Starting phenix.real_space_refine on Fri Oct 10 22:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbb_43119/10_2025/8vbb_43119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbb_43119/10_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_43119/10_2025/8vbb_43119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbb_43119/10_2025/8vbb_43119.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbb_43119/10_2025/8vbb_43119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbb_43119/10_2025/8vbb_43119.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.22, per 1000 atoms: 0.24 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: 0.86 Conformation dependent library (CDL) restraints added in 379.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 2.28 Time building geometry restraints manager: 1.11 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: 19.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 183 TYR 0.016 0.001 TYR L 51 PHE 0.011 0.001 PHE A 741 TRP 0.014 0.001 TRP H 52 HIS 0.005 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00875 ( 9537) covalent geometry : angle 1.03347 (12977) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.52391 ( 4) hydrogen bonds : bond 0.22696 ( 182) hydrogen bonds : angle 9.04764 ( 510) 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 : 0.281 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0798 time to fit residues: 3.2389 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 : 0.345 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 327 ASN A 331 GLN A 410 ASN A 434 HIS A 503 ASN A 513 HIS A 553 ASN A 580 ASN A 587 ASN A 607 ASN A 617 ASN A 703 ASN A 720 ASN A 825 HIS A 837 ASN A 958 GLN A1053 HIS L 112 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.097852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.056399 restraints weight = 39172.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.058648 restraints weight = 24678.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.060002 restraints weight = 18010.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.060769 restraints weight = 14617.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.061499 restraints weight = 12767.935| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9577 Z= 0.115 Angle : 0.515 6.570 12981 Z= 0.274 Chirality : 0.043 0.148 1664 Planarity : 0.003 0.044 1642 Dihedral : 5.962 52.870 2039 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % Rotamer: Outliers : 1.22 % Allowed : 10.44 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.24), residues: 1254 helix: -1.15 (1.06), residues: 25 sheet: -0.97 (0.20), residues: 739 loop : -1.37 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.012 0.001 TYR A 408 PHE 0.008 0.001 PHE A 631 TRP 0.012 0.001 TRP H 52 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9537) covalent geometry : angle 0.51470 (12977) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.63805 ( 4) hydrogen bonds : bond 0.04055 ( 182) hydrogen bonds : angle 5.95753 ( 510) Misc. bond : bond 0.00135 ( 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 32 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7073 (pmm) cc_final: 0.6782 (pmm) outliers start: 12 outliers final: 5 residues processed: 31 average time/residue: 0.0648 time to fit residues: 3.6312 Evaluate side-chains 25 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 897 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN A 914 ASN A 961 HIS A1065 ASN H 101 HIS L 56 GLN L 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.091976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.050834 restraints weight = 39808.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.052410 restraints weight = 28091.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.053253 restraints weight = 22377.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.053966 restraints weight = 19228.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.054308 restraints weight = 17237.118| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 9577 Z= 0.481 Angle : 0.843 9.018 12981 Z= 0.453 Chirality : 0.050 0.165 1664 Planarity : 0.005 0.062 1642 Dihedral : 7.466 55.665 2036 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.69 % Favored : 90.99 % Rotamer: Outliers : 3.55 % Allowed : 12.26 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.23), residues: 1254 helix: -1.04 (1.11), residues: 25 sheet: -1.61 (0.20), residues: 677 loop : -1.90 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 956 TYR 0.025 0.003 TYR L 51 PHE 0.036 0.004 PHE A 741 TRP 0.019 0.002 TRP A 367 HIS 0.013 0.003 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.01028 ( 9537) covalent geometry : angle 0.84291 (12977) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.67226 ( 4) hydrogen bonds : bond 0.03827 ( 182) hydrogen bonds : angle 6.31439 ( 510) Misc. bond : bond 0.00135 ( 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 55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 20 time to evaluate : 0.236 Fit side-chains REVERT: H 75 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8801 (m) outliers start: 35 outliers final: 22 residues processed: 54 average time/residue: 0.0563 time to fit residues: 5.3060 Evaluate side-chains 43 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 462 ILE 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 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 810 THR Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1065 ASN Chi-restraints excluded: chain H residue 75 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 481 HIS ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.094980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.053650 restraints weight = 39821.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.055570 restraints weight = 25784.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.056612 restraints weight = 19462.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.057527 restraints weight = 16225.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.057991 restraints weight = 14184.876| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2269 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= 0.124 Angle : 0.521 7.973 12981 Z= 0.278 Chirality : 0.043 0.150 1664 Planarity : 0.003 0.047 1642 Dihedral : 5.489 58.422 2036 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.23), residues: 1254 helix: -0.89 (1.10), residues: 25 sheet: -1.44 (0.20), residues: 681 loop : -1.56 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1066 TYR 0.014 0.001 TYR A 275 PHE 0.013 0.001 PHE A1061 TRP 0.012 0.001 TRP H 52 HIS 0.004 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9537) covalent geometry : angle 0.52073 (12977) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.39835 ( 4) hydrogen bonds : bond 0.02742 ( 182) hydrogen bonds : angle 5.37573 ( 510) Misc. bond : bond 0.00040 ( 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 42 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 21 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.6050 (pmm) outliers start: 21 outliers final: 14 residues processed: 39 average time/residue: 0.0759 time to fit residues: 5.0068 Evaluate side-chains 32 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET 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 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 703 ASN 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 897 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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** A1065 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.069161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.045788 restraints weight = 37103.