Starting phenix.real_space_refine on Fri Mar 14 04:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbb_43119/03_2025/8vbb_43119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbb_43119/03_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_43119/03_2025/8vbb_43119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbb_43119/03_2025/8vbb_43119.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbb_43119/03_2025/8vbb_43119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbb_43119/03_2025/8vbb_43119.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 5680 2.51 5 N 1646 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9444 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7293 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 8, 'TRANS': 1029} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 921 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "A" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 418 Unusual residues: {'BGC': 38} Classifications: {'undetermined': 38} Link IDs: {None: 37} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 38 Time building chain proxies: 9.02, per 1000 atoms: 0.96 Number of scatterers: 9444 At special positions: 0 Unit cell: (83.375, 98.6, 178.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 2101 8.00 N 1646 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9036 O5 BGC A1601 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9047 O5 BGC A1602 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9300 O5 BGC A1625 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9421 O5 BGC A1636 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9190 O5 BGC A1615 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=38, symmetry=0 Number of additional bonds: simple=38, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 2.5% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.766A pdb=" N PHE A 484 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.216A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.043A pdb=" N VAL A 274 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 310 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 276 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 429 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP A 458 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 431 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 508 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN A 544 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 510 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 5.552A pdb=" N VAL A 162 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 202 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 223 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 267 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 295 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.047A pdb=" N SER A 134 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 217 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 261 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS A 318 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 290 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 342 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.099A pdb=" N TYR A 184 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 249 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP A 243 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.736A pdb=" N ILE A 350 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 415 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 494 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 578 removed outlier: 6.227A pdb=" N ILE A 604 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 632 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 606 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 653 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN A 681 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 654 " --> pdb=" O ASN A 681 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 680 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 729 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N SER A 753 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 731 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL A 776 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 806 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 778 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 801 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 832 " --> pdb=" O LYS A 801 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 803 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 584 through 585 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 584 through 585 current: chain 'A' and resid 635 through 647 removed outlier: 6.526A pdb=" N ASN A 635 " --> pdb=" O THR A 661 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 660 through 661 current: chain 'A' and resid 687 through 699 removed outlier: 7.413A pdb=" N ASN A 692 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN A 721 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR A 694 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 723 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR A 696 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 725 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU A 698 " --> pdb=" O GLN A 725 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 734 through 738 current: chain 'A' and resid 836 through 849 removed outlier: 6.241A pdb=" N ASN A 837 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 865 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 839 " --> pdb=" O ASN A 865 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR A 867 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ALA A 841 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP A 869 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN A 843 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 871 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 845 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR A 873 " --> pdb=" O ALA A 845 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR A 847 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 862 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 891 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU A 864 " --> pdb=" O ASN A 891 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 888 through 892 current: chain 'A' and resid 1036 through 1052 removed outlier: 6.890A pdb=" N ASN A1065 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1038 " --> pdb=" O ASN A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A1067 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN A1040 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A1069 " --> pdb=" O ASN A1040 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A1042 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A1071 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A1044 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA A1073 " --> pdb=" O GLY A1044 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A1046 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A1075 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A1048 " --> pdb=" O THR A1075 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN A1077 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A1050 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1064 " --> pdb=" O THR A1089 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR A1091 " --> pdb=" O ASN A1064 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A1066 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN A1093 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A1068 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR A1095 " --> pdb=" O THR A1068 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N SER A1070 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A1097 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 856 through 857 removed outlier: 6.674A pdb=" N ILE A 856 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 882 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 908 " --> pdb=" O ASN A 934 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 957 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER A 981 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 959 " --> pdb=" O SER A 981 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL A1004 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A1034 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A1006 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AB2, first strand: chain 'H' and resid 29 through 30 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 30 current: chain 'H' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 124 through 127 Processing sheet with id=AB3, first strand: chain 'L' and resid 23 through 25 removed outlier: 3.520A pdb=" N SER L 91 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.023A pdb=" N LEU L 30 " --> pdb=" O GLU L 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 52 through 57 removed outlier: 3.555A pdb=" N GLN L 109 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR L 116 " --> pdb=" O GLN L 109 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 2.92 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: 23.090 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- 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 9537 Z= 0.530 Angle : 1.033 11.883 12977 Z= 0.533 Chirality : 0.103 0.507 1664 Planarity : 0.012 0.469 1642 Dihedral : 12.807 87.775 3878 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.14 % Rotamer: Outliers : 0.41 % Allowed : 11.96 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1254 helix: -1.71 (0.94), residues: 25 sheet: -1.17 (0.19), residues: 764 loop : -1.37 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 52 HIS 0.005 0.001 HIS H 54 PHE 0.011 0.001 PHE A 741 TYR 0.016 0.001 TYR L 51 ARG 0.004 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 1.014 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.1728 time to fit residues: 7.1702 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 705 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 331 GLN A 434 HIS A 503 ASN A 513 HIS A 553 ASN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN A 617 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN A 958 GLN A1053 HIS ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.069088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.046108 restraints weight = 35828.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.046494 restraints weight = 32084.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.046595 restraints weight = 29188.853| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9537 Z= 0.404 Angle : 0.649 6.949 12977 Z= 0.347 Chirality : 0.045 0.149 1664 Planarity : 0.004 0.046 1642 Dihedral : 6.850 59.230 2039 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.74 % Favored : 93.94 % Rotamer: Outliers : 2.53 % Allowed : 12.06 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.23), residues: 1254 helix: -0.89 (1.13), residues: 25 sheet: -1.21 (0.20), residues: 695 loop : -1.65 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.008 0.002 HIS A 707 PHE 0.021 0.002 PHE A 741 TYR 0.020 0.002 TYR L 51 ARG 0.004 0.001 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 18 time to evaluate : 1.062 Fit side-chains REVERT: A 283 MET cc_start: 0.8204 (pmm) cc_final: 0.7856 (pmm) outliers start: 25 outliers final: 13 residues processed: 43 average time/residue: 0.1492 time to fit residues: 11.4934 Evaluate side-chains 31 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 102 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.070954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.047308 restraints weight = 35539.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.047783 restraints weight = 29559.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.048081 restraints weight = 25745.405| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9537 Z= 0.145 Angle : 0.485 6.086 12977 Z= 0.262 Chirality : 0.042 0.142 1664 Planarity : 0.003 0.042 1642 Dihedral : 5.506 56.112 2037 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.27 % Favored : 96.49 % Rotamer: Outliers : 1.22 % Allowed : 12.36 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1254 helix: -0.97 (1.07), residues: 25 sheet: -1.20 (0.19), residues: 730 loop : -1.32 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.004 0.001 HIS A1032 PHE 0.006 0.001 PHE A 631 TYR 0.010 0.001 TYR A 408 ARG 0.003 0.000 ARG A 183 *********************** 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 30 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 1.105 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 28 average time/residue: 0.1561 time to fit residues: 8.2371 Evaluate side-chains 27 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 897 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 HIS A1065 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.070065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.048915 restraints weight = 35369.