Starting phenix.real_space_refine on Tue May 13 01:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbb_43119/05_2025/8vbb_43119.cif" } resolution = 3.97 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= 0.006 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 17 5.16 5 C 5680 2.51 5 N 1646 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9444 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7293 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 8, 'TRANS': 1029} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 921 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "A" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 418 Unusual residues: {'BGC': 38} Classifications: {'undetermined': 38} Link IDs: {None: 37} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 38 Time building chain proxies: 8.70, per 1000 atoms: 0.92 Number of scatterers: 9444 At special positions: 0 Unit cell: (83.375, 98.6, 178.35, 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 17 16.00 O 2101 8.00 N 1646 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " 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 Atom "HETATM 9036 O5 BGC A1601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9047 O5 BGC A1602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9300 O5 BGC A1625 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9421 O5 BGC A1636 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9190 O5 BGC A1615 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=38, symmetry=0 Number of additional bonds: simple=38, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 2.5% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.766A pdb=" N PHE A 484 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.216A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.043A pdb=" N VAL A 274 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 310 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 276 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 429 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP A 458 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 431 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 508 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN A 544 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 510 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 5.552A pdb=" N VAL A 162 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 202 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 223 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 267 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 295 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.047A pdb=" N SER A 134 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 217 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 261 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS A 318 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 290 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 342 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.099A pdb=" N TYR A 184 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 249 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP A 243 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.736A pdb=" N ILE A 350 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 415 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 494 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 578 removed outlier: 6.227A pdb=" N ILE A 604 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 632 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 606 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 653 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN A 681 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 654 " --> pdb=" O ASN A 681 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 680 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 729 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N SER A 753 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 731 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL A 776 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 806 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 778 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 801 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 832 " --> pdb=" O LYS A 801 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 803 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 584 through 585 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 584 through 585 current: chain 'A' and resid 635 through 647 removed outlier: 6.526A pdb=" N ASN A 635 " --> pdb=" O THR A 661 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 660 through 661 current: chain 'A' and resid 687 through 699 removed outlier: 7.413A pdb=" N ASN A 692 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN A 721 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR A 694 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 723 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR A 696 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 725 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU A 698 " --> pdb=" O GLN A 725 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 734 through 738 current: chain 'A' and resid 836 through 849 removed outlier: 6.241A pdb=" N ASN A 837 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 865 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 839 " --> pdb=" O ASN A 865 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR A 867 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ALA A 841 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP A 869 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN A 843 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 871 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 845 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR A 873 " --> pdb=" O ALA A 845 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR A 847 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 862 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 