 ASN A 641 ASN A 658 ASN A 675 GLN A 777 ASN A 787 GLN A 804 GLN A 901 GLN A 913 GLN A 926 GLN A 954 GLN A1005 GLN A1048 HIS C 23 GLN C 30 ASN C 61 ASN C 115 GLN C 207 HIS C 218 GLN C 321 GLN C 394 ASN C 460 ASN C 487 ASN C 493 GLN C 498 GLN C 506 GLN C 544 ASN C 580 GLN C 606 ASN C 710 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN C1005 GLN C1071 GLN C1074 ASN E 23 GLN E 30 ASN E 66 HIS E 188 ASN E 196 ASN E 234 ASN E 370 ASN E 394 ASN E 437 ASN E 474 GLN E 493 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 540 ASN E 613 GLN E 644 GLN E 658 ASN E 777 ASN E 784 GLN E 895 GLN E 935 GLN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN E1048 HIS E1106 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 26078 Z= 0.267 Angle : 0.607 12.487 35524 Z= 0.313 Chirality : 0.046 0.331 4133 Planarity : 0.004 0.047 4570 Dihedral : 3.828 31.678 3462 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.53 (0.14), residues: 3204 helix: 1.21 (0.22), residues: 643 sheet: -1.68 (0.18), residues: 654 loop : -2.88 (0.12), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 610 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 67 residues processed: 693 average time/residue: 1.1263 time to fit residues: 929.0382 Evaluate side-chains 626 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 559 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 40 residues processed: 27 average time/residue: 0.5492 time to fit residues: 24.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 198 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 289 optimal weight: 0.0870 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 564 GLN A 606 ASN A 641 ASN A 777 ASN A 913 GLN A 954 GLN C 30 ASN C 81 ASN C 188 ASN C 196 ASN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN C1108 ASN E 149 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 658 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 26078 Z= 0.249 Angle : 0.596 15.763 35524 Z= 0.305 Chirality : 0.045 0.313 4133 Planarity : 0.004 0.045 4570 Dihedral : 4.184 41.111 3462 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 5.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.11 (0.14), residues: 3204 helix: 1.44 (0.22), residues: 642 sheet: -1.18 (0.18), residues: 672 loop : -2.67 (0.12), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 561 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 79 residues processed: 645 average time/residue: 1.1621 time to fit residues: 886.8524 Evaluate side-chains 603 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 524 time to evaluate : 2.730 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 48 residues processed: 31 average time/residue: 0.5842 time to fit residues: 28.2885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 151 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 196 optimal weight: 0.3980 chunk 293 optimal weight: 0.0170 chunk 310 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 chunk 277 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 360 ASN A 414 GLN A 606 ASN A 913 GLN A 954 GLN C 30 ASN C 121 ASN C 188 ASN C 321 GLN C 437 ASN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1074 ASN E 66 HIS E 115 GLN E 519 HIS E 532 ASN E 658 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 26078 Z= 0.220 Angle : 0.590 14.309 35524 Z= 0.298 Chirality : 0.044 0.229 4133 Planarity : 0.004 0.061 4570 Dihedral : 4.203 40.449 3462 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.86 (0.14), residues: 3204 helix: 1.49 (0.22), residues: 656 sheet: -0.95 (0.19), residues: 683 loop : -2.50 (0.13), residues: 1865 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 542 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 71 residues processed: 627 average time/residue: 1.1713 time to fit residues: 868.5970 Evaluate side-chains 589 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 518 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 49 residues processed: 22 average time/residue: 0.4323 time to fit residues: 18.0544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 264 optimal weight: 0.1980 chunk 214 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 954 GLN C 30 ASN C 81 ASN C 437 ASN C 779 GLN C 954 GLN C1074 ASN E 66 HIS E 81 ASN E 532 ASN E 658 ASN E 762 GLN E 901 GLN E 954 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 26078 Z= 0.343 Angle : 0.649 13.430 35524 Z= 0.331 Chirality : 0.047 0.289 4133 Planarity : 0.004 0.041 4570 Dihedral : 4.557 40.006 3462 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.08 % Favored : 91.89 % Rotamer Outliers : 5.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.78 (0.14), residues: 3204 helix: 1.28 (0.21), residues: 672 sheet: -0.76 (0.19), residues: 702 loop : -2.45 (0.13), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 563 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 95 residues processed: 651 average time/residue: 1.1536 time to fit residues: 889.7105 Evaluate side-chains 627 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 532 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 54 residues processed: 42 average time/residue: 0.4761 time to fit residues: 32.2331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 1.9990 chunk 279 optimal weight: 0.4980 chunk 61 optimal weight: 0.0670 chunk 182 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 143 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 606 ASN A 954 GLN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 437 ASN C1005 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 703 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 26078 Z= 0.214 Angle : 0.615 12.592 35524 Z= 0.311 Chirality : 0.045 0.304 4133 Planarity : 0.004 0.063 4570 Dihedral : 4.453 42.134 3462 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.57 (0.14), residues: 3204 helix: 1.61 (0.22), residues: 656 sheet: -0.69 (0.19), residues: 696 loop : -2.32 (0.13), residues: 1852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 535 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 75 residues processed: 620 average time/residue: 1.1854 time to fit residues: 873.5103 Evaluate side-chains 595 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 520 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 54 residues processed: 21 average time/residue: 0.3886 time to fit residues: 16.