Starting phenix.real_space_refine on Wed Mar 4 21:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.map" model { file = "/net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q62_13850/03_2026/7q62_13850.cif" } resolution = 3.18 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= -0.000 sd= 0.005 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 75 5.16 5 C 10356 2.51 5 N 2653 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9560 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1159} Chain breaks: 3 Chain: "B" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6486 Classifications: {'peptide': 822} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 772} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 16186 At special positions: 0 Unit cell: (106.108, 122.93, 142.34, 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 75 16.00 O 3102 8.00 N 2653 7.00 C 10356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.02 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.11 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.02 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 694 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B 845 " - pdb=" SG CYS B 881 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 120 " " NAG A1502 " - " ASN A 328 " " NAG A1503 " - " ASN A 609 " " NAG A1504 " - " ASN A 857 " " NAG A1505 " - " ASN A 867 " " NAG B1501 " - " ASN B 120 " " NAG B1502 " - " ASN B 328 " " NAG B1503 " - " ASN B 609 " " NAG B1504 " - " ASN B 857 " " NAG B1505 " - " ASN B 867 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 845.3 milliseconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 12.2% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 406 through 409 removed outlier: 4.133A pdb=" N ASN A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.008A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 602' Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.674A pdb=" N VAL A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.704A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 4.343A pdb=" N VAL A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.265A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1010 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1070 removed outlier: 3.845A pdb=" N LYS A1064 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1104 removed outlier: 3.612A pdb=" N LEU A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 4.294A pdb=" N MET A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.331A pdb=" N ASN A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.796A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 3.946A pdb=" N LYS A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A1159 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A1162 " --> pdb=" O LYS A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1207 removed outlier: 3.702A pdb=" N LYS A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 4.039A pdb=" N LYS A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 3.552A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 removed outlier: 3.824A pdb=" N ALA B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.807A pdb=" N LYS B 511 " --> pdb=" O ASN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.719A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.697A pdb=" N ALA B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 8.244A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.797A pdb=" N PHE A 52 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 54 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.759A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 346 removed outlier: 4.038A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 455 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 507 removed outlier: 5.308A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 495 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 487 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB4, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB5, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB6, first strand: chain 'A' and resid 800 through 801 removed outlier: 7.081A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB8, first strand: chain 'A' and resid 921 through 930 Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.599A pdb=" N TYR A1172 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 82 removed outlier: 8.101A pdb=" N LYS B 38 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.814A pdb=" N LEU B 56 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 64 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 126 Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.626A pdb=" N SER B 156 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 172 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B 170 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 160 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 223 Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.230A pdb=" N LEU B 229 