Starting phenix.real_space_refine on Fri Aug 9 08:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2024/7wz2_32902.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2024/7wz2_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_2024/7wz2_32902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2024/7wz2_32902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2024/7wz2_32902.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz2_32902/08_2024/7wz2_32902.cif" } 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-dev-5409/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 dihedrals: 36 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 dihedrals: 33 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.14, per 1000 atoms: 0.52 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: 8.79 Conformation dependent library (CDL) restraints added in 4.2 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: 3.29 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: 12.18 Time building geometry restraints manager: 9.82 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: 15082 17.57 - 35.13: 656 35.13 - 52.70: 157 52.70 - 70.26: 36 70.26 - 87.83: 8 Dihedral angle restraints: 15939 sinusoidal: 6552 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 15936 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 3.040 nonbonded pdb=" OD2 ASP A 737 " pdb=" OG1 THR A 739 " model vdw 2.238 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.253 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.263 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 23.380 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 67.310 Find NCS groups from input model: 1.430 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.390 ------------------------------------------------------------------------------- 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 : 10.242 87.827 9786 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 % Allowed : 8.13 % Favored : 86.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 886 HIS 0.002 0.000 HIS A1064 PHE 0.007 0.001 PHE C 238 TYR 0.011 0.001 TYR E 369 ARG 0.002 0.000 ARG C 905 *********************** 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 : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6922 (tm130) REVERT: A 63 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.6511 (p) REVERT: A 95 THR cc_start: 0.6691 (OUTLIER) cc_final: 0.6394 (t) REVERT: A 165 ASN cc_start: 0.5202 (m-40) cc_final: 0.4784 (t0) REVERT: A 345 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.6219 (p) REVERT: A 354 ASN cc_start: 0.7695 (m-40) cc_final: 0.7393 (m-40) REVERT: A 697 MET cc_start: 0.7893 (ptm) cc_final: 0.7691 (ptm) REVERT: A 820 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: A 914 ASN cc_start: 0.7646 (p0) cc_final: 0.6710 (p0) REVERT: A 933 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7687 (mtpm) REVERT: C 52 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 54 LEU cc_start: 0.8175 (mp) cc_final: 0.7655 (mp) REVERT: C 191 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6855 (mt-10) REVERT: C 195 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7442 (mtpt) REVERT: C 220 PHE cc_start: 0.7992 (t80) cc_final: 0.7768 (t80) REVERT: C 281 GLU cc_start: 0.6548 (pp20) cc_final: 0.6336 (pp20) REVERT: C 282 ASN cc_start: 0.7913 (m-40) cc_final: 0.7323 (m-40) REVERT: C 300 LYS cc_start: 0.8289 (mttt) cc_final: 0.7739 (mttt) REVERT: C 334 ASN cc_start: 0.8301 (t0) cc_final: 0.7871 (t0) REVERT: C 437 ASN cc_start: 0.7321 (t0) cc_final: 0.6992 (t0) REVERT: C 488 CYS cc_start: 0.1452 (OUTLIER) cc_final: 0.1170 (t) REVERT: C 547 THR cc_start: 0.7637 (m) cc_final: 0.7413 (p) REVERT: C 553 THR cc_start: 0.8349 (p) cc_final: 0.8051 (t) REVERT: C 557 LYS cc_start: 0.8215 (mttt) cc_final: 0.7953 (mttm) REVERT: C 568 ASP cc_start: 0.7085 (m-30) cc_final: 0.6772 (m-30) REVERT: C 572 THR cc_start: 0.7856 (p) cc_final: 0.7159 (t) REVERT: C 603 ASN cc_start: 0.7677 (t0) cc_final: 0.7382 (t0) REVERT: C 697 MET cc_start: 0.8086 (ptm) cc_final: 0.7861 (ptp) REVERT: C 861 LEU cc_start: 0.8218 (mt) cc_final: 0.7997 (mt) REVERT: C 933 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7533 (mtmm) REVERT: C 935 GLN cc_start: 0.6871 (mt0) cc_final: 0.5991 (mt0) REVERT: C 950 ASP cc_start: 0.6837 (t70) cc_final: 0.6570 (t0) REVERT: C 994 ASP cc_start: 0.6635 (m-30) cc_final: 0.6119 (m-30) REVERT: C 1107 ARG cc_start: 0.3757 (OUTLIER) cc_final: 0.3360 (ttm170) REVERT: C 1125 ASN cc_start: 0.7418 (p0) cc_final: 0.6990 (p0) REVERT: E 52 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7036 (tp40) REVERT: E 85 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: E 95 THR cc_start: 0.7448 (m) cc_final: 0.7231 (t) REVERT: E 188 ASN cc_start: 0.8022 (m-40) cc_final: 0.7656 (m-40) REVERT: E 189 LEU cc_start: 0.8493 (tp) cc_final: 0.8171 (tp) REVERT: E 190 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7471 (mtt-85) REVERT: E 191 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6824 (mt-10) REVERT: E 220 PHE cc_start: 0.7561 (t80) cc_final: 0.7302 (t80) REVERT: E 281 GLU cc_start: 0.7067 (pp20) cc_final: 0.6277 (pp20) REVERT: E 290 ASP cc_start: 0.7464 (t70) cc_final: 0.6779 (t0) REVERT: E 307 THR cc_start: 0.8480 (t) cc_final: 0.8225 (p) REVERT: E 421 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5645 (m-80) REVERT: E 574 ASP cc_start: 0.6628 (t70) cc_final: 0.6103 (t0) REVERT: E 586 ASP cc_start: 0.7253 (t70) cc_final: 0.6895 (t0) REVERT: E 610 VAL cc_start: 0.7915 (t) cc_final: 0.7530 (m) REVERT: E 658 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6644 (p0) REVERT: E 660 TYR cc_start: 0.7761 (m-80) cc_final: 0.7552 (m-80) REVERT: E 697 MET cc_start: 0.7895 (ptm) cc_final: 0.7686 (ptm) REVERT: E 808 ASP cc_start: 0.6493 (t70) cc_final: 0.6226 (p0) REVERT: E 824 ASN cc_start: 0.8047 (m-40) cc_final: 0.7828 (m110) REVERT: E 954 GLN cc_start: 0.7401 (mt0) cc_final: 0.6936 (mt0) REVERT: E 1118 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6675 (p0) outliers start: 154 outliers final: 34 residues processed: 854 average time/residue: 1.0396 time to fit residues: 1058.9177 Evaluate side-chains 617 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 574 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 421 TYR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.6980 chunk 243 optimal weight: 0.0470 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 164 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 251 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 A 173 GLN A 196 ASN A 218 GLN A 354 ASN 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 580 GLN A 606 ASN A 658 ASN A 675 GLN A 690 GLN A 777 ASN A 787 GLN A 804 GLN A 901 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 957 GLN C 960 ASN C 969 ASN C1071 GLN C1074 ASN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 30 ASN E 66 HIS 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 644 GLN E 777 ASN E 784 GLN E 895 GLN E 935 GLN E 954 GLN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN E1048 HIS E1106 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26078 Z= 0.214 Angle : 0.590 11.977 35524 Z= 0.303 Chirality : 0.045 0.302 4133 Planarity : 0.004 0.044 4570 Dihedral : 6.416 59.092 4270 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.45 % Allowed : 15.91 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.50 (0.14), residues: 3204 helix: 1.22 (0.21), residues: 645 sheet: -1.63 (0.18), residues: 651 loop : -2.88 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS E1088 PHE 0.026 0.001 