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.045974 restraints weight = 32507.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.046202 restraints weight = 28707.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046330 restraints weight = 26343.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046330 restraints weight = 24661.773| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9577 Z= 0.199 Angle : 0.558 6.313 12981 Z= 0.298 Chirality : 0.043 0.159 1664 Planarity : 0.003 0.047 1642 Dihedral : 5.415 58.689 2036 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.74 % Allowed : 13.07 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.23), residues: 1254 helix: -0.76 (1.10), residues: 25 sheet: -1.49 (0.20), residues: 698 loop : -1.57 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.014 0.002 TYR L 110 PHE 0.014 0.002 PHE A 741 TRP 0.011 0.001 TRP H 52 HIS 0.003 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9537) covalent geometry : angle 0.55766 (12977) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.82310 ( 4) hydrogen bonds : bond 0.02693 ( 182) hydrogen bonds : angle 5.37651 ( 510) Misc. bond : bond 0.00054 ( 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 46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 19 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6099 (pptt) REVERT: A 283 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7681 (pmm) outliers start: 27 outliers final: 20 residues processed: 43 average time/residue: 0.0669 time to fit residues: 5.0838 Evaluate side-chains 40 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 191 LYS 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 693 ILE Chi-restraints excluded: chain A residue 703 ASN 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 908 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain H residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 0.0670 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.092571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.051406 restraints weight = 39792.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.053022 restraints weight = 27638.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.053944 restraints weight = 21595.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.054668 restraints weight = 18400.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.055205 restraints weight = 16480.257| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9577 Z= 0.276 Angle : 0.627 6.304 12981 Z= 0.337 Chirality : 0.045 0.158 1664 Planarity : 0.003 0.048 1642 Dihedral : 5.812 59.630 2036 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.34 % Favored : 92.34 % Rotamer: Outliers : 3.24 % Allowed : 13.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.23), residues: 1254 helix: -0.62 (1.14), residues: 25 sheet: -1.69 (0.20), residues: 687 loop : -1.72 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 281 TYR 0.018 0.002 TYR L 110 PHE 0.018 0.002 PHE A 741 TRP 0.012 0.002 TRP H 52 HIS 0.006 0.002 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 9537) covalent geometry : angle 0.62658 (12977) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.78569 ( 4) hydrogen bonds : bond 0.02777 ( 182) hydrogen bonds : angle 5.57537 ( 510) Misc. bond : bond 0.00072 ( 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 53 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 21 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8391 (t0) REVERT: L 93 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7298 (t) outliers start: 32 outliers final: 24 residues processed: 50 average time/residue: 0.0703 time to fit residues: 5.9569 Evaluate side-chains 46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 20 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 99 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 693 ILE Chi-restraints excluded: chain A residue 703 ASN 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 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.066285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.3658 r_free = 0.3658 target = 0.047421 restraints weight = 37561.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 148)---------------| | r_work = 0.3548 r_free = 0.3548 target = 0.045301 restraints weight = 48252.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.045262 restraints weight = 47197.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.045350 restraints weight = 44087.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.045390 restraints weight = 41940.642| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9577 Z= 0.196 Angle : 0.568 9.764 12981 Z= 0.304 Chirality : 0.043 0.155 1664 Planarity : 0.003 0.048 1642 Dihedral : 5.289 59.753 2036 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.23), residues: 1254 helix: -0.52 (1.15), residues: 25 sheet: -1.68 (0.20), residues: 681 loop : -1.69 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 601 TYR 0.017 0.002 TYR L 110 PHE 0.013 0.002 PHE A 741 TRP 0.011 0.001 TRP H 52 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9537) covalent geometry : angle 0.56780 (12977) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.76384 ( 4) hydrogen bonds : bond 0.02565 ( 182) hydrogen bonds : angle 5.32851 ( 510) Misc. bond : bond 0.00052 ( 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 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 21 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 93 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7352 (t) outliers start: 30 outliers final: 26 residues processed: 49 average time/residue: 0.0629 time to fit residues: 5.5341 Evaluate side-chains 47 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 20 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 VAL 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 703 ASN 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 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.066200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 168)---------------| | r_work = 0.3655 r_free = 0.3655 target = 0.047155 restraints weight = 37705.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.045396 restraints weight = 49487.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.045035 restraints weight = 51802.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.045142 restraints weight = 50572.