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B 310 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B 311 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 261 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 346 removed outlier: 5.431A pdb=" N MET B 342 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 344 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 362 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 346 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'B' and resid 451 through 455 Processing sheet with id=AD1, first strand: chain 'B' and resid 498 through 507 removed outlier: 5.152A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY B 495 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER B 488 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 539 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 563 through 567 Processing sheet with id=AD3, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AD4, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 730 removed outlier: 5.938A pdb=" N VAL B 800 " --> pdb=" O LYS B 904 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'B' and resid 790 through 795 640 hydrogen bonds defined for protein. 1758 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: 4.21 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5061 1.34 - 1.46: 4006 1.46 - 1.59: 7390 1.59 - 1.71: 0 1.71 - 1.84: 110 Bond restraints: 16567 Sorted by residual: bond pdb=" CD GLU B 596 " pdb=" OE1 GLU B 596 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.66e+01 bond pdb=" CD GLU A 596 " pdb=" OE1 GLU A 596 " ideal model delta sigma weight residual 1.249 1.321 -0.072 1.90e-02 2.77e+03 1.45e+01 bond pdb=" N ILE A1318 " pdb=" CA ILE A1318 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.61e+00 bond pdb=" N GLY A1031 " pdb=" CA GLY A1031 " ideal model delta sigma weight residual 1.449 1.478 -0.028 9.80e-03 1.04e+04 8.41e+00 bond pdb=" C1 NAG A1504 " pdb=" O5 NAG A1504 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 22455 7.50 - 15.00: 56 15.00 - 22.51: 1 22.51 - 30.01: 0 30.01 - 37.51: 2 Bond angle restraints: 22514 Sorted by residual: angle pdb=" CA CYS A 279 " pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 114.40 151.91 -37.51 2.30e+00 1.89e-01 2.66e+02 angle pdb=" CA CYS A 259 " pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " ideal model delta sigma weight residual 114.40 151.66 -37.26 2.30e+00 1.89e-01 2.62e+02 angle pdb=" N CYS A 259 " pdb=" CA CYS A 259 " pdb=" C CYS A 259 " ideal model delta sigma weight residual 108.99 122.76 -13.77 1.57e+00 4.06e-01 7.69e+01 angle pdb=" N CYS A 279 " pdb=" CA CYS A 279 " pdb=" C CYS A 279 " ideal model delta sigma weight residual 108.79 119.95 -11.16 1.53e+00 4.27e-01 5.32e+01 angle pdb=" C ASN B 103 " pdb=" N ASN B 104 " pdb=" CA ASN B 104 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 ... (remaining 22509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 9123 17.69 - 35.38: 733 35.38 - 53.07: 137 53.07 - 70.76: 39 70.76 - 88.45: 34 Dihedral angle restraints: 10066 sinusoidal: 4126 harmonic: 5940 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 694 " pdb=" CB CYS A 694 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CA GLU A 835 " pdb=" C GLU A 835 " pdb=" N SER A 836 " pdb=" CA SER A 836 " ideal model delta harmonic sigma weight residual 180.00 140.64 39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 10063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2446 0.139 - 0.277: 93 0.277 - 0.416: 10 0.416 - 0.554: 3 0.554 - 0.693: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 857 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA CYS A 259 " pdb=" N CYS A 259 " pdb=" C CYS A 259 " pdb=" CB CYS A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA CYS A 279 " pdb=" N CYS A 279 " pdb=" C CYS A 279 " pdb=" CB CYS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2550 not shown) Planarity restraints: 2899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 837 " 0.029 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 837 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 837 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 837 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 837 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 837 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 837 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 837 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 837 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 44 " 0.057 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 45 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 609 " 0.027 2.00e-02 2.50e+03 2.64e-02 8.73e+00 pdb=" CG ASN B 609 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 609 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 609 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B1503 " 0.030 2.00e-02 2.50e+03 ... (remaining 2896 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4033 2.80 - 3.33: 13141 3.33 - 3.85: 26931 3.85 - 4.38: 29959 