891 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU A 864 " --> pdb=" O ASN A 891 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 888 through 892 current: chain 'A' and resid 1036 through 1052 removed outlier: 6.890A pdb=" N ASN A1065 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1038 " --> pdb=" O ASN A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A1067 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN A1040 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A1069 " --> pdb=" O ASN A1040 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A1042 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A1071 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A1044 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA A1073 " --> pdb=" O GLY A1044 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A1046 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A1075 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A1048 " --> pdb=" O THR A1075 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN A1077 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A1050 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1064 " --> pdb=" O THR A1089 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR A1091 " --> pdb=" O ASN A1064 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A1066 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN A1093 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A1068 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR A1095 " --> pdb=" O THR A1068 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N SER A1070 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A1097 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 856 through 857 removed outlier: 6.674A pdb=" N ILE A 856 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 882 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 908 " --> pdb=" O ASN A 934 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 957 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER A 981 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 959 " --> pdb=" O SER A 981 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL A1004 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A1034 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A1006 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AB2, first strand: chain 'H' and resid 29 through 30 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 30 current: chain 'H' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 124 through 127 Processing sheet with id=AB3, first strand: chain 'L' and resid 23 through 25 removed outlier: 3.520A pdb=" N SER L 91 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.023A pdb=" N LEU L 30 " --> pdb=" O GLU L 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 52 through 57 removed outlier: 3.555A pdb=" N GLN L 109 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR L 116 " --> pdb=" O GLN L 109 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 510 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: 4.17 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3174 1.34 - 1.46: 1595 1.46 - 1.57: 4687 1.57 - 1.69: 51 1.69 - 1.81: 30 Bond restraints: 9537 Sorted by residual: bond pdb=" C2 BGC A1632 " pdb=" C3 BGC A1632 " ideal model delta sigma weight residual 1.522 1.594 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C2 BGC A1606 " pdb=" C3 BGC A1606 " ideal model delta sigma weight residual 1.522 1.592 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C2 BGC A1636 " pdb=" C3 BGC A1636 " ideal model delta sigma weight residual 1.522 1.591 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C2 BGC A1603 " pdb=" C3 BGC A1603 " ideal model delta sigma weight residual 1.522 1.591 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C2 BGC A1615 " pdb=" C3 BGC A1615 " ideal model delta sigma weight residual 1.522 1.590 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 9532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 12456 2.38 - 4.75: 428 4.75 - 7.13: 32 7.13 - 9.51: 59 9.51 - 11.88: 2 Bond angle restraints: 12977 Sorted by residual: angle pdb=" CA PRO A 480 " pdb=" N PRO A 480 " pdb=" CD PRO A 480 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N SER A 829 " pdb=" CA SER A 829 " pdb=" C SER A 829 " ideal model delta sigma weight residual 110.53 104.76 5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" CA GLY A 616 " pdb=" C GLY A 616 " pdb=" O GLY A 616 " ideal model delta sigma weight residual 122.28 118.09 4.19 1.00e+00 1.00e+00 1.76e+01 angle pdb=" N ASN A 667 " pdb=" CA ASN A 667 " pdb=" C ASN A 667 " ideal model delta sigma weight residual 108.69 116.11 -7.42 1.77e+00 3.19e-01 1.76e+01 angle pdb=" CA GLN A 730 " pdb=" C GLN A 730 " pdb=" O GLN A 730 " ideal model delta sigma weight residual 122.13 117.88 4.25 1.13e+00 7.83e-01 1.41e+01 ... (remaining 12972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5583 17.56 - 35.11: 397 35.11 - 52.67: 65 52.67 - 70.22: 30 70.22 - 87.78: 5 Dihedral angle restraints: 6080 sinusoidal: 2606 harmonic: 3474 Sorted by residual: dihedral pdb=" CD ARG A 601 " pdb=" NE ARG A 601 " pdb=" CZ ARG A 601 " pdb=" NH1 ARG A 601 " ideal model delta sinusoidal sigma weight residual 0.00 -73.27 73.27 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA SER A 567 " pdb=" C SER A 567 " pdb=" N GLY A 568 " pdb=" CA GLY A 568 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE L 67 " pdb=" C ILE L 67 " pdb=" N PHE L 68 " pdb=" CA PHE L 68 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1429 0.101 - 0.203: 150 0.203 - 0.304: 29 0.304 - 0.406: 28 0.406 - 0.507: 28 Chirality restraints: 1664 Sorted by residual: chirality pdb=" C3 BGC A1620 " pdb=" C2 BGC A1620 " pdb=" C4 BGC A1620 " pdb=" O3 BGC A1620 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" C3 BGC A1601 " pdb=" C2 BGC A1601 " pdb=" C4 BGC A1601 " pdb=" O3 BGC A1601 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" C3 BGC A1603 " pdb=" C2 BGC A1603 " pdb=" C4 BGC A1603 " pdb=" O3 BGC A1603 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 1661 