Starting phenix.real_space_refine on Wed Jun 25 05:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoa_33342/06_2025/7xoa_33342.cif" } resolution = 3.2 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= 0.021 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 134 5.16 5 C 18667 2.51 5 N 4812 2.21 5 O 5588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 1.77s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 18.59, per 1000 atoms: 0.64 Number of scatterers: 29202 At special positions: 0 Unit cell: (132.664, 136.784, 246.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 134 16.00 O 5588 8.00 N 4812 7.00 C 18667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 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=2.01 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=2.32 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 B 131 " - pdb=" SG CYS B 166 " distance=1.98 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.99 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.60 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.76 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 709 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 3.8 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 49 sheets defined 30.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.633A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.188A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 4.029A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.508A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.787A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.109A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.146A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.702A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.327A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.595A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 3.841A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.533A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.782A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.120A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.541A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.672A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.533A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.560A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.548A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.690A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.556A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.779A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.137A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.034A 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 removed outlier: 3.524A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1033 removed outlier: 3.581A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.781A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.808A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.798A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.147A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.732A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.734A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.375A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.204A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.579A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.528A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.540A pdb=" N ALA D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.649A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.153A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.824A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.747A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.656A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.557A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.569A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.615A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.062A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.817A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.985A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.622A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.599A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.685A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.212A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.810A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.203A 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=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.837A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.525A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.198A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.048A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 126 through 132 removed outlier: 3.550A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.319A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.113A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.513A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.809A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.831A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.515A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.646A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.913A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.299A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.911A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.508A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.549A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.534A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.742A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.832A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.811A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.185A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.566A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.738A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 350 1111 hydrogen bonds defined for protein. 3033 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: 12.56 Time building geometry restraints manager: 8.74 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: 6036 1.33 - 1.45: 7355 1.45 - 1.57: 16336 1.57 - 1.70: 0 1.70 - 1.82: 179 Bond restraints: 29906 Sorted by residual: bond pdb=" CA ALA C 292 " pdb=" CB ALA C 292 " ideal model delta sigma weight residual 1.527 1.497 0.031 7.60e-03 1.73e+04 1.64e+01 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.455 1.474 -0.019 7.00e-03 2.04e+04 7.61e+00 bond pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" CA ALA A 288 " pdb=" CB ALA A 288 " ideal model delta sigma weight residual 1.535 1.483 0.052 1.90e-02 2.77e+03 7.46e+00 ... (remaining 29901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 39977 1.91 - 3.82: 638 3.82 - 5.73: 73 5.73 - 7.63: 16 7.63 - 9.54: 4 Bond angle restraints: 40708 Sorted by residual: angle pdb=" CA PHE A 374 " pdb=" CB PHE A 374 " pdb=" CG PHE A 374 " ideal model delta sigma weight residual 113.80 120.48 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" O PHE A 371 " ideal model delta sigma weight residual 121.46 114.57 6.89 1.17e+00 7.31e-01 3.47e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 118.44 127.21 -8.77 1.59e+00 3.96e-01 3.04e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" O ALA B 520 " ideal model delta sigma weight residual 120.16 112.61 7.55 1.37e+00 5.33e-01 3.04e+01 angle pdb=" O ASP A 287 " pdb=" C ASP A 287 " pdb=" N ALA A 288 " ideal model delta sigma weight residual 123.48 117.24 6.24 1.14e+00 7.69e-01 3.00e+01 ... (remaining 40703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 17786 23.03 - 46.05: 330 46.05 - 69.08: 32 69.08 - 92.10: 19 92.10 - 115.13: 17 Dihedral angle restraints: 18184 sinusoidal: 7482 harmonic: 10702 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -160.06 74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -150.16 64.16 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -142.36 56.36 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 18181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4055 0.062 - 0.124: 560 0.124 - 0.186: 26 0.186 - 0.248: 12 0.248 - 0.310: 6 Chirality restraints: 4659 Sorted by residual: chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA CYS B 131 " pdb=" N CYS B 131 " pdb=" C CYS B 131 " pdb=" CB CYS B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4656 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.306 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG C1311 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 366 " -0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C SER A 366 " 0.078 2.00e-02 2.50e+03 pdb=" O SER A 366 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 288 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C ALA C 288 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA C 288 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL C 289 " 0.018 2.00e-02 2.50e+03 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 111 2.47 - 3.08: 19550 3.08 - 3.69: 42209 3.69 - 4.29: 62475 4.29 - 4.90: 104598 Nonbonded interactions: 228943 Sorted by model distance: nonbonded pdb=" O CYS B 391 " pdb=" NE2 HIS B 519 " model vdw 1.863 3.120 nonbonded pdb=" NH1 ARG C 577 " pdb=" CD1 LEU C 582 " model vdw 1.900 3.540 nonbonded pdb=" CZ PHE B 375 " pdb=" CE2 TYR B 508 " model vdw 2.058 3.640 nonbonded pdb=" SG CYS B 336 " pdb=" O VAL B 362 " model vdw 2.067 3.400 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.170 3.040 ... (remaining 228938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1146 or resid 1301 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 1146 or resid 1301 through 1310)) } 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: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 69.490 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4609 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 : 0.006 0.732 29971 Z= 0.328 Angle : 0.642 29.169 40871 Z= 0.364 Chirality : 0.044 0.310 4659 Planarity : 0.005 0.258 5219 Dihedral : 9.797 115.126 11200 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % 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: -2.65 (0.12), residues: 3618 helix: -0.33 (0.16), residues: 1009 sheet: -1.39 (0.18), residues: 594 loop : -2.76 (0.11), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.002 0.000 HIS B 519 PHE 0.031 0.001 PHE A 374 TYR 0.010 0.001 TYR A 265 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 33) link_NAG-ASN : angle 2.08192 ( 99) hydrogen bonds : bond 0.13630 ( 1111) hydrogen bonds : angle 5.75003 ( 3033) SS BOND : bond 0.17226 ( 32) SS BOND : angle 7.34821 ( 64) covalent geometry : bond 0.00282 (29906) covalent geometry : angle 0.56457 (40708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 693 time to evaluate : 3.341 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: A 313 TYR cc_start: 0.7093 (m-80) cc_final: 0.6783 (m-80) REVERT: A 595 VAL cc_start: 0.8339 (m) cc_final: 0.8052 (t) REVERT: A 698 SER cc_start: 0.8489 (t) cc_final: 0.8222 (p) REVERT: A 737 ASP cc_start: 0.6712 (t70) cc_final: 0.6393 (t0) REVERT: A 821 LEU cc_start: 0.8349 (tt) cc_final: 0.8079 (tp) REVERT: A 822 LEU cc_start: 0.7926 (mt) cc_final: 0.7654 (mp) REVERT: A 875 SER cc_start: 0.8408 (t) cc_final: 0.7922 (m) REVERT: A 881 THR cc_start: 0.7849 (t) cc_final: 0.7628 (t) REVERT: A 929 SER cc_start: 0.8070 (t) cc_final: 0.7828 (p) REVERT: A 1002 GLN cc_start: 0.7169 (tt0) cc_final: 0.6939 (tt0) REVERT: B 290 ASP cc_start: 0.7514 (t0) cc_final: 0.7260 (t0) REVERT: B 340 GLU cc_start: 0.6294 (tp30) cc_final: 0.6035 (tp30) REVERT: B 354 ASN cc_start: 0.7342 (m-40) cc_final: 0.6914 (m-40) REVERT: B 398 ASP cc_start: 0.6368 (m-30) cc_final: 0.6061 (m-30) REVERT: B 420 ASP cc_start: 0.6550 (m-30) cc_final: 0.6325 (m-30) REVERT: B 494 SER cc_start: 0.7248 (m) cc_final: 0.6918 (t) REVERT: B 513 LEU cc_start: 0.7845 (mt) cc_final: 0.7414 (mp) REVERT: B 663 ASP cc_start: 0.6974 (p0) cc_final: 0.6699 (p0) REVERT: B 864 LEU cc_start: 0.7792 (tp) cc_final: 0.7442 (tp) REVERT: B 905 ARG cc_start: 0.6905 (mtt-85) cc_final: 0.6701 (mtp85) REVERT: B 1017 GLU cc_start: 0.6604 (tp30) cc_final: 0.5980 (tp30) REVERT: B 1084 ASP cc_start: 0.6946 (t0) cc_final: 0.6394 (t0) REVERT: B 1123 SER cc_start: 0.7979 (t) cc_final: 0.7694 (t) REVERT: C 45 SER cc_start: 0.8024 (p) cc_final: 0.7740 (p) REVERT: C 303 LEU cc_start: 0.8484 (tp) cc_final: 0.8168 (tt) REVERT: C 305 SER cc_start: 0.8409 (m) cc_final: 0.8184 (m) REVERT: C 595 VAL cc_start: 0.8225 (m) cc_final: 0.7920 (t) REVERT: C 774 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7271 (mm110) REVERT: C 800 PHE cc_start: 0.7373 (m-80) cc_final: 0.5535 (m-80) REVERT: C 822 LEU cc_start: 0.7633 (mt) cc_final: 0.7432 (mt) REVERT: C 907 ASN cc_start: 0.7266 (t0) cc_final: 0.6856 (t0) REVERT: C 1038 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7544 (mmmm) REVERT: D 499 ASP cc_start: -0.1173 (m-30) cc_final: -0.2538 (p0) REVERT: D 557 MET cc_start: -0.1026 (tmm) cc_final: -0.1288 (tmm) outliers start: 2 outliers final: 2 residues processed: 695 average time/residue: 0.4239 time to fit residues: 463.8929 Evaluate side-chains 519 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 374 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 8.9990 chunk 276 optimal weight: 0.5980 chunk 153 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 286 optimal weight: 0.0040 chunk 110 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 173 GLN A 394 ASN A 414 GLN A 505 HIS A 540 ASN A 563 GLN A 607 GLN A 755 GLN A 774 GLN A 784 GLN A 804 GLN A 935 GLN A 955 ASN A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 52 GLN B 81 ASN B 282 ASN B 394 ASN B 613 GLN B 907 ASN B 965 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 173 GLN C 196 ASN C 606 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 907 ASN C1010 GLN C1023 ASN C1106 GLN D 42 GLN D 60 GLN D 86 GLN D 98 GLN D 221 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 345 HIS D 368 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 472 GLN D 522 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.218766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167259 restraints weight = 46344.622| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.41 r_work: 0.3859 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29971 Z= 0.155 Angle : 0.607 11.657 40871 Z= 0.301 Chirality : 0.046 0.341 4659 Planarity : 0.004 0.061 5219 Dihedral : 6.010 100.420 4653 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.34 % Allowed : 9.89 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.79 (0.13), residues: 3618 helix: 0.60 (0.17), residues: 998 sheet: -0.81 (0.19), residues: 577 loop : -2.34 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 168 HIS 0.009 0.001 HIS A1064 PHE 0.030 0.002 PHE D 308 TYR 0.021 0.002 TYR B 365 ARG 0.009 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 33) link_NAG-ASN : angle 2.36622 ( 99) hydrogen bonds : bond 0.03474 ( 1111) hydrogen bonds : angle 4.69871 ( 3033) SS BOND : bond 0.00479 ( 32) SS BOND : angle 1.26660 ( 64) covalent geometry : bond 0.00348 (29906) covalent geometry : angle 0.59449 (40708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 598 time to evaluate : 2.789 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 595 VAL cc_start: 0.8662 (m) cc_final: 0.8455 (t) REVERT: A 698 SER cc_start: 0.8771 (t) cc_final: 0.8435 (p) REVERT: A 737 ASP cc_start: 0.7522 (t70) cc_final: 0.7051 (t0) REVERT: A 739 THR cc_start: 0.7835 (m) cc_final: 0.7364 (t) REVERT: A 756 TYR cc_start: 0.7509 (m-80) cc_final: 0.7208 (m-80) REVERT: A 820 ASP cc_start: 0.8143 (t70) cc_final: 0.7926 (t70) REVERT: A 821 LEU cc_start: 0.8574 (tt) cc_final: 0.8342 (tp) REVERT: A 822 LEU cc_start: 0.8268 (mt) cc_final: 0.8008 (mt) REVERT: A 875 SER cc_start: 0.8802 (t) cc_final: 0.8362 (m) REVERT: A 921 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8288 (mmmm) REVERT: A 935 GLN cc_start: 0.6649 (mt0) cc_final: 0.6442 (mt0) REVERT: A 1010 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8063 (mp10) REVERT: A 1019 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7478 (ttp80) REVERT: A 1139 ASP cc_start: 0.8149 (t0) cc_final: 0.7449 (t0) REVERT: B 340 GLU cc_start: 0.6991 (tp30) cc_final: 0.6674 (tp30) REVERT: B 354 ASN cc_start: 0.8113 (m-40) cc_final: 0.7872 (m-40) REVERT: B 364 ASP cc_start: 0.6961 (t0) cc_final: 0.6673 (t0) REVERT: B 494 SER cc_start: 0.7510 (m) cc_final: 0.7296 (t) REVERT: B 537 LYS cc_start: 0.8596 (ptmt) cc_final: 0.8373 (ptpp) REVERT: B 663 ASP cc_start: 0.7629 (p0) cc_final: 0.7361 (p0) REVERT: B 775 ASP cc_start: 0.7775 (t0) cc_final: 0.7536 (m-30) REVERT: B 790 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8191 (mtmt) REVERT: B 808 ASP cc_start: 0.7007 (t0) cc_final: 0.6596 (t0) REVERT: B 868 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7687 (mp0) REVERT: B 907 ASN cc_start: 0.7917 (t0) cc_final: 0.7670 (t0) REVERT: B 1017 GLU cc_start: 0.7812 (tp30) cc_final: 0.7286 (tp30) REVERT: B 1084 ASP cc_start: 0.7887 (t0) cc_final: 0.7361 (t0) REVERT: B 1123 SER cc_start: 0.8374 (t) cc_final: 0.8159 (t) REVERT: C 53 ASP cc_start: 0.6829 (t0) cc_final: 0.6595 (t0) REVERT: C 298 GLU cc_start: 0.7834 (tt0) cc_final: 0.7610 (tt0) REVERT: C 303 LEU cc_start: 0.8562 (tp) cc_final: 0.8335 (mt) REVERT: C 309 GLU cc_start: 0.7810 (mp0) cc_final: 0.7474 (mp0) REVERT: C 361 CYS cc_start: 0.5286 (OUTLIER) cc_final: 0.4643 (p) REVERT: C 599 THR cc_start: 0.8864 (t) cc_final: 0.8629 (p) REVERT: C 644 GLN cc_start: 0.7674 (tp40) cc_final: 0.7279 (tp-100) REVERT: C 774 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7763 (mp10) REVERT: C 781 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7778 (t) REVERT: C 790 LYS cc_start: 0.8086 (mttp) cc_final: 0.7289 (mttp) REVERT: C 907 ASN cc_start: 0.7853 (t0) cc_final: 0.7310 (t0) REVERT: C 929 SER cc_start: 0.8566 (t) cc_final: 0.8357 (m) REVERT: C 964 LYS cc_start: 0.8610 (tttp) cc_final: 0.8354 (tttm) REVERT: C 1084 ASP cc_start: 0.7736 (t0) cc_final: 0.7497 (t70) REVERT: D 90 THR cc_start: 0.7691 (m) cc_final: 0.7395 (p) REVERT: D 168 TRP cc_start: 0.4408 (t-100) cc_final: 0.4017 (t-100) REVERT: D 174 LYS cc_start: 0.5693 (mtpt) cc_final: 0.5415 (mtpt) REVERT: D 310 GLU cc_start: 0.6007 (mm-30) cc_final: 0.5712 (mm-30) REVERT: D 328 TRP cc_start: 0.6272 (m100) cc_final: 0.5908 (m100) REVERT: D 332 MET cc_start: -0.1434 (ttp) cc_final: -0.1737 (tmm) REVERT: D 342 VAL cc_start: 0.4872 (OUTLIER) cc_final: 0.4516 (p) REVERT: D 359 LYS cc_start: 0.4056 (mtmt) cc_final: 0.3762 (mttt) REVERT: D 499 ASP cc_start: -0.3132 (m-30) cc_final: -0.4803 (t0) outliers start: 74 outliers final: 32 residues processed: 636 average time/residue: 0.4169 time to fit residues: 412.7525 Evaluate side-chains 574 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 539 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 56 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 19 optimal weight: 0.0370 chunk 43 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 198 optimal weight: 0.2980 chunk 192 optimal weight: 0.2980 chunk 78 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 299 optimal weight: 0.8980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 388 ASN A 564 GLN A 657 ASN A 774 GLN B 30 ASN B 282 ASN B 755 GLN B 907 ASN C 81 ASN C 394 ASN C 606 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1010 GLN C1023 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.215941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163431 restraints weight = 45556.244| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.43 r_work: 0.3826 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29971 Z= 0.116 Angle : 0.528 12.389 40871 Z= 0.264 Chirality : 0.043 0.255 4659 Planarity : 0.004 0.061 5219 Dihedral : 4.815 91.078 4651 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.22 % Allowed : 12.07 % Favored : 85.71 % 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: -1.38 (0.13), residues: 3618 helix: 1.03 (0.17), residues: 989 sheet: -0.77 (0.18), residues: 649 loop : -2.08 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 48 HIS 0.008 0.001 HIS D 505 PHE 0.047 0.001 PHE D 308 TYR 0.016 0.001 TYR B 380 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 33) link_NAG-ASN : angle 2.03572 ( 99) hydrogen bonds : bond 0.03200 ( 1111) hydrogen bonds : angle 4.58413 ( 3033) SS BOND : bond 0.00332 ( 32) SS BOND : angle 1.08037 ( 64) covalent geometry : bond 0.00267 (29906) covalent geometry : angle 0.51760 (40708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 562 time to evaluate : 3.250 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 296 LEU cc_start: 0.8636 (tp) cc_final: 0.8418 (tp) REVERT: A 656 VAL cc_start: 0.8488 (t) cc_final: 0.8274 (m) REVERT: A 698 SER cc_start: 0.8785 (t) cc_final: 0.8398 (p) REVERT: A 739 THR cc_start: 0.7934 (m) cc_final: 0.7688 (t) REVERT: A 745 ASP cc_start: 0.6677 (p0) cc_final: 0.6146 (p0) REVERT: A 781 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (t) REVERT: A 820 ASP cc_start: 0.8081 (t70) cc_final: 0.7664 (m-30) REVERT: A 821 LEU cc_start: 0.8472 (tt) cc_final: 0.8258 (tp) REVERT: A 822 LEU cc_start: 0.8337 (mt) cc_final: 0.8053 (mp) REVERT: A 875 SER cc_start: 0.8780 (t) cc_final: 0.8392 (m) REVERT: A 1010 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8091 (mp10) REVERT: A 1130 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 1139 ASP cc_start: 0.8271 (t0) cc_final: 0.7604 (t0) REVERT: B 34 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: B 303 LEU cc_start: 0.7727 (mp) cc_final: 0.7477 (mp) REVERT: B 340 GLU cc_start: 0.7128 (tp30) cc_final: 0.6840 (tp30) REVERT: B 354 ASN cc_start: 0.8093 (m-40) cc_final: 0.7760 (m-40) REVERT: B 364 ASP cc_start: 0.7049 (t0) cc_final: 0.6736 (t0) REVERT: B 420 ASP cc_start: 0.7262 (m-30) cc_final: 0.6904 (m-30) REVERT: B 494 SER cc_start: 0.7571 (m) cc_final: 0.7348 (t) REVERT: B 599 THR cc_start: 0.8628 (t) cc_final: 0.8415 (p) REVERT: B 710 ASN cc_start: 0.8089 (p0) cc_final: 0.7837 (p0) REVERT: B 808 ASP cc_start: 0.7104 (t0) cc_final: 0.6671 (t0) REVERT: B 907 ASN cc_start: 0.7919 (t0) cc_final: 0.7453 (t0) REVERT: B 1017 GLU cc_start: 0.7974 (tp30) cc_final: 0.7717 (tp30) REVERT: B 1084 ASP cc_start: 0.7913 (t0) cc_final: 0.7424 (t0) REVERT: B 1123 SER cc_start: 0.8419 (t) cc_final: 0.8096 (t) REVERT: B 1144 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7815 (mt-10) REVERT: C 53 ASP cc_start: 0.6978 (t0) cc_final: 0.6684 (t0) REVERT: C 309 GLU cc_start: 0.7746 (mp0) cc_final: 0.7465 (mp0) REVERT: C 361 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.4710 (p) REVERT: C 644 GLN cc_start: 0.7799 (tp40) cc_final: 0.7386 (tp-100) REVERT: C 650 LEU cc_start: 0.8176 (tp) cc_final: 0.7873 (tp) REVERT: C 776 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8048 (ttpp) REVERT: C 821 LEU cc_start: 0.8488 (tt) cc_final: 0.8284 (tt) REVERT: C 907 ASN cc_start: 0.7882 (t0) cc_final: 0.7371 (t0) REVERT: C 929 SER cc_start: 0.8581 (t) cc_final: 0.8355 (m) REVERT: C 983 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7628 (ttm170) REVERT: D 48 TRP cc_start: 0.6115 (t-100) cc_final: 0.5664 (t-100) REVERT: D 90 THR cc_start: 0.7680 (m) cc_final: 0.6565 (p) REVERT: D 168 TRP cc_start: 0.4265 (t-100) cc_final: 0.3979 (t-100) REVERT: D 174 LYS cc_start: 0.5669 (mtpt) cc_final: 0.5409 (mtpt) REVERT: D 328 TRP cc_start: 0.6598 (m100) cc_final: 0.6338 (m100) REVERT: D 332 MET cc_start: -0.1168 (ttp) cc_final: -0.1940 (tmm) REVERT: D 342 VAL cc_start: 0.4886 (OUTLIER) cc_final: 0.4499 (p) REVERT: D 349 TRP cc_start: 0.4978 (m100) cc_final: 0.4108 (m100) REVERT: D 359 LYS cc_start: 0.4368 (mtmt) cc_final: 0.3255 (mtpt) REVERT: D 408 MET cc_start: 0.6854 (mmt) cc_final: 0.6541 (mmt) REVERT: D 499 ASP cc_start: -0.3194 (m-30) cc_final: -0.4865 (t0) outliers start: 70 outliers final: 38 residues processed: 600 average time/residue: 0.4424 time to fit residues: 415.1844 Evaluate side-chains 574 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 531 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 171 optimal weight: 0.0870 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 300 optimal weight: 0.7980 chunk 340 optimal weight: 0.2980 chunk 230 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 282 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1106 GLN C 606 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.213592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160374 restraints weight = 45841.906| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.47 r_work: 0.3777 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 29971 Z= 0.129 Angle : 0.550 16.192 40871 Z= 0.275 Chirality : 0.044 0.306 4659 Planarity : 0.004 0.061 5219 Dihedral : 4.736 88.059 4651 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.50 % Allowed : 13.81 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.18 (0.13), residues: 3618 helix: 1.17 (0.17), residues: 992 sheet: -0.48 (0.19), residues: 606 loop : -1.99 (0.12), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 PHE 0.044 0.001 PHE D 308 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 33) link_NAG-ASN : angle 2.00974 ( 99) hydrogen bonds : bond 0.03246 ( 1111) hydrogen bonds : angle 4.59720 ( 3033) SS BOND : bond 0.00679 ( 32) SS BOND : angle 2.18466 ( 64) covalent geometry : bond 0.00303 (29906) covalent geometry : angle 0.53538 (40708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 550 time to evaluate : 3.323 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: A 296 LEU cc_start: 0.8607 (tp) cc_final: 0.8390 (tp) REVERT: A 586 ASP cc_start: 0.7664 (m-30) cc_final: 0.7441 (m-30) REVERT: A 646 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7648 (mmt180) REVERT: A 698 SER cc_start: 0.8757 (t) cc_final: 0.8361 (p) REVERT: A 737 ASP cc_start: 0.7587 (t70) cc_final: 0.7137 (t0) REVERT: A 739 THR cc_start: 0.7926 (m) cc_final: 0.7550 (t) REVERT: A 796 TYR cc_start: 0.7783 (t80) cc_final: 0.7423 (t80) REVERT: A 821 LEU cc_start: 0.8429 (tt) cc_final: 0.8213 (tp) REVERT: A 822 LEU cc_start: 0.8370 (mt) cc_final: 0.8130 (mp) REVERT: A 875 SER cc_start: 0.8801 (t) cc_final: 0.8430 (m) REVERT: A 1010 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8059 (mp10) REVERT: A 1130 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 1139 ASP cc_start: 0.8322 (t0) cc_final: 0.7693 (t0) REVERT: B 34 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7568 (mtp-110) REVERT: B 195 LYS cc_start: 0.7132 (ptmt) cc_final: 0.6911 (pttp) REVERT: B 276 LEU cc_start: 0.7234 (tp) cc_final: 0.6999 (tt) REVERT: B 303 LEU cc_start: 0.7752 (mp) cc_final: 0.7503 (mp) REVERT: B 340 GLU cc_start: 0.7307 (tp30) cc_final: 0.7019 (tp30) REVERT: B 354 ASN cc_start: 0.8016 (m-40) cc_final: 0.7704 (m-40) REVERT: B 364 ASP cc_start: 0.7156 (t0) cc_final: 0.6678 (t70) REVERT: B 420 ASP cc_start: 0.7342 (m-30) cc_final: 0.6991 (m-30) REVERT: B 599 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 619 GLU cc_start: 0.6627 (mp0) cc_final: 0.6360 (mp0) REVERT: B 808 ASP cc_start: 0.7215 (t0) cc_final: 0.6838 (t0) REVERT: B 907 ASN cc_start: 0.8007 (t0) cc_final: 0.7534 (t0) REVERT: B 1084 ASP cc_start: 0.7921 (t0) cc_final: 0.7440 (t0) REVERT: B 1123 SER cc_start: 0.8431 (t) cc_final: 0.8139 (t) REVERT: C 53 ASP cc_start: 0.7123 (t0) cc_final: 0.6916 (t0) REVERT: C 129 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8145 (ptpp) REVERT: C 309 GLU cc_start: 0.7897 (mp0) cc_final: 0.7546 (mp0) REVERT: C 361 CYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4738 (p) REVERT: C 535 LYS cc_start: 0.8136 (mttm) cc_final: 0.7935 (mptt) REVERT: C 592 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6619 (t80) REVERT: C 644 GLN cc_start: 0.7720 (tp40) cc_final: 0.7390 (tp-100) REVERT: C 756 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6922 (t80) REVERT: C 821 LEU cc_start: 0.8448 (tt) cc_final: 0.8217 (tp) REVERT: C 907 ASN cc_start: 0.7926 (t0) cc_final: 0.7438 (t0) REVERT: C 929 SER cc_start: 0.8597 (t) cc_final: 0.8364 (m) REVERT: C 964 LYS cc_start: 0.8576 (tttm) cc_final: 0.8325 (tttm) REVERT: C 983 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7615 (ttm170) REVERT: C 1038 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8336 (mmtm) REVERT: D 31 ASN cc_start: 0.6673 (t0) cc_final: 0.5260 (m-40) REVERT: D 48 TRP cc_start: 0.6222 (t-100) cc_final: 0.5999 (t-100) REVERT: D 168 TRP cc_start: 0.4442 (t-100) cc_final: 0.4143 (t-100) REVERT: D 174 LYS cc_start: 0.5706 (mtpt) cc_final: 0.5454 (mtpt) REVERT: D 249 MET cc_start: -0.1247 (OUTLIER) cc_final: -0.1588 (mmm) REVERT: D 332 MET cc_start: -0.1289 (ttp) cc_final: -0.2159 (tmm) REVERT: D 342 VAL cc_start: 0.4908 (OUTLIER) cc_final: 0.4517 (p) REVERT: D 349 TRP cc_start: 0.5071 (m100) cc_final: 0.4436 (m100) REVERT: D 359 LYS cc_start: 0.4324 (mtmt) cc_final: 0.3670 (mttt) REVERT: D 383 MET cc_start: 0.7640 (tmm) cc_final: 0.6241 (mmm) REVERT: D 408 MET cc_start: 0.6831 (mmt) cc_final: 0.6539 (mmt) REVERT: D 499 ASP cc_start: -0.3169 (m-30) cc_final: -0.3874 (p0) outliers start: 79 outliers final: 44 residues processed: 589 average time/residue: 0.4475 time to fit residues: 414.2424 Evaluate side-chains 578 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 527 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 38 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 244 optimal weight: 0.3980 chunk 260 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 295 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 183 optimal weight: 0.2980 chunk 179 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 173 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1002 GLN B1005 GLN B1106 GLN C 606 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C1002 GLN D 76 GLN D 121 ASN D 368 ASN D 417 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.210698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156847 restraints weight = 44861.640| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.44 r_work: 0.3727 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29971 Z= 0.144 Angle : 0.564 12.853 40871 Z= 0.281 Chirality : 0.044 0.270 4659 Planarity : 0.004 0.060 5219 Dihedral : 4.745 85.411 4651 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.95 % Allowed : 13.69 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.12 (0.13), residues: 3618 helix: 1.13 (0.17), residues: 992 sheet: -0.35 (0.19), residues: 605 loop : -1.94 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.006 0.001 HIS C1064 PHE 0.043 0.002 PHE D 308 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 33) link_NAG-ASN : angle 2.17598 ( 99) hydrogen bonds : bond 0.03442 ( 1111) hydrogen bonds : angle 4.64996 ( 3033) SS BOND : bond 0.00483 ( 32) SS BOND : angle 1.75486 ( 64) covalent geometry : bond 0.00340 (29906) covalent geometry : angle 0.55037 (40708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 563 time to evaluate : 3.180 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: A 275 PHE cc_start: 0.7894 (m-80) cc_final: 0.7467 (m-80) REVERT: A 290 ASP cc_start: 0.8209 (t0) cc_final: 0.7920 (m-30) REVERT: A 646 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7782 (mmt180) REVERT: A 739 THR cc_start: 0.8034 (m) cc_final: 0.7810 (t) REVERT: A 820 ASP cc_start: 0.7943 (t70) cc_final: 0.7551 (t70) REVERT: A 821 LEU cc_start: 0.8387 (tt) cc_final: 0.8181 (tp) REVERT: A 875 SER cc_start: 0.8759 (t) cc_final: 0.8402 (m) REVERT: A 1010 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7999 (mp10) REVERT: A 1130 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 1139 ASP cc_start: 0.8261 (t0) cc_final: 0.7625 (t0) REVERT: B 34 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7583 (mtp-110) REVERT: B 195 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6982 (pttp) REVERT: B 276 LEU cc_start: 0.7309 (tp) cc_final: 0.7086 (tt) REVERT: B 303 LEU cc_start: 0.7854 (mp) cc_final: 0.7603 (mp) REVERT: B 340 GLU cc_start: 0.7510 (tp30) cc_final: 0.7220 (tp30) REVERT: B 354 ASN cc_start: 0.7977 (m-40) cc_final: 0.7623 (m-40) REVERT: B 364 ASP cc_start: 0.7236 (t0) cc_final: 0.6900 (t70) REVERT: B 420 ASP cc_start: 0.7387 (m-30) cc_final: 0.6990 (m-30) REVERT: B 599 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 619 GLU cc_start: 0.6639 (mp0) cc_final: 0.6378 (mp0) REVERT: B 710 ASN cc_start: 0.8201 (p0) cc_final: 0.7969 (p0) REVERT: B 776 LYS cc_start: 0.8628 (tttt) cc_final: 0.8370 (tttp) REVERT: B 808 ASP cc_start: 0.7343 (t0) cc_final: 0.6983 (t0) REVERT: B 821 LEU cc_start: 0.8300 (mp) cc_final: 0.8085 (mp) REVERT: B 907 ASN cc_start: 0.8014 (t0) cc_final: 0.7568 (t0) REVERT: B 929 SER cc_start: 0.8302 (t) cc_final: 0.8073 (m) REVERT: B 966 LEU cc_start: 0.9242 (mt) cc_final: 0.9017 (mp) REVERT: B 1084 ASP cc_start: 0.7936 (t0) cc_final: 0.7440 (t0) REVERT: B 1123 SER cc_start: 0.8471 (t) cc_final: 0.8164 (t) REVERT: B 1144 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7776 (mt-10) REVERT: C 45 SER cc_start: 0.8481 (p) cc_final: 0.8155 (t) REVERT: C 53 ASP cc_start: 0.7326 (t0) cc_final: 0.7099 (t0) REVERT: C 65 PHE cc_start: 0.7225 (m-10) cc_final: 0.6772 (m-10) REVERT: C 121 ASN cc_start: 0.7580 (t0) cc_final: 0.7376 (t0) REVERT: C 129 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8156 (ptpp) REVERT: C 305 SER cc_start: 0.9025 (t) cc_final: 0.8798 (t) REVERT: C 361 CYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4669 (p) REVERT: C 592 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6708 (t80) REVERT: C 644 GLN cc_start: 0.7754 (tp40) cc_final: 0.7440 (tp-100) REVERT: C 756 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 821 LEU cc_start: 0.8469 (tt) cc_final: 0.8260 (tt) REVERT: C 907 ASN cc_start: 0.7962 (t0) cc_final: 0.7530 (t0) REVERT: C 964 LYS cc_start: 0.8588 (tttm) cc_final: 0.8342 (tttm) REVERT: C 983 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7655 (ttm170) REVERT: C 1017 GLU cc_start: 0.7774 (tp30) cc_final: 0.7265 (tp30) REVERT: C 1038 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8424 (mmtm) REVERT: C 1128 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8210 (p) REVERT: D 165 TRP cc_start: -0.0041 (t60) cc_final: -0.2609 (t60) REVERT: D 168 TRP cc_start: 0.4548 (t-100) cc_final: 0.4191 (t-100) REVERT: D 174 LYS cc_start: 0.5718 (mtpt) cc_final: 0.5456 (mtpt) REVERT: D 332 MET cc_start: -0.1270 (ttp) cc_final: -0.2495 (tmm) REVERT: D 342 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4487 (p) REVERT: D 349 TRP cc_start: 0.5173 (m100) cc_final: 0.4032 (m100) REVERT: D 359 LYS cc_start: 0.4326 (mtmt) cc_final: 0.3861 (mttt) REVERT: D 380 GLN cc_start: 0.6461 (mm-40) cc_final: 0.6191 (mt0) REVERT: D 383 MET cc_start: 0.7837 (tmm) cc_final: 0.6416 (mmm) REVERT: D 408 MET cc_start: 0.6879 (mmt) cc_final: 0.6610 (mmt) REVERT: D 499 ASP cc_start: -0.3720 (m-30) cc_final: -0.3964 (p0) REVERT: D 571 GLU cc_start: 0.6852 (tt0) cc_final: 0.6515 (mt-10) outliers start: 93 outliers final: 49 residues processed: 611 average time/residue: 0.4768 time to fit residues: 457.7570 Evaluate side-chains 587 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 530 time to evaluate : 5.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 368 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 266 optimal weight: 0.8980 chunk 316 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 320 optimal weight: 9.9990 chunk 347 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 774 GLN B 282 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 925 ASN B1106 GLN B1125 ASN C 606 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 784 GLN D 368 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.208603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154372 restraints weight = 44603.734| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.63 r_work: 0.3678 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29971 Z= 0.160 Angle : 0.579 12.764 40871 Z= 0.291 Chirality : 0.045 0.300 4659 Planarity : 0.004 0.059 5219 Dihedral : 4.806 83.506 4651 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.85 % Allowed : 14.20 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.08 (0.13), residues: 3618 helix: 1.07 (0.17), residues: 998 sheet: -0.23 (0.20), residues: 570 loop : -1.87 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 275 HIS 0.007 0.001 HIS A1064 PHE 0.056 0.002 PHE D 308 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 33) link_NAG-ASN : angle 2.10387 ( 99) hydrogen bonds : bond 0.03631 ( 1111) hydrogen bonds : angle 4.74331 ( 3033) SS BOND : bond 0.00567 ( 32) SS BOND : angle 1.90801 ( 64) covalent geometry : bond 0.00379 (29906) covalent geometry : angle 0.56595 (40708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 548 time to evaluate : 3.220 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 33 THR cc_start: 0.8462 (t) cc_final: 0.8247 (t) REVERT: A 238 PHE cc_start: 0.4918 (t80) cc_final: 0.4394 (t80) REVERT: A 555 SER cc_start: 0.8299 (p) cc_final: 0.7855 (m) REVERT: A 586 ASP cc_start: 0.7681 (m-30) cc_final: 0.7082 (m-30) REVERT: A 646 ARG cc_start: 0.8143 (mmt180) cc_final: 0.7904 (mmt180) REVERT: A 718 PHE cc_start: 0.8483 (p90) cc_final: 0.8224 (p90) REVERT: A 739 THR cc_start: 0.8142 (m) cc_final: 0.7941 (t) REVERT: A 875 SER cc_start: 0.8789 (t) cc_final: 0.8460 (m) REVERT: A 1118 ASP cc_start: 0.8034 (t0) cc_final: 0.7727 (t0) REVERT: A 1130 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 1136 THR cc_start: 0.8553 (t) cc_final: 0.8334 (p) REVERT: A 1139 ASP cc_start: 0.8292 (t0) cc_final: 0.7646 (t0) REVERT: B 195 LYS cc_start: 0.7294 (ptmt) cc_final: 0.7066 (pttp) REVERT: B 273 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7161 (mmt90) REVERT: B 340 GLU cc_start: 0.7684 (tp30) cc_final: 0.7380 (tp30) REVERT: B 409 GLN cc_start: 0.8495 (tt0) cc_final: 0.8270 (tt0) REVERT: B 420 ASP cc_start: 0.7464 (m-30) cc_final: 0.7038 (m-30) REVERT: B 599 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 619 GLU cc_start: 0.6772 (mp0) cc_final: 0.6452 (mp0) REVERT: B 651 ILE cc_start: 0.8569 (pt) cc_final: 0.8076 (mt) REVERT: B 710 ASN cc_start: 0.8266 (p0) cc_final: 0.8055 (p0) REVERT: B 774 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: B 776 LYS cc_start: 0.8693 (tttt) cc_final: 0.8398 (tttp) REVERT: B 808 ASP cc_start: 0.7475 (t0) cc_final: 0.7083 (t0) REVERT: B 821 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 907 ASN cc_start: 0.8002 (t0) cc_final: 0.7595 (t0) REVERT: B 929 SER cc_start: 0.8302 (t) cc_final: 0.8036 (m) REVERT: B 934 ILE cc_start: 0.8032 (tt) cc_final: 0.7685 (tp) REVERT: B 966 LEU cc_start: 0.9271 (mt) cc_final: 0.9058 (mp) REVERT: B 1005 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: B 1019 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7811 (ttm110) REVERT: B 1084 ASP cc_start: 0.7970 (t0) cc_final: 0.7452 (t0) REVERT: B 1123 SER cc_start: 0.8500 (t) cc_final: 0.8290 (t) REVERT: B 1125 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (p0) REVERT: B 1144 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7788 (mt-10) REVERT: C 45 SER cc_start: 0.8455 (p) cc_final: 0.8121 (t) REVERT: C 53 ASP cc_start: 0.7433 (t0) cc_final: 0.7200 (t0) REVERT: C 121 ASN cc_start: 0.7724 (t0) cc_final: 0.7459 (t0) REVERT: C 129 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (ptpp) REVERT: C 287 ASP cc_start: 0.7843 (m-30) cc_final: 0.7572 (m-30) REVERT: C 305 SER cc_start: 0.9041 (t) cc_final: 0.8816 (t) REVERT: C 361 CYS cc_start: 0.5276 (OUTLIER) cc_final: 0.4665 (p) REVERT: C 535 LYS cc_start: 0.8147 (mttm) cc_final: 0.7911 (mptt) REVERT: C 592 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6774 (t80) REVERT: C 644 GLN cc_start: 0.7790 (tp40) cc_final: 0.7515 (tp40) REVERT: C 650 LEU cc_start: 0.8257 (tp) cc_final: 0.8028 (tp) REVERT: C 722 VAL cc_start: 0.8449 (m) cc_final: 0.8219 (t) REVERT: C 907 ASN cc_start: 0.8030 (t0) cc_final: 0.7625 (t0) REVERT: C 964 LYS cc_start: 0.8645 (tttm) cc_final: 0.8410 (tttm) REVERT: C 983 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7701 (ttm170) REVERT: C 1038 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8484 (mmtm) REVERT: C 1128 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (p) REVERT: D 31 ASN cc_start: 0.6664 (t0) cc_final: 0.5961 (t0) REVERT: D 165 TRP cc_start: 0.0077 (t60) cc_final: -0.2388 (t60) REVERT: D 168 TRP cc_start: 0.4596 (t-100) cc_final: 0.4236 (t-100) REVERT: D 174 LYS cc_start: 0.5748 (mtpt) cc_final: 0.5491 (mtpt) REVERT: D 203 TRP cc_start: 0.1990 (OUTLIER) cc_final: 0.1520 (m-10) REVERT: D 332 MET cc_start: -0.1103 (ttp) cc_final: -0.2197 (tmm) REVERT: D 342 VAL cc_start: 0.4925 (OUTLIER) cc_final: 0.4524 (p) REVERT: D 359 LYS cc_start: 0.4453 (mtmt) cc_final: 0.4164 (mttt) REVERT: D 380 GLN cc_start: 0.6546 (mm-40) cc_final: 0.6284 (mt0) REVERT: D 383 MET cc_start: 0.7906 (tmm) cc_final: 0.6370 (mmm) REVERT: D 406 GLU cc_start: 0.7749 (tp30) cc_final: 0.7518 (mm-30) REVERT: D 408 MET cc_start: 0.6799 (mmt) cc_final: 0.6517 (mmt) REVERT: D 452 PHE cc_start: 0.3891 (t80) cc_final: 0.2989 (t80) outliers start: 90 outliers final: 49 residues processed: 595 average time/residue: 0.4322 time to fit residues: 398.8675 Evaluate side-chains 593 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 532 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 296 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 222 optimal weight: 0.0370 chunk 26 optimal weight: 0.7980 chunk 345 optimal weight: 20.0000 chunk 268 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 606 ASN A 657 ASN A 774 GLN B 282 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B1106 GLN B1125 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 322 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.208596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154787 restraints weight = 44702.255| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.39 r_work: 0.3698 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29971 Z= 0.141 Angle : 0.575 13.016 40871 Z= 0.287 Chirality : 0.045 0.552 4659 Planarity : 0.004 0.072 