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.048510 restraints weight = 29752.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.048300 restraints weight = 27858.616| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9537 Z= 0.165 Angle : 0.475 6.231 12977 Z= 0.255 Chirality : 0.042 0.144 1664 Planarity : 0.003 0.043 1642 Dihedral : 4.875 55.086 2037 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Rotamer: Outliers : 1.82 % Allowed : 12.16 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.24), residues: 1254 helix: -0.85 (1.07), residues: 25 sheet: -1.05 (0.20), residues: 705 loop : -1.42 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS H 54 PHE 0.007 0.001 PHE A 741 TYR 0.010 0.001 TYR L 110 ARG 0.003 0.000 ARG A 183 *********************** 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 36 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7703 (pmm) outliers start: 18 outliers final: 15 residues processed: 32 average time/residue: 0.1463 time to fit residues: 8.6017 Evaluate side-chains 34 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 961 HIS L 56 GLN L 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.092134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.051234 restraints weight = 39627.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.052864 restraints weight = 27546.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.053902 restraints weight = 21482.820| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 9537 Z= 0.560 Angle : 0.712 7.550 12977 Z= 0.385 Chirality : 0.047 0.158 1664 Planarity : 0.004 0.048 1642 Dihedral : 6.613 58.989 2037 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.21 % Favored : 91.47 % Rotamer: Outliers : 3.65 % Allowed : 11.96 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1254 helix: -1.22 (1.03), residues: 26 sheet: -1.51 (0.20), residues: 670 loop : -1.79 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 367 HIS 0.009 0.002 HIS A 707 PHE 0.027 0.003 PHE A 741 TYR 0.022 0.003 TYR L 110 ARG 0.005 0.001 ARG A 956 *********************** 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 56 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 20 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6244 (pmm) outliers start: 36 outliers final: 24 residues processed: 54 average time/residue: 0.1470 time to fit residues: 13.6284 Evaluate side-chains 44 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 19 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 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 908 ILE Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1065 ASN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 111 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 116 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** A 703 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 = 0.4303 r_free = 0.4303 target = 0.095095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.053363 restraints weight = 39273.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.055231 restraints weight = 25776.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.056406 restraints weight = 19489.899| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9537 Z= 0.178 Angle : 0.503 6.823 12977 Z= 0.269 Chirality : 0.042 0.150 1664 Planarity : 0.003 0.046 1642 Dihedral : 4.869 56.620 2037 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.99 % Favored : 95.77 % Rotamer: Outliers : 2.23 % Allowed : 13.27 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.24), residues: 1254 helix: -0.59 (1.12), residues: 25 sheet: -1.48 (0.20), residues: 687 loop : -1.50 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.004 0.001 HIS H 54 PHE 0.007 0.001 PHE A 156 TYR 0.010 0.001 TYR L 110 ARG 0.002 0.000 ARG A 183 *********************** 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 41 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 19 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.6053 (pmm) REVERT: L 93 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7245 (t) outliers start: 22 outliers final: 15 residues processed: 38 average time/residue: 0.1677 time to fit residues: 11.0990 Evaluate side-chains 35 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 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 L residue 69 TYR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6399 > 50: distance: 88 - 92: 3.602 distance: 93 - 94: 7.539 distance: 94 - 95: 5.747 distance: 94 - 96: 4.346 distance: 96 - 97: 3.616 distance: 98 - 99: 5.931 distance: 98 - 104: 7.788 distance: 100 - 101: 7.215 distance: 101 - 103: 3.170 distance: 104 - 105: 8.398 distance: 105 - 106: 9.438 distance: 105 - 108: 7.837 distance: 106 - 107: 8.108 distance: 106 - 109: 4.798 distance: 109 - 110: 7.085 distance: 110 - 111: 3.813 distance: 110 - 113: 3.917 distance: 111 - 112: 8.449 distance: 111 - 117: 10.508 distance: 113 - 114: 6.800 distance: 113 - 115: 9.742 distance: 114 - 116: 7.031 distance: 117 - 118: 10.603 distance: 118 - 119: 9.939 distance: 118 - 121: 10.658 distance: 119 - 120: 19.424 distance: 119 - 125: 17.930 distance: 121 - 122: 8.663 distance: 122 - 123: 24.875 distance: 122 - 124: 10.249 distance: 126 - 127: 18.904 distance: 126 - 129: 22.400 distance: 127 - 128: 8.276 distance: 127 - 133: 28.978 distance: 129 - 130: 8.423 distance: 130 - 131: 10.459 distance: 130 - 132: 17.623 distance: 133 - 134: 18.134 distance: 134 - 135: 18.809 distance: 134 - 137: 21.952 distance: 135 - 136: 15.781 distance: 135 - 142: 6.851 distance: 137 - 138: 16.608 distance: 138 - 139: 23.831 distance: 139 - 140: 36.816 distance: 140 - 141: 29.438 distance: 142 - 143: 13.305 distance: 143 - 144: 6.392 distance: 144 - 145: 22.595 distance: 144 - 146: 17.044 distance: 146 - 147: 15.972 distance: 147 - 148: 12.760 distance: 147 - 150: 24.163 distance: 148 - 149: 20.199 distance: 148 - 154: 13.360 distance: 150 - 151: 20.344 distance: 151 - 152: 4.137 distance: 151 - 153: 9.652 distance: 154 - 155: 9.493 distance: 155 - 156: 3.185 distance: 155 - 158: 17.642 distance: 156 - 157: 23.152 distance: 156 - 162: 10.750 distance: 158 - 159: 24.114 distance: 159 - 160: 6.954 distance: 159 - 161: 12.438