PHE C 400 TYR 0.019 0.001 TYR A 508 ARG 0.007 0.001 ARG C1014 *********************** 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 727 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 604 time to evaluate : 2.892 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: A 48 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7365 (mt) REVERT: A 52 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 55 PHE cc_start: 0.7943 (m-80) cc_final: 0.7729 (m-80) REVERT: A 191 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6478 (mt-10) REVERT: A 231 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6721 (tp) REVERT: A 354 ASN cc_start: 0.7770 (m110) cc_final: 0.7499 (m-40) REVERT: A 362 VAL cc_start: 0.8263 (t) cc_final: 0.7978 (p) REVERT: A 378 LYS cc_start: 0.7163 (pttm) cc_final: 0.6894 (pttm) REVERT: A 420 ASP cc_start: 0.7026 (p0) cc_final: 0.6586 (p0) REVERT: A 421 TYR cc_start: 0.7751 (m-10) cc_final: 0.7438 (m-10) REVERT: A 451 TYR cc_start: 0.7890 (m-10) cc_final: 0.7606 (m-10) REVERT: A 492 LEU cc_start: 0.7902 (mt) cc_final: 0.7695 (mm) REVERT: A 493 GLN cc_start: 0.6639 (tp40) cc_final: 0.6393 (tp40) REVERT: A 651 ILE cc_start: 0.8294 (mt) cc_final: 0.8092 (mm) REVERT: A 776 LYS cc_start: 0.7947 (tppp) cc_final: 0.7735 (ttpp) REVERT: A 820 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: A 914 ASN cc_start: 0.7568 (p0) cc_final: 0.7181 (p0) REVERT: A 1019 ARG cc_start: 0.7451 (ttm170) cc_final: 0.7245 (ttm170) REVERT: A 1114 ILE cc_start: 0.8365 (mp) cc_final: 0.8139 (tt) REVERT: A 1122 VAL cc_start: 0.8454 (t) cc_final: 0.8164 (p) REVERT: A 1144 GLU cc_start: 0.6610 (mp0) cc_final: 0.6387 (mp0) REVERT: C 52 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6750 (tm-30) REVERT: C 122 ASN cc_start: 0.6209 (m-40) cc_final: 0.5985 (m-40) REVERT: C 206 LYS cc_start: 0.8095 (tptm) cc_final: 0.7877 (tptm) REVERT: C 220 PHE cc_start: 0.8049 (t80) cc_final: 0.7735 (t80) REVERT: C 282 ASN cc_start: 0.7922 (m-40) cc_final: 0.7423 (m-40) REVERT: C 356 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7735 (tptp) REVERT: C 437 ASN cc_start: 0.7150 (t0) cc_final: 0.6950 (t0) REVERT: C 553 THR cc_start: 0.8268 (p) cc_final: 0.8005 (t) REVERT: C 568 ASP cc_start: 0.7097 (m-30) cc_final: 0.6808 (m-30) REVERT: C 572 THR cc_start: 0.7890 (p) cc_final: 0.7144 (t) REVERT: C 586 ASP cc_start: 0.6871 (t70) cc_final: 0.6669 (m-30) REVERT: C 697 MET cc_start: 0.8108 (ptm) cc_final: 0.7792 (ptp) REVERT: C 719 THR cc_start: 0.8132 (t) cc_final: 0.7893 (t) REVERT: C 776 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7237 (ttpp) REVERT: C 855 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.4964 (t80) REVERT: C 861 LEU cc_start: 0.8358 (mt) cc_final: 0.8135 (mt) REVERT: C 950 ASP cc_start: 0.6934 (t70) cc_final: 0.6674 (t0) REVERT: C 1107 ARG cc_start: 0.3625 (OUTLIER) cc_final: 0.3295 (ttm170) REVERT: E 41 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7919 (mttt) REVERT: E 52 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7126 (tp40) REVERT: E 95 THR cc_start: 0.7378 (m) cc_final: 0.7042 (t) REVERT: E 188 ASN cc_start: 0.8106 (m-40) cc_final: 0.7785 (m-40) REVERT: E 189 LEU cc_start: 0.8406 (tp) cc_final: 0.8122 (tp) REVERT: E 236 THR cc_start: 0.6989 (p) cc_final: 0.6761 (m) REVERT: E 281 GLU cc_start: 0.6961 (pp20) cc_final: 0.6596 (pp20) REVERT: E 290 ASP cc_start: 0.7635 (t70) cc_final: 0.7084 (t0) REVERT: E 402 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7534 (pt) REVERT: E 574 ASP cc_start: 0.6762 (t70) cc_final: 0.6279 (t0) REVERT: E 586 ASP cc_start: 0.7236 (t70) cc_final: 0.6931 (t0) REVERT: E 610 VAL cc_start: 0.7849 (t) cc_final: 0.7438 (m) REVERT: E 808 ASP cc_start: 0.6569 (t70) cc_final: 0.6308 (p0) REVERT: E 869 MET cc_start: 0.8362 (mtt) cc_final: 0.7931 (mtp) REVERT: E 935 