5219 Dihedral : 4.834 81.929 4651 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.82 % Allowed : 14.64 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3618 helix: 1.19 (0.17), residues: 995 sheet: -0.17 (0.20), residues: 579 loop : -1.85 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D 275 HIS 0.005 0.001 HIS A1064 PHE 0.052 0.002 PHE D 308 TYR 0.018 0.001 TYR B1067 ARG 0.014 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 33) link_NAG-ASN : angle 2.34297 ( 99) hydrogen bonds : bond 0.03562 ( 1111) hydrogen bonds : angle 4.72534 ( 3033) SS BOND : bond 0.00414 ( 32) SS BOND : angle 1.75708 ( 64) covalent geometry : bond 0.00335 (29906) covalent geometry : angle 0.55973 (40708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 546 time to evaluate : 2.935 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 106 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: A 555 SER cc_start: 0.8334 (p) cc_final: 0.7969 (t) REVERT: A 602 THR cc_start: 0.7758 (p) cc_final: 0.7471 (m) REVERT: A 650 LEU cc_start: 0.8458 (pt) cc_final: 0.8250 (pt) REVERT: A 739 THR cc_start: 0.8144 (m) cc_final: 0.7861 (t) REVERT: A 875 SER cc_start: 0.8756 (t) cc_final: 0.8433 (m) REVERT: A 1010 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7862 (mp10) REVERT: A 1118 ASP cc_start: 0.8035 (t0) cc_final: 0.7723 (t0) REVERT: A 1130 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 1136 THR cc_start: 0.8523 (t) cc_final: 0.8313 (p) REVERT: B 48 LEU cc_start: 0.7924 (mm) cc_final: 0.7688 (mp) REVERT: B 273 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7211 (mmt90) REVERT: B 290 ASP cc_start: 0.8131 (t70) cc_final: 0.7905 (t0) REVERT: B 303 LEU cc_start: 0.8026 (mp) cc_final: 0.7755 (mp) REVERT: B 340 GLU cc_start: 0.7649 (tp30) cc_final: 0.7394 (tp30) REVERT: B 364 ASP cc_start: 0.7368 (t0) cc_final: 0.7140 (t70) REVERT: B 401 VAL cc_start: 0.7948 (p) cc_final: 0.7739 (t) REVERT: B 420 ASP cc_start: 0.7440 (m-30) cc_final: 0.6989 (m-30) REVERT: B 599 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 619 GLU cc_start: 0.6675 (mp0) cc_final: 0.6390 (mp0) REVERT: B 651 ILE cc_start: 0.8532 (pt) cc_final: 0.8094 (mt) REVERT: B 710 ASN cc_start: 0.8263 (p0) cc_final: 0.8058 (p0) REVERT: B 776 LYS cc_start: 0.8656 (tttt) cc_final: 0.8370 (tttp) REVERT: B 808 ASP cc_start: 0.7433 (t0) cc_final: 0.7056 (t0) REVERT: B 821 LEU cc_start: 0.8416 (mp) cc_final: 0.8205 (mp) REVERT: B 907 ASN cc_start: 0.7962 (t0) cc_final: 0.7549 (t0) REVERT: B 929 SER cc_start: 0.8235 (t) cc_final: 0.7970 (m) REVERT: B 970 PHE cc_start: 0.8409 (m-80) cc_final: 0.7958 (m-80) REVERT: B 1019 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7812 (ttm110) REVERT: B 1084 ASP cc_start: 0.7904 (t0) cc_final: 0.7396 (t0) REVERT: B 1123 SER cc_start: 0.8479 (t) cc_final: 0.8255 (t) REVERT: B 1144 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7788 (mt-10) REVERT: C 44 ARG cc_start: 0.8628 (mpt180) cc_final: 0.8096 (mtt180) REVERT: C 45 SER cc_start: 0.8440 (p) cc_final: 0.8099 (t) REVERT: C 65 PHE cc_start: 0.7454 (m-10) cc_final: 0.7215 (m-10) REVERT: C 121 ASN cc_start: 0.7622 (t0) cc_final: 0.7299 (t0) REVERT: C 129 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (ptpp) REVERT: C 305 SER cc_start: 0.9016 (t) cc_final: 0.8808 (t) REVERT: C 361 CYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4551 (p) REVERT: C 535 LYS cc_start: 0.8114 (mttm) cc_final: 0.7900 (mptt) REVERT: C 592 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6725 (t80) REVERT: C 644 GLN cc_start: 0.7774 (tp40) cc_final: 0.7551 (tp40) REVERT: C 756 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 907 ASN cc_start: 0.8011 (t0) cc_final: 0.7616 (t0) REVERT: C 964 LYS cc_start: 0.8629 (tttm) cc_final: 0.8387 (tttm) REVERT: C 998 THR cc_start: 0.8678 (t) cc_final: 0.8447 (p) REVERT: C 1038 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8485 (mmtm) REVERT: C 1128 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8304 (p) REVERT: D 165 TRP cc_start: 0.0238 (t60) cc_final: -0.2299 (t60) REVERT: D 168 TRP cc_start: 0.4581 (t-100) cc_final: 0.4208 (t-100) REVERT: D 174 LYS cc_start: 0.5799 (mtpt) cc_final: 0.5521 (mtpt) REVERT: D 203 TRP cc_start: 0.1917 (OUTLIER) cc_final: 0.1555 (m-10) REVERT: D 262 LEU cc_start: 0.5720 (pt) cc_final: 0.5282 (tt) REVERT: D 313 LYS cc_start: 0.6221 (pttm) cc_final: 0.5920 (tmtt) REVERT: D 322 HIS cc_start: 0.0053 (OUTLIER) cc_final: -0.0460 (t70) REVERT: D 332 MET cc_start: -0.1379 (ttp) cc_final: -0.2352 (tmm) REVERT: D 342 VAL cc_start: 0.4827 (OUTLIER) cc_final: 0.4474 (p) REVERT: D 349 TRP cc_start: 0.5182 (m100) cc_final: 0.4018 (m100) REVERT: D 359 LYS cc_start: 0.4438 (mtmt) cc_final: 0.4063 (mttt) REVERT: D 406 GLU cc_start: 0.7770 (tp30) cc_final: 0.7514 (mm-30) REVERT: D 408 MET cc_start: 0.6803 (mmt) cc_final: 0.6501 (mmt) REVERT: D 452 PHE cc_start: 0.3693 (t80) cc_final: 0.2820 (t80) REVERT: D 457 GLU cc_start: 0.6518 (mm-30) cc_final: 0.6257 (pp20) outliers start: 89 outliers final: 59 residues processed: 594 average time/residue: 0.4413 time to fit residues: 404.1799 Evaluate side-chains 612 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 542 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 116 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 281 optimal weight: 0.1980 chunk 262 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 164 optimal weight: 0.9990 chunk 355 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 217 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 606 ASN A 774 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 81 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 322 HIS D 368 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.210753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154931 restraints weight = 43818.436| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.91 r_work: 0.3674 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29971 Z= 0.121 Angle : 0.573 14.900 40871 Z= 0.284 Chirality : 0.044 0.412 4659 Planarity : 0.004 0.076 5219 Dihedral : 4.727 80.227 4649 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.28 % Allowed : 15.43 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3618 helix: 1.20 (0.17), residues: 994 sheet: -0.21 (0.19), residues: 621 loop : -1.76 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP D 275 HIS 0.008 0.001 HIS D 322 PHE 0.054 0.001 PHE D 308 TYR 0.019 0.001 TYR B 655 ARG 0.014 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 33) link_NAG-ASN : angle 2.23679 ( 99) hydrogen bonds : bond 0.03388 ( 1111) hydrogen bonds : angle 4.70930 ( 3033) SS BOND : bond 0.00325 ( 32) SS BOND : angle 2.17089 ( 64) covalent geometry : bond 0.00286 (29906) covalent geometry : angle 0.55641 (40708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 536 time to evaluate : 3.098 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 303 LEU cc_start: 0.8486 (mp) cc_final: 0.8270 (mp) REVERT: A 543 PHE cc_start: 0.8637 (m-10) cc_final: 0.8424 (m-80) REVERT: A 555 SER cc_start: 0.8344 (p) cc_final: 0.8083 (t) REVERT: A 602 THR cc_start: 0.7761 (p) cc_final: 0.7513 (m) REVERT: A 650 LEU cc_start: 0.8437 (pt) cc_final: 0.8227 (pt) REVERT: A 739 THR cc_start: 0.8093 (m) cc_final: 0.7846 (t) REVERT: A 820 ASP cc_start: 0.7804 (t0) cc_final: 0.7534 (m-30) REVERT: A 875 SER cc_start: 0.8763 (t) cc_final: 0.8430 (m) REVERT: A 1010 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7927 (mp10) REVERT: A 1127 ASP cc_start: 0.7591 (t0) cc_final: 0.7285 (t70) REVERT: A 1139 ASP cc_start: 0.8286 (t0) cc_final: 0.7869 (t70) REVERT: B 52 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7605 (tp40) REVERT: B 273 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7274 (mmt90) REVERT: B 290 ASP cc_start: 0.8103 (t70) cc_final: 0.7890 (t0) REVERT: B 303 LEU cc_start: 0.8029 (mp) cc_final: 0.7752 (mp) REVERT: B 364 ASP cc_start: 0.7494 (t0) cc_final: 0.7271 (t70) REVERT: B 401 VAL cc_start: 0.7954 (p) cc_final: 0.7748 (t) REVERT: B 409 GLN cc_start: 0.8621 (tt0) cc_final: 0.8339 (tt0) REVERT: B 420 ASP cc_start: 0.7490 (m-30) cc_final: 0.7014 (m-30) REVERT: B 599 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 619 GLU cc_start: 0.6542 (mp0) cc_final: 0.6274 (mp0) REVERT: B 651 ILE cc_start: 0.8570 (pt) cc_final: 0.8161 (mt) REVERT: B 658 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8084 (p0) REVERT: B 710 ASN cc_start: 0.8302 (p0) cc_final: 0.8083 (p0) REVERT: B 808 ASP cc_start: 0.7434 (t0) cc_final: 0.7056 (t0) REVERT: B 821 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 907 ASN cc_start: 0.7978 (t0) cc_final: 0.7577 (t0) REVERT: B 929 SER cc_start: 0.8279 (t) cc_final: 0.8008 (m) REVERT: B 1019 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7939 (ttm110) REVERT: B 1084 ASP cc_start: 0.7945 (t0) cc_final: 0.7435 (t0) REVERT: B 1144 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7798 (mt-10) REVERT: C 45 SER cc_start: 0.8447 (p) cc_final: 0.8123 (t) REVERT: C 121 ASN cc_start: 0.7652 (t0) cc_final: 0.7342 (t0) REVERT: C 129 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8245 (ptpp) REVERT: C 239 GLN cc_start: 0.8019 (tp40) cc_final: 0.7737 (tp40) REVERT: C 305 SER cc_start: 0.9036 (t) cc_final: 0.8818 (t) REVERT: C 307 THR cc_start: 0.8355 (p) cc_final: 0.8034 (p) REVERT: C 361 CYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4746 (p) REVERT: C 592 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6791 (t80) REVERT: C 644 GLN cc_start: 0.7817 (tp40) cc_final: 0.7605 (tp-100) REVERT: C 651 ILE cc_start: 0.8604 (pt) cc_final: 0.8238 (mt) REVERT: C 756 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7385 (t80) REVERT: C 907 ASN cc_start: 0.8024 (t0) cc_final: 0.7626 (t0) REVERT: C 964 LYS cc_start: 0.8661 (tttm) cc_final: 0.8419 (tttm) REVERT: C 983 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7714 (ttm170) REVERT: C 998 THR cc_start: 0.8673 (t) cc_final: 0.8456 (p) REVERT: C 1038 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8484 (mmtm) REVERT: C 1128 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8305 (p) REVERT: D 168 TRP cc_start: 0.4581 (t-100) cc_final: 0.4237 (t-100) REVERT: D 174 LYS cc_start: 0.5820 (mtpt) cc_final: 0.5518 (mtpt) REVERT: D 203 TRP cc_start: 0.1760 (OUTLIER) cc_final: 0.1410 (m-10) REVERT: D 262 LEU cc_start: 0.5664 (pt) cc_final: 0.5205 (tt) REVERT: D 313 LYS cc_start: 0.6278 (pttm) cc_final: 0.5906 (tmtt) REVERT: D 322 HIS cc_start: 0.0369 (OUTLIER) cc_final: -0.0068 (t70) REVERT: D 332 MET cc_start: -0.1373 (ttp) cc_final: -0.2175 (tmm) REVERT: D 342 VAL cc_start: 0.4905 (OUTLIER) cc_final: 0.4560 (p) REVERT: D 349 TRP cc_start: 0.5194 (m100) cc_final: 0.3856 (m100) REVERT: D 359 LYS cc_start: 0.4401 (mtmt) cc_final: 0.3904 (mttt) REVERT: D 381 TYR cc_start: 0.7860 (t80) cc_final: 0.7637 (t80) REVERT: D 406 GLU cc_start: 0.7778 (tp30) cc_final: 0.7506 (mm-30) REVERT: D 408 MET cc_start: 0.6783 (mmt) cc_final: 0.6466 (mmt) REVERT: D 452 PHE cc_start: 0.3949 (t80) cc_final: 0.1214 (m-80) REVERT: D 457 GLU cc_start: 0.6510 (mm-30) cc_final: 0.6274 (pp20) REVERT: D 480 MET cc_start: 0.4817 (mtp) cc_final: 0.4557 (mtt) outliers start: 72 outliers final: 50 residues processed: 577 average time/residue: 0.4332 time to fit residues: 388.6569 Evaluate side-chains 590 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 529 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 140 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 100 optimal weight: 0.2980 chunk 353 optimal weight: 0.4980 chunk 230 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 606 ASN A 774 GLN B 234 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 HIS D 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.206659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151980 restraints weight = 44330.098| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.77 r_work: 0.3654 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29971 Z= 0.149 Angle : 0.589 14.611 40871 Z= 0.294 Chirality : 0.045 0.340 4659 Planarity : 0.004 0.073 5219 Dihedral : 4.735 78.829 4649 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.47 % Allowed : 15.49 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3618 helix: 1.15 (0.17), residues: 1002 sheet: -0.18 (0.21), residues: 551 loop : -1.73 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 275 HIS 0.014 0.001 HIS D 322 PHE 0.054 0.002 PHE D 308 TYR 0.022 0.001 TYR B 453 ARG 0.013 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 33) link_NAG-ASN : angle 2.20727 ( 99) hydrogen bonds : bond 0.03639 ( 1111) hydrogen bonds : angle 4.75112 ( 3033) SS BOND : bond 0.00334 ( 32) SS BOND : angle 1.94153 ( 64) covalent geometry : bond 0.00355 (29906) covalent geometry : angle 0.57486 (40708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 547 time to evaluate : 3.256 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 239 GLN cc_start: 0.7030 (pm20) cc_final: 0.6246 (pp30) REVERT: A 303 LEU cc_start: 0.8535 (mp) cc_final: 0.8316 (mp) REVERT: A 555 SER cc_start: 0.8366 (p) cc_final: 0.8158 (t) REVERT: A 602 THR cc_start: 0.7883 (p) cc_final: 0.7678 (m) REVERT: A 605 SER cc_start: 0.7613 (t) cc_final: 0.7242 (m) REVERT: A 650 LEU cc_start: 0.8462 (pt) cc_final: 0.8255 (pt) REVERT: A 739 THR cc_start: 0.8120 (m) cc_final: 0.7863 (t) REVERT: A 820 ASP cc_start: 0.7893 (t0) cc_final: 0.7581 (m-30) REVERT: A 875 SER cc_start: 0.8755 (t) cc_final: 0.8426 (m) REVERT: A 1118 ASP cc_start: 0.8100 (t0) cc_final: 0.7741 (t0) REVERT: A 1127 ASP cc_start: 0.7609 (t0) cc_final: 0.7300 (t70) REVERT: B 52 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7659 (tp40) REVERT: B 273 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7360 (mmt90) REVERT: B 298 GLU cc_start: 0.7307 (tp30) cc_final: 0.6913 (tt0) REVERT: B 303 LEU cc_start: 0.8102 (mp) cc_final: 0.7831 (mp) REVERT: B 409 GLN cc_start: 0.8644 (tt0) cc_final: 0.8348 (tt0) REVERT: B 420 ASP cc_start: 0.7533 (m-30) cc_final: 0.7041 (m-30) REVERT: B 599 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 619 GLU cc_start: 0.6645 (mp0) cc_final: 0.6365 (mp0) REVERT: B 651 ILE cc_start: 0.8609 (pt) cc_final: 0.8230 (mt) REVERT: B 658 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (p0) REVERT: B 710 ASN cc_start: 0.8324 (p0) cc_final: 0.8117 (p0) REVERT: B 739 THR cc_start: 0.8257 (m) cc_final: 0.8015 (p) REVERT: B 740 MET cc_start: 0.7908 (mtp) cc_final: 0.7575 (ttm) REVERT: B 808 ASP cc_start: 0.7439 (t0) cc_final: 0.7020 (t0) REVERT: B 821 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 907 ASN cc_start: 0.8026 (t0) cc_final: 0.7598 (t0) REVERT: B 929 SER cc_start: 0.8244 (t) cc_final: 0.7955 (m) REVERT: B 950 ASP cc_start: 0.7968 (m-30) cc_final: 0.7750 (m-30) REVERT: B 1017 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: B 1019 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7840 (ttm110) REVERT: B 1084 ASP cc_start: 0.7951 (t0) cc_final: 0.7444 (t0) REVERT: B 1127 ASP cc_start: 0.8118 (m-30) cc_final: 0.7860 (m-30) REVERT: C 45 SER cc_start: 0.8481 (p) cc_final: 0.8151 (t) REVERT: C 121 ASN cc_start: 0.7686 (t0) cc_final: 0.7364 (t0) REVERT: C 239 GLN cc_start: 0.8060 (tp40) cc_final: 0.7757 (tp40) REVERT: C 273 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7558 (mmm160) REVERT: C 305 SER cc_start: 0.9017 (t) cc_final: 0.8808 (t) REVERT: C 307 THR cc_start: 0.8431 (p) cc_final: 0.8108 (p) REVERT: C 361 CYS cc_start: 0.5273 (OUTLIER) cc_final: 0.4719 (p) REVERT: C 535 LYS cc_start: 0.8152 (mttm) cc_final: 0.7905 (mmtm) REVERT: C 592 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6851 (t80) REVERT: C 651 ILE cc_start: 0.8566 (pt) cc_final: 0.8283 (mt) REVERT: C 756 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7351 (t80) REVERT: C 907 ASN cc_start: 0.8045 (t0) cc_final: 0.7670 (t0) REVERT: C 964 LYS cc_start: 0.8675 (tttm) cc_final: 0.8441 (tttm) REVERT: C 979 ASP cc_start: 0.8167 (t0) cc_final: 0.7929 (t0) REVERT: C 983 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7715 (ttm170) REVERT: C 998 THR cc_start: 0.8682 (t) cc_final: 0.8468 (p) REVERT: C 1038 LYS cc_start: 0.8803 (mmmm) cc_final: 0.8510 (mmtm) REVERT: C 1107 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7589 (mtt180) REVERT: C 1128 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 31 ASN cc_start: 0.6652 (t0) cc_final: 0.6017 (t0) REVERT: D 168 TRP cc_start: 0.4701 (t-100) cc_final: 0.4360 (t-100) REVERT: D 174 LYS cc_start: 0.5837 (mtpt) cc_final: 0.5504 (mtpt) REVERT: D 203 TRP cc_start: 0.1866 (OUTLIER) cc_final: 0.1515 (m-10) REVERT: D 262 LEU cc_start: 0.5831 (pt) cc_final: 0.5414 (tt) REVERT: D 313 LYS cc_start: 0.6181 (pttm) cc_final: 0.5849 (tmtt) REVERT: D 322 HIS cc_start: 0.0437 (OUTLIER) cc_final: 0.0022 (t70) REVERT: D 332 MET cc_start: -0.0948 (ttp) cc_final: -0.1877 (tmm) REVERT: D 342 VAL cc_start: 0.4943 (OUTLIER) cc_final: 0.4603 (p) REVERT: D 