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 601 " -1.047 9.50e-02 1.11e+02 4.69e-01 1.33e+02 pdb=" NE ARG A 601 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 601 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 601 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 479 " 0.081 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 480 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 313 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C ASP A 313 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 313 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 314 " -0.011 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 1 2.15 - 2.84: 3264 2.84 - 3.52: 13434 3.52 - 4.21: 23955 4.21 - 4.90: 41142 Nonbonded interactions: 81796 Sorted by model distance: nonbonded pdb=" ND2 ASN A 580 " pdb=" C1 BGC A1614 " model vdw 1.459 3.550 nonbonded pdb=" O ASN H 50 " pdb=" O6 BGC A1630 " model vdw 2.209 3.040 nonbonded pdb=" ND2 ASN A 524 " pdb=" O2 BGC A1627 " model vdw 2.211 2.496 nonbonded pdb=" ND2 ASN A 652 " pdb=" O2 BGC A1610 " model vdw 2.253 3.120 nonbonded pdb=" O SER L 49 " pdb=" OH TYR L 90 " model vdw 2.264 3.040 ... (remaining 81791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.009 0.155 9577 Z= 0.483 Angle : 1.033 11.883 12981 Z= 0.533 Chirality : 0.103 0.507 1664 Planarity : 0.012 0.469 1642 Dihedral : 12.807 87.775 3878 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.14 % Rotamer: Outliers : 0.41 % Allowed : 11.96 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1254 helix: -1.71 (0.94), residues: 25 sheet: -1.17 (0.19), residues: 764 loop : -1.37 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 52 HIS 0.005 0.001 HIS H 54 PHE 0.011 0.001 PHE A 741 TYR 0.016 0.001 TYR L 51 ARG 0.004 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.22696 ( 182) hydrogen bonds : angle 9.04764 ( 510) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.52391 ( 4) covalent geometry : bond 0.00875 ( 9537) covalent geometry : angle 1.03347 (12977) Misc. bond : bond 0.00623 ( 38) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 1.007 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.1732 time to fit residues: 7.0653 Evaluate side-chains 21 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 705 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 331 GLN A 434 HIS A 503 ASN A 513 HIS A 553 ASN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN A 617 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN A 958 GLN A1053 HIS ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.069088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.046139 restraints weight = 35828.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.046407 restraints weight = 32823.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.046556 restraints weight = 30398.498| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9577 Z= 0.276 Angle : 0.649 6.949 12981 Z= 0.347 Chirality : 0.045 0.149 1664 Planarity : 0.004 0.046 1642 Dihedral : 6.850 59.230 2039 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.74 % Favored : 93.94 % Rotamer: Outliers : 2.53 % Allowed : 12.06 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.23), residues: 1254 helix: -0.89 (1.13), residues: 25 sheet: -1.21 (0.20), residues: 695 loop : -1.65 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.008 0.002 HIS A 707 PHE 0.021 0.002 PHE A 741 TYR 0.020 0.002 TYR L 51 ARG 0.004 0.001 ARG A 956 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 182) hydrogen bonds : angle 6.05685 ( 510) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.81572 ( 4) covalent geometry : bond 0.00588 ( 9537) covalent geometry : angle 0.64943 (12977) Misc. bond : bond 0.00112 ( 38) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 18 time to evaluate : 1.042 Fit side-chains REVERT: A 283 MET cc_start: 0.8215 (pmm) cc_final: 0.7852 (pmm) outliers start: 25 outliers final: 13 residues processed: 43 average time/residue: 0.1432 time to fit residues: 10.9935 Evaluate side-chains 31 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 735 ASN ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.070321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.046711 restraints weight = 35759.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.047134 restraints weight = 29371.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.047529 restraints weight = 26148.709| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9577 Z= 0.129 Angle : 0.500 5.971 12981 Z= 0.270 Chirality : 0.042 0.141 1664 Planarity : 0.003 0.043 1642 Dihedral : 5.714 57.446 2037 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.42 % Allowed : 12.56 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.24), residues: 1254 helix: -0.95 (1.08), residues: 25 sheet: -1.23 (0.19), residues: 730 loop : -1.40 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.003 0.001 HIS H 54 PHE 0.008 0.001 PHE A1061 TYR 0.012 0.001 TYR A 408 ARG 0.003 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 182) hydrogen bonds : angle 5.37354 ( 510) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.61792 ( 4) covalent geometry : bond 0.00269 ( 9537) covalent geometry : angle 0.49980 (12977) Misc. bond : bond 0.00047 ( 38) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 30 average time/residue: 0.1504 time to fit residues: 8.3288 Evaluate side-chains 27 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 897 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN L 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.069018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.046198 restraints weight = 35981.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.046280 restraints weight = 33146.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.046462 restraints weight = 30624.302| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9577 Z= 0.192 Angle : 0.537 5.784 12981 Z= 0.290 Chirality : 0.043 0.148 1664 Planarity : 0.003 0.045 1642 Dihedral : 5.460 58.508 2037 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 2.84 % Allowed : 11.85 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.23), residues: 1254 helix: -0.81 (1.10), residues: 25 sheet: -1.25 (0.20), residues: 697 loop : -1.52 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.004 0.001 HIS A 707 PHE 0.012 0.002 PHE A 741 TYR 0.014 0.002 TYR L 110 ARG 0.003 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02724 ( 182) hydrogen bonds : angle 5.21103 ( 510) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.44878 ( 4) covalent geometry : bond 0.00408 ( 9537) covalent geometry : angle 0.53662 (12977) Misc. bond : bond 0.00054 ( 38) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6337 (p) REVERT: A 283 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7746 (pmm) REVERT: A 720 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8329 (t0) REVERT: H 75 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8759 (m) outliers start: 28 outliers final: 17 residues processed: 43 average time/residue: 0.1581 time to fit residues: 11.7463 Evaluate side-chains 38 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 17 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN L 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.092839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.051669 restraints weight = 39677.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.053354 restraints weight = 27435.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.054273 restraints weight = 21321.615| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9577 Z= 0.295 Angle : 0.633 6.383 12981 Z= 0.343 Chirality : 0.045 0.154 1664 Planarity : 0.003 0.047 1642 Dihedral : 6.069 59.682 2037 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.10 % Favored : 92.58 % Rotamer: Outliers : 3.95 % Allowed : 12.06 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1254 helix: -0.95 (1.10), residues: 26 sheet: -1.52 (0.20), residues: 680 loop : -1.72 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 367 HIS 0.006 0.002 HIS A 707 PHE 0.020 0.002 PHE A 741 TYR 0.018 0.002 TYR L 110 ARG 0.004 0.001 ARG A 956 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 182) hydrogen bonds : angle 5.55384 ( 510) SS BOND : bond 0.00775 ( 2) SS BOND : angle 0.64743 ( 4) covalent geometry : bond 0.00626 ( 9537) covalent geometry : angle 0.63305 (12977) Misc. bond : bond 0.00077 ( 38) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 20 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6184 (pmm) REVERT: A 719 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8812 (m) REVERT: A 720 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8396 (t0) REVERT: L 23 MET cc_start: 0.8162 (mmm) cc_final: 0.7863 (mmm) outliers start: 39 outliers final: 25 residues processed: 58 average time/residue: 0.1494 time to fit residues: 15.0070 Evaluate side-chains 48 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 20 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1065 ASN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 HIS L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.094250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.052873 restraints weight = 39198.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.054643 restraints weight = 25956.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.055642 restraints weight = 19875.537| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9577 Z= 0.150 Angle : 0.515 6.606 12981 Z= 0.277 Chirality : 0.043 0.148 1664 Planarity : 0.003 0.046 1642 Dihedral : 5.178 59.701 2037 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.82 % Rotamer: Outliers : 2.94 % Allowed : 12.97 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1254 helix: -0.62 (1.12), residues: 25 sheet: -1.51 (0.20), residues: 704 loop : -1.53 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS H 54 PHE 0.008 0.001 PHE A 741 TYR 0.013 0.001 TYR L 110 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02512 ( 182) hydrogen bonds : angle 5.13885 ( 510) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.69186 ( 4) covalent geometry : bond 0.00318 ( 9537) covalent geometry : angle 0.51468 (12977) Misc. bond : bond 0.00041 ( 38) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 22 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8343 (t0) REVERT: L 23 MET cc_start: 0.8193 (mmm) cc_final: 0.7926 (mmm) REVERT: L 93 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7213 (t) outliers start: 29 outliers final: 20 residues processed: 48 average time/residue: 0.1409 time to fit residues: 12.0359 Evaluate side-chains 43 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 21 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.093461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.051809 restraints weight = 39545.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.053626 restraints weight = 26890.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.054617 restraints weight = 20710.442| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9577 Z= 0.216 Angle : 0.565 6.574 12981 Z= 0.302 Chirality : 0.043 0.150 1664 Planarity : 0.003 0.046 1642 Dihedral : 5.092 58.227 2037 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.18 % Favored : 92.58 % Rotamer: Outliers : 3.04 % Allowed : 13.68 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1254 helix: -0.91 (1.06), residues: 26 sheet: -1.56 (0.20), residues: 691 loop : -1.64 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.004 0.001 HIS A 707 PHE 0.014 0.002 PHE A 741 TYR 0.017 0.002 TYR L 110 ARG 0.003 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 182) hydrogen bonds : angle 5.18355 ( 510) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.64606 ( 4) covalent geometry : bond 0.00459 ( 9537) covalent geometry : angle 0.56464 (12977) Misc. bond : bond 0.00056 ( 38) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 24 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8793 (m) REVERT: A 720 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8342 (t0) REVERT: L 23 MET cc_start: 0.8153 (mmm) cc_final: 0.7904 (mmm) REVERT: L 93 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7272 (t) outliers start: 30 outliers final: 25 residues processed: 53 average time/residue: 0.1421 time to fit residues: 13.1189 Evaluate side-chains 49 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 21 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.064853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.043773 restraints weight = 37475.