GLN cc_start: 0.7561 (tt0) cc_final: 0.6920 (tt0) REVERT: E 949 GLN cc_start: 0.7840 (tp40) cc_final: 0.7591 (mm-40) REVERT: E 954 GLN cc_start: 0.7410 (mt0) cc_final: 0.6992 (mt0) REVERT: E 1014 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.7159 (mtt-85) REVERT: E 1017 GLU cc_start: 0.6855 (tt0) cc_final: 0.6562 (tt0) outliers start: 123 outliers final: 56 residues processed: 676 average time/residue: 1.1135 time to fit residues: 892.3711 Evaluate side-chains 619 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 555 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1118 ASP 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: 0.3980 chunk 198 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 315 optimal weight: 0.6980 chunk 260 optimal weight: 7.9990 chunk 289 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 414 GLN A 542 ASN A 564 GLN A 606 ASN A 658 ASN A 954 GLN A 960 ASN C 30 ASN C 81 ASN C 188 ASN C 196 ASN C 641 ASN C 710 ASN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN E 703 ASN E 777 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26078 Z= 0.242 Angle : 0.591 15.745 35524 Z= 0.303 Chirality : 0.045 0.263 4133 Planarity : 0.004 0.044 4570 Dihedral : 6.017 58.335 4241 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.92 % Allowed : 17.75 % Favored : 77.33 % 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: 1.30 (0.21), residues: 658 sheet: -1.19 (0.18), residues: 691 loop : -2.65 (0.12), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.004 0.001 HIS A 146 PHE 0.024 0.002 PHE C 168 TYR 0.021 0.001 TYR E 660 ARG 0.009 0.001 ARG C1014 *********************** 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 704 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 568 time to evaluate : 2.544 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: A 52 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 191 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6149 (mt-10) REVERT: A 237 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6680 (mtp-110) REVERT: A 347 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: A 351 TYR cc_start: 0.7917 (p90) cc_final: 0.7697 (p90) REVERT: A 354 ASN cc_start: 0.7825 (m110) cc_final: 0.7531 (m-40) REVERT: A 362 VAL cc_start: 0.8257 (t) cc_final: 0.8015 (p) REVERT: A 378 LYS cc_start: 0.7206 (pttm) cc_final: 0.6905 (pttm) REVERT: A 380 TYR cc_start: 0.8370 (m-80) cc_final: 0.8104 (m-80) REVERT: A 452 LEU cc_start: 0.8564 (mt) cc_final: 0.8361 (mt) REVERT: A 505 TYR cc_start: 0.7238 (m-80) cc_final: 0.7013 (m-80) REVERT: A 820 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: A 950 ASP cc_start: 0.6822 (m-30) cc_final: 0.6514 (m-30) REVERT: A 1031 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 1122 VAL cc_start: 0.8541 (t) cc_final: 0.8263 (p) REVERT: C 153 MET cc_start: 0.7138 (ptp) cc_final: 0.6905 (pmm) REVERT: C 191 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 206 LYS cc_start: 0.8140 (tptm) cc_final: 0.7927 (tptm) REVERT: C 220 PHE cc_start: 0.8147 (t80) cc_final: 0.7714 (t80) REVERT: C 231 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8209 (mt) REVERT: C 356 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7639 (tppp) REVERT: C 568 ASP cc_start: 0.7135 (m-30) cc_final: 0.6856 (m-30) REVERT: C 572 THR cc_start: 0.7930 (p) cc_final: 0.7255 (t) REVERT: C 674 TYR cc_start: 0.8325 (t80) cc_final: 0.7793 (t80) REVERT: C 675 GLN cc_start: 0.5528 (OUTLIER) cc_final: 0.5256 (mp10) REVERT: C 697 MET cc_start: 0.8116 (ptm) cc_final: 0.7842 (ptp) REVERT: C 780 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6380 (mt-10) REVERT: C 804 GLN cc_start: 0.7319 (pt0) cc_final: 0.7003 (pt0) REVERT: C 855 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4862 (t80) REVERT: C 861 LEU cc_start: 0.8347 (mt) cc_final: 0.8105 (mt) REVERT: C 900 MET cc_start: 0.7578 (mtm) cc_final: 0.7368 (mtt) REVERT: C 921 LYS cc_start: 0.7505 (mmmm) cc_final: 0.7228 (mmmm) REVERT: C 935 GLN cc_start: 0.7076 (mt0) cc_final: 0.6411 (mt0) REVERT: C 950 ASP cc_start: 0.6979 (t70) cc_final: 0.6368 (t0) REVERT: C 954 GLN cc_start: 0.7427 (mt0) cc_final: 0.7098 (mt0) REVERT: E 41 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7933 (mtmt) REVERT: E 95 THR cc_start: 0.7450 (m) cc_final: 0.7125 (t) REVERT: E 188 ASN cc_start: 0.8119 (m-40) cc_final: 0.7850 (m110) REVERT: E 189 LEU cc_start: 0.8534 (tp) cc_final: 0.8290 (tp) REVERT: E 285 ILE cc_start: 0.8202 (mt) cc_final: 0.7967 (mt) REVERT: E 290 ASP cc_start: 0.7618 (t70) cc_final: 0.6979 (t0) REVERT: E 402 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7548 (pt) REVERT: E 574 ASP cc_start: 0.6854 (t70) cc_final: 0.6313 (t0) REVERT: E 586 ASP cc_start: 0.7211 (t70) cc_final: 0.6877 (t0) REVERT: E 690 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (mm110) REVERT: E 808 ASP cc_start: 0.6638 (t70) cc_final: 0.6390 (p0) REVERT: E 869 MET cc_start: 0.8440 (mtt) cc_final: 0.8118 (mtp) REVERT: E 950 ASP cc_start: 0.6913 (t70) cc_final: 0.6514 (t70) REVERT: E 954 GLN cc_start: 0.7480 (mt0) cc_final: 0.7123 (mt0) REVERT: E 1014 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7375 (mtt-85) REVERT: E 1017 GLU cc_start: 0.6891 (tt0) cc_final: 0.6583 (tt0) REVERT: E 1055 SER cc_start: 0.8189 (t) cc_final: 0.7940 (p) outliers start: 136 outliers final: 69 residues processed: 648 average time/residue: 1.1280 time to fit residues: 864.7754 Evaluate side-chains 614 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 536 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 690 GLN Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 310 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 606 ASN A 777 ASN A 954 GLN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 196 ASN C 641 ASN C 710 ASN C 762 GLN C 779 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN C1108 ASN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 81 ASN E 115 GLN E 121 ASN E 519 HIS E 532 ASN E 901 GLN E1125 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26078 Z= 0.284 Angle : 0.613 14.724 35524 Z= 0.312 Chirality : 0.046 0.252 4133 Planarity : 0.004 0.043 4570 Dihedral : 6.010 58.182 4232 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.88 % Allowed : 19.23 % Favored : 75.89 % 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: -1.87 (0.14), residues: 3204 helix: 1.33 (0.21), residues: 669 sheet: -0.96 (0.18), residues: 685 loop : -2.48 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS E1048 PHE 0.018 0.002 PHE E 86 TYR 0.017 0.002 TYR E 28 ARG 0.009 0.001 ARG E 567 *********************** 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 676 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 541 time to evaluate : 2.756 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: A 52 GLN cc_start: 0.7225 (tm-30) cc_final: 0.7017 (tm-30) REVERT: A 237 ARG cc_start: 0.7146 (mmm160) cc_final: 0.6626 (mtp-110) REVERT: A 347 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: A 354 ASN cc_start: 0.7865 (m110) cc_final: 0.7610 (m-40) REVERT: A 362 VAL cc_start: 0.8283 (t) cc_final: 0.8040 (p) REVERT: A 378 LYS cc_start: 0.7221 (pttm) cc_final: 0.6881 (pttm) REVERT: A 380 TYR cc_start: 0.8350 (m-80) cc_final: 0.8051 (m-80) REVERT: A 505 TYR cc_start: 0.7243 (m-80) cc_final: 0.7016 (m-80) REVERT: A 820 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: A 950 ASP cc_start: 0.6825 (m-30) cc_final: 0.6501 (m-30) REVERT: A 1031 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 1122 VAL cc_start: 0.8556 (t) cc_final: 0.8310 (p) REVERT: C 153 MET cc_start: 0.7201 (ptp) cc_final: 0.6862 (mpp) REVERT: C 180 GLU cc_start: 0.7088 (tt0) cc_final: 0.6864 (tm-30) REVERT: C 191 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6949 (mt-10) REVERT: C 220 PHE cc_start: 0.8181 (t80) cc_final: 0.7724 (t80) REVERT: C 231 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (mt) REVERT: C 356 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7602 (tppp) REVERT: C 568 ASP cc_start: 0.7191 (m-30) cc_final: 0.6894 (m-30) REVERT: C 572 THR cc_start: 0.8006 (p) cc_final: 0.7331 (t) REVERT: C 674 TYR cc_start: 0.8316 (t80) cc_final: 0.7786 (t80) REVERT: C 675 GLN cc_start: 0.5587 (OUTLIER) cc_final: 0.5318 (mp10) REVERT: C 697 MET cc_start: 0.8119 (ptm) cc_final: 0.7874 (ptp) REVERT: C 776 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7558 (ttpp) REVERT: C 780 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6414 (mt-10) REVERT: C 855 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.4894 (t80) REVERT: C 861 LEU cc_start: 0.8339 (mt) cc_final: 0.8094 (mt) REVERT: C 921 LYS cc_start: 0.7518 (mmmm) cc_final: 0.7236 (mmmm) REVERT: C 935 GLN cc_start: 0.7018 (mt0) cc_final: 0.6800 (mt0) REVERT: C 950 ASP cc_start: 0.6973 (t70) cc_final: 0.6367 (t0) REVERT: C 954 GLN cc_start: 0.7467 (mt0) cc_final: 0.7145 (mt0) REVERT: E 41 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7974 (mtmt) REVERT: E 95 THR cc_start: 0.7573 (m) cc_final: 0.7239 (t) REVERT: E 129 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7137 (mtpp) REVERT: E 188 ASN cc_start: 0.8107 (m-40) cc_final: 0.7856 (m-40) REVERT: E 189 LEU cc_start: 0.8607 (tp) cc_final: 0.8361 (tp) REVERT: E 285 ILE cc_start: 0.8207 (mt) cc_final: 0.7994 (mt) REVERT: E 376 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7948 (p) REVERT: E 453 TYR cc_start: 0.6915 (p90) cc_final: 0.6658 (p90) REVERT: E 574 ASP cc_start: 0.6921 (t70) cc_final: 0.6331 (t0) REVERT: E 586 ASP cc_start: 0.7199 (t70) cc_final: 0.6868 (t0) REVERT: E 808 ASP cc_start: 0.6644 (t70) cc_final: 0.6366 (p0) REVERT: E 869 MET cc_start: 0.8458 (mtt) cc_final: 0.8254 (mtp) REVERT: E 935 GLN cc_start: 0.7348 (tt0) cc_final: 0.7139 (tt0) REVERT: E 950 ASP cc_start: 0.6904 (t70) cc_final: 0.6455 (t70) REVERT: E 954 GLN cc_start: 0.7518 (mt0) cc_final: 0.7123 (mt0) REVERT: E 983 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.6990 (mtm110) REVERT: E 1014 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7358 (mtt-85) REVERT: E 1055 SER cc_start: 0.8197 (t) cc_final: 0.7988 (p) outliers start: 135 outliers final: 78 residues processed: 626 average time/residue: 1.1569 time to fit residues: 858.7409 Evaluate side-chains 612 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 526 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 158 ARG Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.9980 chunk 176 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 264 optimal weight: 0.2980 chunk 214 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 278 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 606 ASN A 954 GLN C 121 ASN C 137 ASN C 188 ASN C 321 GLN C 641 ASN C 690 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 532 ASN E 644 GLN E 658 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26078 Z= 0.232 Angle : 0.595 13.199 35524 Z= 0.301 Chirality : 0.045 0.217 4133 Planarity : 0.004 0.045 4570 Dihedral : 5.906 56.508 4229 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.70 % Allowed : 20.32 % Favored : 74.98 % 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: -1.73 (0.14), residues: 3204 helix: 1.41 (0.21), residues: 671 sheet: -0.85 (0.19), residues: 698 loop : -2.40 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS E1088 PHE 0.021 0.001 PHE C 168 TYR 0.019 0.001 TYR A 28 ARG 0.008 0.000 ARG E 567 *********************** 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 