349 TRP cc_start: 0.5214 (m100) cc_final: 0.4030 (m100) REVERT: D 359 LYS cc_start: 0.4711 (mtmt) cc_final: 0.4301 (mttt) REVERT: D 381 TYR cc_start: 0.7935 (t80) cc_final: 0.7698 (t80) REVERT: D 406 GLU cc_start: 0.7735 (tp30) cc_final: 0.7503 (mm-30) REVERT: D 408 MET cc_start: 0.6745 (mmt) cc_final: 0.6475 (mmt) REVERT: D 452 PHE cc_start: 0.3779 (t80) cc_final: 0.1320 (m-80) REVERT: D 480 MET cc_start: 0.4708 (mtp) cc_final: 0.4449 (mtt) outliers start: 78 outliers final: 58 residues processed: 589 average time/residue: 0.4370 time to fit residues: 400.0060 Evaluate side-chains 610 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 541 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 255 optimal weight: 0.0170 chunk 108 optimal weight: 0.0980 chunk 158 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 606 ASN A 774 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN D 322 HIS D 368 ASN D 397 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.207925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153819 restraints weight = 44576.848| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.77 r_work: 0.3672 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29971 Z= 0.112 Angle : 0.572 14.505 40871 Z= 0.283 Chirality : 0.044 0.338 4659 Planarity : 0.004 0.058 5219 Dihedral : 4.657 77.322 4649 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.19 % Allowed : 16.10 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3618 helix: 1.18 (0.17), residues: 1004 sheet: -0.21 (0.21), residues: 561 loop : -1.68 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 275 HIS 0.020 0.001 HIS D 322 PHE 0.055 0.001 PHE D 308 TYR 0.018 0.001 TYR B 453 ARG 0.013 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 33) link_NAG-ASN : angle 2.47906 ( 99) hydrogen bonds : bond 0.03360 ( 1111) hydrogen bonds : angle 4.70966 ( 3033) SS BOND : bond 0.00277 ( 32) SS BOND : angle 1.65008 ( 64) covalent geometry : bond 0.00261 (29906) covalent geometry : angle 0.55590 (40708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 542 time to evaluate : 3.084 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 303 LEU cc_start: 0.8531 (mp) cc_final: 0.8298 (mp) REVERT: A 304 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: A 555 SER cc_start: 0.8380 (p) cc_final: 0.8147 (t) REVERT: A 605 SER cc_start: 0.7580 (t) cc_final: 0.7210 (m) REVERT: A 650 LEU cc_start: 0.8447 (pt) cc_final: 0.8217 (pt) REVERT: A 739 THR cc_start: 0.8057 (m) cc_final: 0.7811 (t) REVERT: A 773 GLU cc_start: 0.8058 (tt0) cc_final: 0.7846 (tt0) REVERT: A 811 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7936 (mtpt) REVERT: A 820 ASP cc_start: 0.7883 (t0) cc_final: 0.7562 (m-30) REVERT: A 875 SER cc_start: 0.8790 (t) cc_final: 0.8462 (m) REVERT: A 1019 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7701 (ttp-170) REVERT: A 1127 ASP cc_start: 0.7666 (t0) cc_final: 0.7302 (t0) REVERT: B 273 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7308 (mmt90) REVERT: B 298 GLU cc_start: 0.7284 (tp30) cc_final: 0.6925 (tt0) REVERT: B 409 GLN cc_start: 0.8644 (tt0) cc_final: 0.8308 (tt0) REVERT: B 420 ASP cc_start: 0.7572 (m-30) cc_final: 0.7047 (m-30) REVERT: B 599 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 651 ILE cc_start: 0.8578 (pt) cc_final: 0.8218 (mt) REVERT: B 658 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 710 ASN cc_start: 0.8307 (p0) cc_final: 0.8081 (p0) REVERT: B 740 MET cc_start: 0.7844 (mtp) cc_final: 0.7564 (ttm) REVERT: B 808 ASP cc_start: 0.7414 (t0) cc_final: 0.7038 (t0) REVERT: B 821 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8317 (mp) REVERT: B 907 ASN cc_start: 0.8010 (t0) cc_final: 0.7585 (t0) REVERT: B 929 SER cc_start: 0.8272 (t) cc_final: 0.7986 (m) REVERT: B 1017 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: B 1019 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7151 (ttm110) REVERT: B 1084 ASP cc_start: 0.7956 (t0) cc_final: 0.7456 (t0) REVERT: B 1127 ASP cc_start: 0.8090 (m-30) cc_final: 0.7796 (m-30) REVERT: B 1138 TYR cc_start: 0.7995 (t80) cc_final: 0.7698 (t80) REVERT: B 1144 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7789 (mt-10) REVERT: C 45 SER cc_start: 0.8446 (p) cc_final: 0.8113 (t) REVERT: C 121 ASN cc_start: 0.7666 (t0) cc_final: 0.7353 (t0) REVERT: C 129 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8197 (ptpp) REVERT: C 239 GLN cc_start: 0.8012 (tp40) cc_final: 0.7724 (tp40) REVERT: C 305 SER cc_start: 0.9011 (t) cc_final: 0.8804 (t) REVERT: C 307 THR cc_start: 0.8443 (p) cc_final: 0.8142 (p) REVERT: C 361 CYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4571 (p) REVERT: C 592 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6849 (t80) REVERT: C 651 ILE cc_start: 0.8538 (pt) cc_final: 0.8246 (mt) REVERT: C 756 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7393 (t80) REVERT: C 907 ASN cc_start: 0.8009 (t0) cc_final: 0.7617 (t0) REVERT: C 964 LYS cc_start: 0.8661 (tttm) cc_final: 0.8421 (tttm) REVERT: C 979 ASP cc_start: 0.8166 (t0) cc_final: 0.7925 (t0) REVERT: C 983 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7664 (ttm170) REVERT: C 1017 GLU cc_start: 0.7771 (tp30) cc_final: 0.7322 (tp30) REVERT: C 1038 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8481 (mmtm) REVERT: C 1128 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 1136 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8316 (p) REVERT: D 31 ASN cc_start: 0.6672 (t0) cc_final: 0.6047 (t0) REVERT: D 168 TRP cc_start: 0.4707 (t-100) cc_final: 0.4362 (t-100) REVERT: D 203 TRP cc_start: 0.1817 (OUTLIER) cc_final: 0.1494 (m-10) REVERT: D 262 LEU cc_start: 0.5891 (pt) cc_final: 0.5495 (tt) REVERT: D 313 LYS cc_start: 0.6104 (pttm) cc_final: 0.5758 (tmtt) REVERT: D 322 HIS cc_start: 0.0309 (OUTLIER) cc_final: -0.0158 (t70) REVERT: D 332 MET cc_start: -0.1147 (ttp) cc_final: -0.2012 (tmm) REVERT: D 342 VAL cc_start: 0.4950 (OUTLIER) cc_final: 0.4640 (p) REVERT: D 349 TRP cc_start: 0.5213 (m100) cc_final: 0.4063 (m100) REVERT: D 359 LYS cc_start: 0.4690 (mtmt) cc_final: 0.4337 (mttt) REVERT: D 381 TYR cc_start: 0.7894 (t80) cc_final: 0.7661 (t80) REVERT: D 406 GLU cc_start: 0.7725 (tp30) cc_final: 0.7501 (mm-30) REVERT: D 408 MET cc_start: 0.6723 (mmt) cc_final: 0.6456 (mmt) REVERT: D 452 PHE cc_start: 0.3689 (t80) cc_final: 0.1279 (m-80) REVERT: D 457 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6288 (pp20) REVERT: D 480 MET cc_start: 0.4687 (mtp) cc_final: 0.4430 (mtt) REVERT: D 571 GLU cc_start: 0.6859 (tt0) cc_final: 0.6533 (mt-10) outliers start: 69 outliers final: 49 residues processed: 579 average time/residue: 0.5049 time to fit residues: 456.3208 Evaluate side-chains 604 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 542 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 330 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 252 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 342 optimal weight: 0.3980 chunk 112 optimal weight: 0.3980 chunk 346 optimal weight: 30.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 388 ASN A 774 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 405 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 299 ASN D 322 HIS D 368 ASN D 397 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.207308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152298 restraints weight = 44041.107| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.87 r_work: 0.3627 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29971 Z= 0.156 Angle : 0.610 14.285 40871 Z= 0.303 Chirality : 0.046 0.586 4659 Planarity : 0.004 0.067 5219 Dihedral : 4.727 75.820 4649 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.19 % Allowed : 16.35 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3618 helix: 1.19 (0.17), residues: 997 sheet: -0.09 (0.21), residues: 540 loop : -1.64 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 275 HIS 0.026 0.001 HIS D 322 PHE 0.054 0.002 PHE D 308 TYR 0.027 0.002 TYR B 453 ARG 0.014 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 33) link_NAG-ASN : angle 2.50512 ( 99) hydrogen bonds : bond 0.03732 ( 1111) hydrogen bonds : angle 4.77587 ( 3033) SS BOND : bond 0.00333 ( 32) SS BOND : angle 1.83474 ( 64) covalent geometry : bond 0.00374 (29906) covalent geometry : angle 0.59437 (40708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23970.38 seconds wall clock time: 418 minutes 1.60 seconds (25081.60 seconds total)