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.044109 restraints weight = 32147.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.044266 restraints weight = 28389.869| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9577 Z= 0.179 Angle : 0.542 10.578 12981 Z= 0.291 Chirality : 0.043 0.149 1664 Planarity : 0.003 0.046 1642 Dihedral : 4.774 57.418 2037 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % Rotamer: Outliers : 3.04 % Allowed : 13.78 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1254 helix: -0.88 (1.06), residues: 26 sheet: -1.61 (0.20), residues: 689 loop : -1.57 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.003 0.001 HIS A 318 PHE 0.011 0.002 PHE A 741 TYR 0.014 0.002 TYR L 110 ARG 0.003 0.000 ARG A 601 Details of bonding type rmsd hydrogen bonds : bond 0.02476 ( 182) hydrogen bonds : angle 5.03826 ( 510) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.56239 ( 4) covalent geometry : bond 0.00382 ( 9537) covalent geometry : angle 0.54231 (12977) Misc. bond : bond 0.00047 ( 38) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 21 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8602 (m) REVERT: L 93 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7293 (t) outliers start: 30 outliers final: 27 residues processed: 50 average time/residue: 0.1477 time to fit residues: 13.0588 Evaluate side-chains 49 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 20 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 0.0470 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.092505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.051406 restraints weight = 39833.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.053036 restraints weight = 27535.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.053912 restraints weight = 21620.876| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9577 Z= 0.236 Angle : 0.591 8.502 12981 Z= 0.316 Chirality : 0.044 0.153 1664 Planarity : 0.003 0.047 1642 Dihedral : 5.174 58.567 2037 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.39 % Rotamer: Outliers : 3.24 % Allowed : 13.58 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.23), residues: 1254 helix: -0.84 (1.07), residues: 26 sheet: -1.66 (0.20), residues: 669 loop : -1.81 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 52 HIS 0.004 0.002 HIS A 707 PHE 0.017 0.002 PHE A 741 TYR 0.017 0.002 TYR L 110 ARG 0.003 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02599 ( 182) hydrogen bonds : angle 5.30567 ( 510) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.18006 ( 4) covalent geometry : bond 0.00503 ( 9537) covalent geometry : angle 0.59046 (12977) Misc. bond : bond 0.00059 ( 38) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 22 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 29 residues processed: 53 average time/residue: 0.1499 time to fit residues: 14.0384 Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 22 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.092183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.050966 restraints weight = 40208.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.052591 restraints weight = 28188.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.053445 restraints weight = 22192.099| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9577 Z= 0.253 Angle : 0.616 7.220 12981 Z= 0.330 Chirality : 0.044 0.170 1664 Planarity : 0.003 0.047 1642 Dihedral : 5.484 58.916 2037 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.66 % Favored : 92.11 % Rotamer: Outliers : 2.94 % Allowed : 13.88 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1254 helix: -1.00 (1.04), residues: 26 sheet: -1.75 (0.20), residues: 664 loop : -1.91 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 52 HIS 0.005 0.002 HIS A 318 PHE 0.018 0.002 PHE A 741 TYR 0.017 0.002 TYR L 110 ARG 0.004 0.001 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02676 ( 182) hydrogen bonds : angle 5.44198 ( 510) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.89487 ( 4) covalent geometry : bond 0.00539 ( 9537) covalent geometry : angle 0.61577 (12977) Misc. bond : bond 0.00064 ( 38) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 22 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 28 residues processed: 50 average time/residue: 0.1415 time to fit residues: 12.5053 Evaluate side-chains 50 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 22 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.092555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.051442 restraints weight = 39887.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.053083 restraints weight = 27781.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.054001 restraints weight = 21710.099| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9577 Z= 0.198 Angle : 0.572 7.312 12981 Z= 0.305 Chirality : 0.043 0.161 1664 Planarity : 0.003 0.047 1642 Dihedral : 5.189 57.253 2037 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.50 % Rotamer: Outliers : 2.84 % Allowed : 13.98 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.23), residues: 1254 helix: -0.87 (1.06), residues: 26 sheet: -1.72 (0.20), residues: 666 loop : -1.90 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 52 HIS 0.005 0.001 HIS A 318 PHE 0.013 0.002 PHE A 741 TYR 0.015 0.002 TYR L 110 ARG 0.003 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02520 ( 182) hydrogen bonds : angle 5.31782 ( 510) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.70634 ( 4) covalent geometry : bond 0.00423 ( 9537) covalent geometry : angle 0.57198 (12977) Misc. bond : bond 0.00051 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.88 seconds wall clock time: 66 minutes 8.98 seconds (3968.98 seconds total)