666 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 536 time to evaluate : 2.670 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: A 52 GLN cc_start: 0.7228 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 347 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 354 ASN cc_start: 0.7862 (m110) cc_final: 0.7627 (m-40) REVERT: A 362 VAL cc_start: 0.8258 (t) cc_final: 0.8035 (p) REVERT: A 378 LYS cc_start: 0.7240 (pttm) cc_final: 0.6894 (pttm) REVERT: A 380 TYR cc_start: 0.8371 (m-80) cc_final: 0.8082 (m-80) REVERT: A 585 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 820 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: A 950 ASP cc_start: 0.6817 (m-30) cc_final: 0.6504 (m-30) REVERT: A 1031 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 1122 VAL cc_start: 0.8566 (t) cc_final: 0.8312 (p) REVERT: C 180 GLU cc_start: 0.7082 (tt0) cc_final: 0.6838 (tm-30) REVERT: C 191 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6938 (mt-10) REVERT: C 220 PHE cc_start: 0.8182 (t80) cc_final: 0.7743 (t80) REVERT: C 231 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8201 (mt) REVERT: C 356 LYS cc_start: 0.8005 (tppp) cc_final: 0.7542 (tppp) REVERT: C 546 LEU cc_start: 0.8050 (tp) cc_final: 0.7789 (tt) REVERT: C 568 ASP cc_start: 0.7197 (m-30) cc_final: 0.6913 (m-30) REVERT: C 572 THR cc_start: 0.8011 (p) cc_final: 0.7391 (t) REVERT: C 675 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.5303 (mp10) REVERT: C 697 MET cc_start: 0.8106 (ptm) cc_final: 0.7819 (ptp) REVERT: C 719 THR cc_start: 0.8201 (p) cc_final: 0.7877 (t) REVERT: C 776 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7755 (ttpp) REVERT: C 855 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4758 (t80) REVERT: C 858 LEU cc_start: 0.8322 (mt) cc_final: 0.8107 (mt) REVERT: C 861 LEU cc_start: 0.8336 (mt) cc_final: 0.8085 (mt) REVERT: C 921 LYS cc_start: 0.7525 (mmmm) cc_final: 0.7236 (mmmm) REVERT: C 950 ASP cc_start: 0.6959 (t70) cc_final: 0.6322 (t0) REVERT: C 954 GLN cc_start: 0.7448 (mt0) cc_final: 0.7135 (mt0) REVERT: E 41 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7987 (mtmt) REVERT: E 95 THR cc_start: 0.7558 (m) cc_final: 0.7215 (t) REVERT: E 105 ILE cc_start: 0.7941 (pt) cc_final: 0.7619 (mp) REVERT: E 129 LYS cc_start: 0.7284 (mtmt) cc_final: 0.7031 (mtpp) REVERT: E 149 ASN cc_start: 0.1253 (OUTLIER) cc_final: 0.0741 (p0) REVERT: E 158 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7601 (mtm110) REVERT: E 188 ASN cc_start: 0.8093 (m-40) cc_final: 0.7847 (m-40) REVERT: E 189 LEU cc_start: 0.8633 (tp) cc_final: 0.8415 (tp) REVERT: E 285 ILE cc_start: 0.8213 (mt) cc_final: 0.7987 (mt) REVERT: E 376 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7949 (t) REVERT: E 574 ASP cc_start: 0.6923 (t70) cc_final: 0.6303 (t0) REVERT: E 586 ASP cc_start: 0.7173 (t70) cc_final: 0.6705 (t0) REVERT: E 808 ASP cc_start: 0.6664 (t70) cc_final: 0.6377 (p0) REVERT: E 869 MET cc_start: 0.8461 (mtt) cc_final: 0.8255 (mtp) REVERT: E 950 ASP cc_start: 0.6886 (t70) cc_final: 0.6543 (t70) REVERT: E 954 GLN cc_start: 0.7542 (mt0) cc_final: 0.7135 (mt0) REVERT: E 990 GLU cc_start: 0.6875 (tp30) cc_final: 0.6651 (mm-30) REVERT: E 1014 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7334 (mtt-85) REVERT: E 1055 SER cc_start: 0.8150 (t) cc_final: 0.7944 (p) outliers start: 130 outliers final: 77 residues processed: 621 average time/residue: 1.1133 time to fit residues: 815.0702 Evaluate side-chains 608 residues out of total 2817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 521 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 158 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1141 LEU 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: 0.3980 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: