Starting phenix.real_space_refine on Thu Jun 26 14:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz7_26881/06_2025/7uz7_26881.cif" } resolution = 2.9 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19419 2.51 5 N 5019 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 1.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30552 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 21.23, per 1000 atoms: 0.69 Number of scatterers: 30552 At special positions: 0 Unit cell: (164.736, 161.408, 188.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5982 8.00 N 5019 7.00 C 19419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.7 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 60 sheets defined 19.9% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.725A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.069A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.813A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.667A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.579A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.596A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.730A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.664A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 976 through 984 removed outlier: 3.625A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.794A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.548A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.720A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.065A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.809A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 984 removed outlier: 3.619A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.679A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.754A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.789A pdb=" N ASN M 36 " --> pdb=" O ASN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.742A pdb=" N ASN P 36 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.894A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.792A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.194A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 435 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.682A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.647A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.642A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.906A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.615A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.948A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.692A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.723A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.100A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.638A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.187A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.720A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.517A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.111A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.637A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.735A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.970A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 66 through 67 removed outlier: 5.082A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.031A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.169A pdb=" N GLU L 125 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.975A pdb=" N GLN M 3 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 66 through 67 removed outlier: 5.087A pdb=" N TRP M 52 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS M 43 " --> pdb=" O TRP M 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 54 " --> pdb=" O TRP M 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.801A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.670A pdb=" N GLU N 125 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR N 122 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.984A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL P 19 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 66 through 67 removed outlier: 5.048A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 122 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.846A pdb=" N THR Q 5 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS Q 23 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE Q 87 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE Q 54 " --> pdb=" O TRP Q 41 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN Q 43 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU Q 52 " --> pdb=" O GLN Q 43 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3174 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: 14.21 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 4372 1.25 - 1.39: 8349 1.39 - 1.54: 17592 1.54 - 1.68: 773 1.68 - 1.82: 171 Bond restraints: 31257 Sorted by residual: bond pdb=" CG PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.503 1.100 0.403 3.40e-02 8.65e+02 1.40e+02 bond pdb=" CG PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N ASN C 801 " pdb=" CA ASN C 801 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.98e+00 ... (remaining 31252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 42537 4.49 - 8.98: 39 8.98 - 13.47: 0 13.47 - 17.96: 4 17.96 - 22.45: 2 Bond angle restraints: 42582 Sorted by residual: angle pdb=" N PRO A1079 " pdb=" CD PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 103.20 80.75 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" N PRO B1079 " pdb=" CD PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 97.65 14.35 1.40e+00 5.10e-01 1.05e+02 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 98.42 13.58 1.40e+00 5.10e-01 9.41e+01 angle pdb=" CA PRO A1079 " pdb=" CB PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 104.50 89.34 15.16 1.90e+00 2.77e-01 6.37e+01 ... (remaining 42577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 17978 21.67 - 43.35: 968 43.35 - 65.02: 139 65.02 - 86.69: 47 86.69 - 108.36: 11 Dihedral angle restraints: 19143 sinusoidal: 7920 harmonic: 11223 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 167.97 -74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 104 " pdb=" CB CYS N 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.23 -70.23 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 104 " pdb=" CB CYS Q 104 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4130 0.058 - 0.115: 747 0.115 - 0.173: 63 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 4941 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.228 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG A1307 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.226 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG B1307 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " -0.222 2.00e-02 2.50e+03 1.89e-01 4.49e+02 pdb=" C7 NAG C1307 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.008 2.00e-02 2.50e+03 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 521 2.68 - 3.23: 29270 3.23 - 3.79: 47533 3.79 - 4.34: 65317 4.34 - 4.90: 107380 Nonbonded interactions: 250021 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.121 3.040 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLN B 804 " pdb=" NE2 GLN B 935 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.209 3.040 ... (remaining 250016 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 7.360 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: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.130 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.140 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.005 0.403 31344 Z= 0.189 Angle : 0.620 22.452 42801 Z= 0.330 Chirality : 0.044 0.289 4944 Planarity : 0.006 0.195 5457 Dihedral : 13.463 108.363 11811 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3813 helix: 1.79 (0.21), residues: 672 sheet: 0.32 (0.17), residues: 888 loop : -0.64 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.002 0.001 HIS B 655 PHE 0.023 0.001 PHE A 906 TYR 0.025 0.001 TYR B 248 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 42) link_NAG-ASN : angle 2.24448 ( 126) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.47864 ( 9) hydrogen bonds : bond 0.21353 ( 1074) hydrogen bonds : angle 9.00623 ( 3174) SS BOND : bond 0.00313 ( 42) SS BOND : angle 0.92101 ( 84) covalent geometry : bond 0.00460 (31257) covalent geometry : angle 0.60739 (42582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6905 (m-90) cc_final: 0.6613 (m-90) REVERT: A 120 VAL cc_start: 0.7684 (t) cc_final: 0.7455 (m) REVERT: B 104 TRP cc_start: 0.7650 (m-90) cc_final: 0.7262 (m-90) REVERT: B 265 TYR cc_start: 0.7589 (p90) cc_final: 0.7309 (p90) REVERT: N 4 MET cc_start: 0.2404 (tpt) cc_final: 0.2153 (tpt) REVERT: N 122 THR cc_start: 0.1325 (p) cc_final: 0.0575 (p) REVERT: Q 4 MET cc_start: 0.2405 (tpp) cc_final: 0.2165 (tpp) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 1.1640 time to fit residues: 347.3973 Evaluate side-chains 153 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 345 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1010 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN B1010 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 117 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.229298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.157566 restraints weight = 43921.463| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.75 r_work: 0.3308 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 31344 Z= 0.288 Angle : 0.692 12.688 42801 Z= 0.350 Chirality : 0.049 0.292 4944 Planarity : 0.005 0.057 5457 Dihedral : 7.744 78.573 5085 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.09 % Allowed : 8.87 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3813 helix: 1.28 (0.21), residues: 657 sheet: 0.43 (0.18), residues: 831 loop : -0.76 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.008 0.001 HIS C1088 PHE 0.033 0.002 PHE B1121 TYR 0.030 0.002 TYR B1067 ARG 0.009 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 42) link_NAG-ASN : angle 2.43671 ( 126) link_BETA1-4 : bond 0.00129 ( 3) link_BETA1-4 : angle 2.04095 ( 9) hydrogen bonds : bond 0.04874 ( 1074) hydrogen bonds : angle 6.72615 ( 3174) SS BOND : bond 0.00764 ( 42) SS BOND : angle 1.30334 ( 84) covalent geometry : bond 0.00686 (31257) covalent geometry : angle 0.67802 (42582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.5355 (p0) cc_final: 0.5044 (p0) REVERT: B 190 ARG cc_start: 0.7839 (ptp-110) cc_final: 0.7547 (mtm-85) REVERT: B 265 TYR cc_start: 0.7263 (p90) cc_final: 0.6830 (p90) REVERT: C 177 MET cc_start: 0.7085 (mpt) cc_final: 0.6883 (tpt) REVERT: C 190 ARG cc_start: 0.6913 (mtp-110) cc_final: 0.6658 (mmt90) REVERT: C 1029 MET cc_start: 0.8261 (tpp) cc_final: 0.7926 (tpp) REVERT: N 4 MET cc_start: 0.4315 (tpt) cc_final: 0.3905 (tpt) REVERT: Q 4 MET cc_start: 0.4229 (tpp) cc_final: 0.3891 (mmm) outliers start: 36 outliers final: 16 residues processed: 194 average time/residue: 1.1385 time to fit residues: 274.5816 Evaluate side-chains 151 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 311 optimal weight: 0.6980 chunk 319 optimal weight: 0.0670 chunk 171 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 371 optimal weight: 0.0060 chunk 67 optimal weight: 0.9990 chunk 365 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.234815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.164573 restraints weight = 44339.954| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.71 r_work: 0.3382 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31344 Z= 0.109 Angle : 0.566 12.497 42801 Z= 0.283 Chirality : 0.044 0.275 4944 Planarity : 0.004 0.046 5457 Dihedral : 6.599 58.949 5082 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.97 % Allowed : 11.53 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 3813 helix: 1.90 (0.20), residues: 672 sheet: 0.52 (0.18), residues: 825 loop : -0.76 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.002 0.000 HIS A1048 PHE 0.015 0.001 PHE B 898 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 42) link_NAG-ASN : angle 2.15956 ( 126) link_BETA1-4 : bond 0.00482 ( 3) link_BETA1-4 : angle 1.30298 ( 9) hydrogen bonds : bond 0.03928 ( 1074) hydrogen bonds : angle 5.93711 ( 3174) SS BOND : bond 0.00234 ( 42) SS BOND : angle 0.86581 ( 84) covalent geometry : bond 0.00238 (31257) covalent geometry : angle 0.55364 (42582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 3.195 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: A 820 ASP cc_start: 0.7295 (m-30) cc_final: 0.7085 (m-30) REVERT: B 265 TYR cc_start: 0.6957 (p90) cc_final: 0.6495 (p90) REVERT: C 190 ARG cc_start: 0.6833 (mtp-110) cc_final: 0.6599 (mmt90) REVERT: C 811 LYS cc_start: 0.7388 (ptpt) cc_final: 0.7180 (ptmm) REVERT: N 4 MET cc_start: 0.4202 (tpt) cc_final: 0.3773 (tpt) REVERT: N 38 TYR cc_start: 0.5524 (m-10) cc_final: 0.5311 (m-10) REVERT: Q 4 MET cc_start: 0.4223 (tpp) cc_final: 0.3837 (mmm) outliers start: 32 outliers final: 16 residues processed: 191 average time/residue: 1.0867 time to fit residues: 260.1556 Evaluate side-chains 162 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 188 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 275 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 chunk 15 optimal weight: 0.0040 chunk 47 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 overall best weight: 1.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.233673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.162751 restraints weight = 44371.461| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.69 r_work: 0.3351 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31344 Z= 0.138 Angle : 0.565 12.546 42801 Z= 0.282 Chirality : 0.045 0.278 4944 Planarity : 0.004 0.044 5457 Dihedral : 6.044 57.624 5082 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 13.02 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.13), residues: 3813 helix: 1.77 (0.20), residues: 678 sheet: 0.45 (0.17), residues: 855 loop : -0.73 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.018 0.001 PHE C 106 TYR 0.025 0.001 TYR C 170 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 42) link_NAG-ASN : angle 2.15980 ( 126) link_BETA1-4 : bond 0.00207 ( 3) link_BETA1-4 : angle 1.52860 ( 9) hydrogen bonds : bond 0.03740 ( 1074) hydrogen bonds : angle 5.72265 ( 3174) SS BOND : bond 0.00372 ( 42) SS BOND : angle 0.90710 ( 84) covalent geometry : bond 0.00320 (31257) covalent geometry : angle 0.55235 (42582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 3.020 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: A 820 ASP cc_start: 0.7326 (m-30) cc_final: 0.7072 (m-30) REVERT: B 235 ILE cc_start: 0.6625 (tp) cc_final: 0.6290 (tt) REVERT: B 265 TYR cc_start: 0.6938 (p90) cc_final: 0.6471 (p90) REVERT: B 1092 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7472 (pt0) REVERT: C 177 MET cc_start: 0.7201 (mpt) cc_final: 0.6928 (tpt) REVERT: H 122 THR cc_start: 0.2947 (OUTLIER) cc_final: 0.2745 (t) REVERT: N 4 MET cc_start: 0.4204 (tpt) cc_final: 0.3806 (tpt) REVERT: Q 4 MET cc_start: 0.4250 (tpp) cc_final: 0.3877 (mmm) outliers start: 54 outliers final: 35 residues processed: 200 average time/residue: 0.9720 time to fit residues: 246.1034 Evaluate side-chains 180 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 217 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 375 optimal weight: 40.0000 chunk 225 optimal weight: 9.9990 chunk 356 optimal weight: 50.0000 chunk 198 optimal weight: 2.9990 chunk 350 optimal weight: 30.0000 chunk 195 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 949 GLN A1011 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN C 207 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN L 44 GLN N 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.227031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.154405 restraints weight = 44217.870| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.69 r_work: 0.3268 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 31344 Z= 0.313 Angle : 0.676 12.302 42801 Z= 0.339 Chirality : 0.049 0.292 4944 Planarity : 0.004 0.045 5457 Dihedral : 6.195 58.864 5082 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.33 % Allowed : 13.78 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3813 helix: 1.20 (0.20), residues: 678 sheet: 0.25 (0.17), residues: 915 loop : -0.84 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.007 0.001 HIS C1088 PHE 0.036 0.002 PHE B1121 TYR 0.029 0.002 TYR B1067 ARG 0.003 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 42) link_NAG-ASN : angle 2.53996 ( 126) link_BETA1-4 : bond 0.00251 ( 3) link_BETA1-4 : angle 2.39940 ( 9) hydrogen bonds : bond 0.04305 ( 1074) hydrogen bonds : angle 5.94275 ( 3174) SS BOND : bond 0.00840 ( 42) SS BOND : angle 1.26315 ( 84) covalent geometry : bond 0.00748 (31257) covalent geometry : angle 0.65983 (42582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: A 745 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 122 ASN cc_start: 0.5526 (p0) cc_final: 0.5232 (p0) REVERT: B 177 MET cc_start: 0.8037 (ppp) cc_final: 0.7800 (ppp) REVERT: C 1089 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: N 4 MET cc_start: 0.4544 (tpt) cc_final: 0.4150 (tpt) REVERT: Q 4 MET cc_start: 0.4690 (tpp) cc_final: 0.4184 (mmm) outliers start: 77 outliers final: 43 residues processed: 206 average time/residue: 1.0418 time to fit residues: 271.7729 Evaluate side-chains 182 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 22 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 286 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 308 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 351 optimal weight: 0.0050 chunk 355 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1005 GLN B 81 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.234098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.145143 restraints weight = 43726.136| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.64 r_work: 0.3340 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31344 Z= 0.112 Angle : 0.558 12.249 42801 Z= 0.279 Chirality : 0.044 0.286 4944 Planarity : 0.004 0.040 5457 Dihedral : 5.723 57.208 5082 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.94 % Allowed : 14.87 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 3813 helix: 1.72 (0.20), residues: 678 sheet: 0.40 (0.17), residues: 876 loop : -0.74 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 PHE 0.017 0.001 PHE B 898 TYR 0.025 0.001 TYR C 170 ARG 0.008 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 42) link_NAG-ASN : angle 2.21582 ( 126) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.39884 ( 9) hydrogen bonds : bond 0.03557 ( 1074) hydrogen bonds : angle 5.49121 ( 3174) SS BOND : bond 0.00284 ( 42) SS BOND : angle 0.88613 ( 84) covalent geometry : bond 0.00249 (31257) covalent geometry : angle 0.54458 (42582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 3.045 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: A 190 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7680 (mtm-85) REVERT: A 574 ASP cc_start: 0.7561 (t0) cc_final: 0.7216 (t0) REVERT: A 745 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 122 ASN cc_start: 0.5558 (p0) cc_final: 0.5285 (p0) REVERT: B 1092 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7413 (pt0) REVERT: C 177 MET cc_start: 0.6784 (tpt) cc_final: 0.6164 (mmt) REVERT: C 269 TYR cc_start: 0.8484 (m-80) cc_final: 0.8270 (m-80) REVERT: C 574 ASP cc_start: 0.7698 (t0) cc_final: 0.7243 (t0) REVERT: C 787 GLN cc_start: 0.8266 (mt0) cc_final: 0.8006 (mt0) REVERT: C 988 GLU cc_start: 0.8216 (mp0) cc_final: 0.8001 (mp0) REVERT: N 4 MET cc_start: 0.5046 (tpt) cc_final: 0.4661 (tpt) REVERT: Q 4 MET cc_start: 0.5006 (tpp) cc_final: 0.4489 (mmm) outliers start: 64 outliers final: 39 residues processed: 210 average time/residue: 1.0332 time to fit residues: 273.1211 Evaluate side-chains 184 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 252 optimal weight: 50.0000 chunk 182 optimal weight: 0.0870 chunk 286 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 231 optimal weight: 50.0000 chunk 287 optimal weight: 3.9990 chunk 317 optimal weight: 40.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.227061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.154652 restraints weight = 44246.252| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.71 r_work: 0.3271 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 31344 Z= 0.285 Angle : 0.658 12.067 42801 Z= 0.330 Chirality : 0.048 0.305 4944 Planarity : 0.004 0.044 5457 Dihedral : 5.936 57.624 5082 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.06 % Allowed : 15.65 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.31 (0.13), residues: 3813 helix: 1.24 (0.20), residues: 678 sheet: 0.11 (0.16), residues: 939 loop : -0.81 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.006 0.001 HIS C1088 PHE 0.041 0.002 PHE B1121 TYR 0.027 0.002 TYR C 170 ARG 0.009 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 42) link_NAG-ASN : angle 2.53213 ( 126) link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 2.39554 ( 9) hydrogen bonds : bond 0.04148 ( 1074) hydrogen bonds : angle 5.76543 ( 3174) SS BOND : bond 0.00840 ( 42) SS BOND : angle 1.18482 ( 84) covalent geometry : bond 0.00689 (31257) covalent geometry : angle 0.64155 (42582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 149 time to evaluate : 2.979 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: A 281 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: A 574 ASP cc_start: 0.7657 (t0) cc_final: 0.7261 (t0) REVERT: A 745 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8001 (p0) REVERT: A 988 GLU cc_start: 0.7878 (mp0) cc_final: 0.7561 (mp0) REVERT: A 1092 GLU cc_start: 0.8230 (tp30) cc_final: 0.7417 (pt0) REVERT: B 122 ASN cc_start: 0.5705 (p0) cc_final: 0.5392 (p0) REVERT: C 697 MET cc_start: 0.8465 (ptt) cc_final: 0.8171 (ptm) REVERT: C 787 GLN cc_start: 0.8343 (mt0) cc_final: 0.8082 (mt0) REVERT: C 988 GLU cc_start: 0.8160 (mp0) cc_final: 0.7928 (mp0) REVERT: N 4 MET cc_start: 0.4296 (tpt) cc_final: 0.3924 (tpt) REVERT: P 39 MET cc_start: 0.3634 (ptm) cc_final: 0.3180 (ttp) REVERT: Q 4 MET cc_start: 0.4512 (tpp) cc_final: 0.4114 (tpt) outliers start: 68 outliers final: 41 residues processed: 209 average time/residue: 1.0638 time to fit residues: 279.6101 Evaluate side-chains 180 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 131 optimal weight: 0.0030 chunk 182 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 314 optimal weight: 0.7980 chunk 223 optimal weight: 30.0000 chunk 261 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.233961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.145177 restraints weight = 43851.871| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.64 r_work: 0.3335 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31344 Z= 0.111 Angle : 0.562 12.106 42801 Z= 0.281 Chirality : 0.044 0.303 4944 Planarity : 0.004 0.042 5457 Dihedral : 5.508 54.781 5082 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 15.96 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.07 (0.13), residues: 3813 helix: 1.70 (0.20), residues: 678 sheet: 0.43 (0.17), residues: 855 loop : -0.80 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 PHE 0.018 0.001 PHE C1089 TYR 0.024 0.001 TYR B 170 ARG 0.014 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 42) link_NAG-ASN : angle 2.19184 ( 126) link_BETA1-4 : bond 0.00211 ( 3) link_BETA1-4 : angle 1.28138 ( 9) hydrogen bonds : bond 0.03486 ( 1074) hydrogen bonds : angle 5.35469 ( 3174) SS BOND : bond 0.00285 ( 42) SS BOND : angle 0.89646 ( 84) covalent geometry : bond 0.00252 (31257) covalent geometry : angle 0.54918 (42582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 3.377 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: A 281 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: A 574 ASP cc_start: 0.7600 (t0) cc_final: 0.7229 (t0) REVERT: A 745 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7930 (p0) REVERT: A 1092 GLU cc_start: 0.8283 (tp30) cc_final: 0.7419 (pt0) REVERT: B 65 PHE cc_start: 0.7031 (m-80) cc_final: 0.6830 (m-80) REVERT: B 122 ASN cc_start: 0.5644 (p0) cc_final: 0.5395 (p0) REVERT: B 745 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 988 GLU cc_start: 0.8029 (mp0) cc_final: 0.7783 (mp0) REVERT: B 1092 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7399 (pt0) REVERT: C 177 MET cc_start: 0.6789 (tpt) cc_final: 0.6131 (mmt) REVERT: C 574 ASP cc_start: 0.7665 (t0) cc_final: 0.7276 (t0) REVERT: C 675 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 787 GLN cc_start: 0.8252 (mt0) cc_final: 0.8027 (mt0) REVERT: C 988 GLU cc_start: 0.8320 (mp0) cc_final: 0.8091 (mp0) REVERT: L 4 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4837 (tpt) REVERT: N 4 MET cc_start: 0.5338 (tpt) cc_final: 0.4972 (tpt) REVERT: Q 4 MET cc_start: 0.5233 (tpp) cc_final: 0.4707 (mmm) REVERT: Q 116 LEU cc_start: 0.0234 (OUTLIER) cc_final: -0.0129 (pp) outliers start: 55 outliers final: 37 residues processed: 196 average time/residue: 1.0581 time to fit residues: 261.0946 Evaluate side-chains 183 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 163 optimal weight: 0.0060 chunk 110 optimal weight: 1.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.231982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142095 restraints weight = 43489.013| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.62 r_work: 0.3291 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31344 Z= 0.199 Angle : 0.604 12.240 42801 Z= 0.301 Chirality : 0.046 0.322 4944 Planarity : 0.004 0.044 5457 Dihedral : 5.556 56.162 5082 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.73 % Allowed : 16.11 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3813 helix: 1.49 (0.20), residues: 678 sheet: 0.20 (0.16), residues: 939 loop : -0.75 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 PHE 0.029 0.002 PHE B1121 TYR 0.021 0.001 TYR B1067 ARG 0.017 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 42) link_NAG-ASN : angle 2.31695 ( 126) link_BETA1-4 : bond 0.00065 ( 3) link_BETA1-4 : angle 1.90336 ( 9) hydrogen bonds : bond 0.03761 ( 1074) hydrogen bonds : angle 5.46570 ( 3174) SS BOND : bond 0.00584 ( 42) SS BOND : angle 1.00441 ( 84) covalent geometry : bond 0.00478 (31257) covalent geometry : angle 0.58969 (42582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 3.288 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: A 281 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: A 574 ASP cc_start: 0.7642 (t0) cc_final: 0.7271 (t0) REVERT: A 745 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 1092 GLU cc_start: 0.8268 (tp30) cc_final: 0.7359 (pt0) REVERT: B 122 ASN cc_start: 0.5705 (p0) cc_final: 0.5441 (p0) REVERT: B 745 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8024 (p0) REVERT: B 988 GLU cc_start: 0.8062 (mp0) cc_final: 0.7821 (mp0) REVERT: B 1092 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7410 (pt0) REVERT: C 675 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7684 (tm-30) REVERT: C 697 MET cc_start: 0.8463 (ptt) cc_final: 0.8178 (ptm) REVERT: C 787 GLN cc_start: 0.8339 (mt0) cc_final: 0.8093 (mt0) REVERT: C 988 GLU cc_start: 0.8287 (mp0) cc_final: 0.8040 (mp0) REVERT: L 4 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.5057 (tpt) REVERT: N 4 MET cc_start: 0.5540 (tpt) cc_final: 0.5181 (tpt) REVERT: P 39 MET cc_start: 0.3505 (ptm) cc_final: 0.3102 (ttp) REVERT: Q 4 MET cc_start: 0.5490 (tpp) cc_final: 0.4988 (mmm) REVERT: Q 116 LEU cc_start: 0.0375 (OUTLIER) cc_final: -0.0004 (pp) outliers start: 57 outliers final: 40 residues processed: 195 average time/residue: 1.0816 time to fit residues: 265.5244 Evaluate side-chains 184 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 116 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 126 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 351 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 355 optimal weight: 0.0270 chunk 314 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 211 optimal weight: 0.5980 overall best weight: 3.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.226218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153852 restraints weight = 44391.298| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.67 r_work: 0.3251 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 31344 Z= 0.311 Angle : 0.686 13.337 42801 Z= 0.344 Chirality : 0.050 0.358 4944 Planarity : 0.004 0.049 5457 Dihedral : 5.864 57.159 5082 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.67 % Allowed : 16.17 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.42 (0.13), residues: 3813 helix: 1.08 (0.20), residues: 660 sheet: 0.05 (0.16), residues: 954 loop : -0.85 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.009 0.001 HIS C1048 PHE 0.039 0.002 PHE B1121 TYR 0.030 0.002 TYR B1067 ARG 0.009 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 42) link_NAG-ASN : angle 2.61989 ( 126) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 2.45902 ( 9) hydrogen bonds : bond 0.04234 ( 1074) hydrogen bonds : angle 5.75391 ( 3174) SS BOND : bond 0.00888 ( 42) SS BOND : angle 1.31024 ( 84) covalent geometry : bond 0.00745 (31257) covalent geometry : angle 0.66940 (42582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 3.090 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: A 574 ASP cc_start: 0.7786 (t0) cc_final: 0.7310 (t0) REVERT: A 745 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8079 (p0) REVERT: A 1092 GLU cc_start: 0.8204 (tp30) cc_final: 0.7368 (pt0) REVERT: B 122 ASN cc_start: 0.5789 (p0) cc_final: 0.5470 (p0) REVERT: B 740 MET cc_start: 0.8936 (tpp) cc_final: 0.8638 (ttp) REVERT: B 745 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8047 (p0) REVERT: B 988 GLU cc_start: 0.7954 (mp0) cc_final: 0.7745 (mp0) REVERT: C 269 TYR cc_start: 0.8375 (m-80) cc_final: 0.8072 (m-80) REVERT: C 558 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7969 (mmtm) REVERT: C 697 MET cc_start: 0.8516 (ptt) cc_final: 0.8220 (ptm) REVERT: C 787 GLN cc_start: 0.8348 (mt0) cc_final: 0.8073 (mt0) REVERT: C 988 GLU cc_start: 0.8249 (mp0) cc_final: 0.8036 (mp0) REVERT: N 4 MET cc_start: 0.4773 (tpt) cc_final: 0.4402 (tpt) REVERT: P 39 MET cc_start: 0.3696 (ptm) cc_final: 0.3270 (ttp) REVERT: Q 4 MET cc_start: 0.4923 (tpp) cc_final: 0.4410 (mmm) REVERT: Q 116 LEU cc_start: 0.0345 (OUTLIER) cc_final: -0.0051 (pp) outliers start: 55 outliers final: 37 residues processed: 190 average time/residue: 1.0656 time to fit residues: 253.5710 Evaluate side-chains 175 residues out of total 3363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 323 optimal weight: 40.0000 chunk 126 optimal weight: 50.0000 chunk 17 optimal weight: 0.0060 chunk 43 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 345 optimal weight: 40.0000 chunk 164 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.214434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143631 restraints weight = 43073.520| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.69 r_work: 0.3236 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 31344 Z= 0.254 Angle : 0.648 13.058 42801 Z= 0.324 Chirality : 0.048 0.344 4944 Planarity : 0.004 0.050 5457 Dihedral : 5.798 56.152 5082 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.42 % Allowed : 16.71 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.43 (0.13), residues: 3813 helix: 1.12 (0.20), residues: 660 sheet: 0.08 (0.17), residues: 930 loop : -0.89 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.006 0.001 HIS C1048 PHE 0.031 0.002 PHE B1121 TYR 0.026 0.001 TYR B1067 ARG 0.019 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 42) link_NAG-ASN : angle 2.50537 ( 126) link_BETA1-4 : bond 0.00123 ( 3) link_BETA1-4 : angle 2.09545 ( 9) hydrogen bonds : bond 0.03987 ( 1074) hydrogen bonds : angle 5.63172 ( 3174) SS BOND : bond 0.00748 ( 42) SS BOND : angle 1.21152 ( 84) covalent geometry : bond 0.00608 (31257) covalent geometry : angle 0.63235 (42582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27780.96 seconds wall clock time: 475 minutes 21.25 seconds (28521.25 seconds total)