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 173 optimal weight: 0.0050 chunk 309 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 540 ASN A 606 ASN A 655 HIS A 954 GLN C 437 ASN C 655 HIS C1005 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 66 HIS E 188 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 913 GLN E1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 26078 Z= 0.304 Angle : 0.643 12.365 35524 Z= 0.327 Chirality : 0.046 0.257 4133 Planarity : 0.004 0.043 4570 Dihedral : 4.496 40.652 3462 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 4.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.54 (0.14), residues: 3204 helix: 1.48 (0.22), residues: 660 sheet: -0.61 (0.19), residues: 698 loop : -2.26 (0.13), residues: 1846 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 526 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 81 residues processed: 608 average time/residue: 1.2272 time to fit residues: 885.6321 Evaluate side-chains 596 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 515 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 60 residues processed: 21 average time/residue: 0.4959 time to fit residues: 18.3169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 chunk 210 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 606 ASN A 655 HIS A 954 GLN C 30 ASN C 61 ASN C 121 ASN C 655 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 644 GLN E1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 26078 Z= 0.271 Angle : 0.632 13.290 35524 Z= 0.322 Chirality : 0.046 0.430 4133 Planarity : 0.004 0.045 4570 Dihedral : 4.532 41.850 3462 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.47 (0.14), residues: 3204 helix: 1.50 (0.21), residues: 660 sheet: -0.56 (0.19), residues: 704 loop : -2.20 (0.13), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 529 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 80 residues processed: 603 average time/residue: 1.1940 time to fit residues: 850.5715 Evaluate side-chains 601 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 521 time to evaluate : 2.799 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 58 residues processed: 22 average time/residue: 0.4225 time to fit residues: 17.7603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.5980 chunk 296 optimal weight: 0.0020 chunk 270 optimal weight: 0.8980 chunk 288 optimal weight: 0.6980 chunk 173 optimal weight: 0.0980 chunk 125 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 272 optimal weight: 1.9990 chunk 287 optimal weight: 0.0070 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 606 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN C 655 HIS ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 165 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 26078 Z= 0.187 Angle : 0.612 12.669 35524 Z= 0.311 Chirality : 0.045 0.325 4133 Planarity : 0.004 0.045 4570 Dihedral : 4.431 38.093 3462 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.34 (0.15), residues: 3204 helix: 1.72 (0.22), residues: 650 sheet: -0.49 (0.19), residues: 695 loop : -2.14 (0.13), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 522 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 69 residues processed: 590 average time/residue: 1.1965 time to fit residues: 833.4415 Evaluate side-chains 579 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 510 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 58 residues processed: 12 average time/residue: 1.1113 time to fit residues: 20.0881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 211 optimal weight: 0.3980 chunk 319 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 196 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 606 ASN A 655 HIS A 777 ASN A 935 GLN A 954 GLN C 61 ASN C 321 GLN C 655 HIS C1088 HIS C1106 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 188 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 26078 Z= 0.274 Angle : 0.642 13.292 35524 Z= 0.328 Chirality : 0.046 0.283 4133 Planarity : 0.004 0.049 4570 Dihedral : 4.529 38.986 3462 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.38 (0.15), residues: 3204 helix: 1.55 (0.21), residues: 660 sheet: -0.51 (0.19), residues: 700 loop : -2.13 (0.13), residues: 1844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6408 Ramachandran restraints generated. 3204 Oldfield, 0 Emsley, 3204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 529 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 69 residues processed: 590 average time/residue: 1.2282 time to fit residues: 854.6211 Evaluate side-chains 585 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 516 time to evaluate : 2.811 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 60 residues processed: 10 average time/residue: 0.5794 time to fit residues: 11.7758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 chunk 234 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 655 HIS ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 954 GLN C 655 HIS ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 409 GLN E 532 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129923 restraints weight = 36509.646| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.15 r_work: 0.3629 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 26078 Z= 0.215 Angle : 0.631 12.994 35524 Z= 0.321 Chirality : 0.045 0.275 4133 Planarity : 0.004 0.041 4570 Dihedral : 4.488 37.511 3462 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.30 (0.15), residues: 3204 helix: 1.72 (0.21), residues: 651 sheet: -0.48 (0.19), residues: 701 loop : -2.10 (0.13), residues: 1852 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12941.71 seconds wall clock time: 228 minutes 38.04 seconds (13718.04 seconds total)