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.045203 restraints weight = 46691.678| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9577 Z= 0.201 Angle : 0.571 8.174 12981 Z= 0.304 Chirality : 0.043 0.153 1664 Planarity : 0.003 0.048 1642 Dihedral : 5.029 58.790 2036 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.10 % Favored : 92.66 % Rotamer: Outliers : 3.24 % Allowed : 13.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.23), residues: 1254 helix: -0.67 (1.12), residues: 26 sheet: -1.79 (0.20), residues: 667 loop : -1.69 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 601 TYR 0.016 0.002 TYR L 110 PHE 0.013 0.002 PHE A 741 TRP 0.011 0.001 TRP H 52 HIS 0.004 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9537) covalent geometry : angle 0.57088 (12977) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.65684 ( 4) hydrogen bonds : bond 0.02551 ( 182) hydrogen bonds : angle 5.21232 ( 510) Misc. bond : bond 0.00052 ( 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 55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 23 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6433 (p) REVERT: L 93 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (t) outliers start: 32 outliers final: 29 residues processed: 53 average time/residue: 0.0632 time to fit residues: 5.9285 Evaluate side-chains 52 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 21 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 VAL 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 703 ASN 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 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1065 ASN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.092256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.051152 restraints weight = 39739.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.052758 restraints weight = 27749.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.053580 restraints weight = 21817.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.054351 restraints weight = 18760.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.054730 restraints weight = 16786.265| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3497 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= 0.241 Angle : 0.615 13.223 12981 Z= 0.326 Chirality : 0.044 0.164 1664 Planarity : 0.003 0.048 1642 Dihedral : 5.223 59.187 2036 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.58 % Favored : 92.19 % Rotamer: Outliers : 3.24 % Allowed : 13.78 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.23), residues: 1254 helix: -1.30 (1.01), residues: 26 sheet: -1.83 (0.20), residues: 654 loop : -1.80 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 183 TYR 0.018 0.002 TYR L 110 PHE 0.018 0.002 PHE A 741 TRP 0.012 0.002 TRP H 52 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9537) covalent geometry : angle 0.61446 (12977) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.79665 ( 4) hydrogen bonds : bond 0.02696 ( 182) hydrogen bonds : angle 5.55296 ( 510) Misc. bond : bond 0.00060 ( 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 53 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 21 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 93 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7336 (t) outliers start: 32 outliers final: 28 residues processed: 51 average time/residue: 0.0637 time to fit residues: 5.8375 Evaluate side-chains 50 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 21 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET 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 703 ASN 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 897 THR Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1065 ASN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.065207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.045215 restraints weight = 37327.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.044623 restraints weight = 34804.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.044638 restraints weight = 31866.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.044682 restraints weight = 31817.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.044696 restraints weight = 30749.144| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9577 Z= 0.146 Angle : 0.546 10.429 12981 Z= 0.289 Chirality : 0.043 0.168 1664 Planarity : 0.003 0.048 1642 Dihedral : 4.645 57.421 2036 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 2.53 % Allowed : 14.49 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.23), residues: 1254 helix: -1.43 (0.99), residues: 26 sheet: -1.73 (0.20), residues: 647 loop : -1.82 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 601 TYR 0.015 0.001 TYR L 110 PHE 0.009 0.001 PHE H 124 TRP 0.009 0.001 TRP H 52 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9537) covalent geometry : angle 0.54560 (12977) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.56008 ( 4) hydrogen bonds : bond 0.02502 ( 182) hydrogen bonds : angle 5.24212 ( 510) Misc. bond : bond 0.00038 ( 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 47 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 22 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 24 residues processed: 45 average time/residue: 0.0661 time to fit residues: 5.2707 Evaluate side-chains 45 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 21 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET 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 689 THR Chi-restraints excluded: chain A residue 703 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.091776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.050543 restraints weight = 39850.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.052063 restraints weight = 28411.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.052951 restraints weight = 22500.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.053649 restraints weight = 19289.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.054173 restraints weight = 17356.546| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3736 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= 0.292 Angle : 0.661 10.384 12981 Z= 0.353 Chirality : 0.045 0.168 1664 Planarity : 0.003 0.049 1642 Dihedral : 5.502 59.947 2036 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.13 % Favored : 89.63 % Rotamer: Outliers : 2.84 % Allowed : 14.49 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.23), residues: 1254 helix: -1.70 (1.00), residues: 26 sheet: -1.93 (0.20), residues: 651 loop : -1.90 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 956 TYR 0.020 0.002 TYR L 110 PHE 0.021 0.002 PHE A 741 TRP 0.013 0.002 TRP H 52 HIS 0.006 0.002 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 9537) covalent geometry : angle 0.66129 (12977) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.71117 ( 4) hydrogen bonds : bond 0.02781 ( 182) hydrogen bonds : angle 5.64562 ( 510) Misc. bond : bond 0.00072 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.04 seconds wall clock time: 39 minutes 57.23 seconds (2397.23 seconds total)