4.38 - 4.90: 52543 Nonbonded interactions: 126607 Sorted by model distance: nonbonded pdb=" OD1 ASP A 127 " pdb=" OH TYR A 131 " model vdw 2.276 3.040 nonbonded pdb=" O ALA B 827 " pdb=" OH TYR B 832 " model vdw 2.327 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.333 3.040 nonbonded pdb=" OD1 ASP B 127 " pdb=" OH TYR B 131 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR A1238 " pdb=" OE1 GLN A1239 " model vdw 2.341 3.040 ... (remaining 126602 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 16595 Z= 0.269 Angle : 1.163 37.509 22580 Z= 0.576 Chirality : 0.067 0.693 2553 Planarity : 0.008 0.105 2889 Dihedral : 14.476 88.447 6200 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.75 (0.17), residues: 2031 helix: -2.90 (0.26), residues: 204 sheet: -0.24 (0.17), residues: 917 loop : -1.65 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 774 TYR 0.049 0.003 TYR B 306 PHE 0.030 0.003 PHE A1286 TRP 0.069 0.003 TRP A 837 HIS 0.007 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00570 (16567) covalent geometry : angle 1.13339 (22514) SS BOND : bond 0.01958 ( 18) SS BOND : angle 2.47744 ( 36) hydrogen bonds : bond 0.09654 ( 628) hydrogen bonds : angle 6.67293 ( 1758) link_NAG-ASN : bond 0.01558 ( 10) link_NAG-ASN : angle 6.78288 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.614 Fit side-chains REVERT: A 266 TRP cc_start: 0.6368 (m-10) cc_final: 0.6051 (m-90) REVERT: A 394 ASP cc_start: 0.7664 (p0) cc_final: 0.7412 (p0) REVERT: A 578 GLU cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: A 985 LEU cc_start: 0.9067 (mm) cc_final: 0.8834 (mm) REVERT: A 1015 MET cc_start: 0.7157 (pmm) cc_final: 0.6045 (tmm) REVERT: A 1065 TRP cc_start: 0.6221 (m100) cc_final: 0.5448 (m100) REVERT: A 1173 TRP cc_start: 0.6464 (m-90) cc_final: 0.5897 (m-90) REVERT: A 1297 MET cc_start: 0.7573 (pmm) cc_final: 0.7273 (pmm) REVERT: B 298 MET cc_start: 0.7018 (ppp) cc_final: 0.6725 (ppp) REVERT: B 306 TYR cc_start: 0.7928 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1115 time to fit residues: 32.3009 Evaluate side-chains 133 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 164 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 855 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.116616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.083309 restraints weight = 42302.268| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.91 r_work: 0.3334 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16595 Z= 0.131 Angle : 0.691 17.418 22580 Z= 0.338 Chirality : 0.046 0.524 2553 Planarity : 0.005 0.055 2889 Dihedral : 6.144 57.102 2402 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.50 % Allowed : 6.99 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 are not related in a simple way. whole: -1.18 (0.18), residues: 2031 helix: -1.64 (0.30), residues: 217 sheet: -0.10 (0.17), residues: 905 loop : -1.17 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 774 TYR 0.016 0.001 TYR B 491 PHE 0.037 0.001 PHE A1286 TRP 0.041 0.002 TRP A 837 HIS 0.002 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00288 (16567) covalent geometry : angle 0.65507 (22514) SS BOND : bond 0.00399 ( 18) SS BOND : angle 2.89738 ( 36) hydrogen bonds : bond 0.03368 ( 628) hydrogen bonds : angle 5.47374 ( 1758) link_NAG-ASN : bond 0.01464 ( 10) link_NAG-ASN : angle 5.22394 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6339 (m-10) cc_final: 0.5970 (m-90) REVERT: A 394 ASP cc_start: 0.8039 (p0) cc_final: 0.7735 (p0) REVERT: A 578 GLU cc_start: 0.8534 (tt0) cc_final: 0.7936 (tt0) REVERT: A 619 TRP cc_start: 0.6583 (p90) cc_final: 0.5854 (p-90) REVERT: A 837 TRP cc_start: 0.4251 (m-90) cc_final: 0.3806 (m-90) REVERT: A 985 LEU cc_start: 0.9075 (mm) cc_final: 0.8802 (mm) REVERT: A 1065 TRP cc_start: 0.6003 (m100) cc_final: 0.5320 (m100) REVERT: A 1142 TYR cc_start: 0.8966 (t80) cc_final: 0.8683 (t80) REVERT: B 157 MET cc_start: 0.8286 (ppp) cc_final: 0.7661 (ppp) REVERT: B 298 MET cc_start: 0.7332 (ppp) cc_final: 0.6932 (ppp) REVERT: B 387 PHE cc_start: 0.9145 (t80) cc_final: 0.8925 (t80) outliers start: 9 outliers final: 5 residues processed: 156 average time/residue: 0.1140 time to fit residues: 28.7393 Evaluate side-chains 140 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 965 GLN A1011 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 331 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 865 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.112412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.077965 restraints weight = 43169.216| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.93 r_work: 0.3216 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 16595 Z= 0.254 Angle : 0.735 17.583 22580 Z= 0.362 Chirality : 0.048 0.525 2553 Planarity : 0.004 0.056 2889 Dihedral : 6.053 55.490 2402 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 1.29 % Allowed : 9.17 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.97 (0.18), residues: 2031 helix: -0.65 (0.33), residues: 214 sheet: -0.18 (0.17), residues: 912 loop : -1.01 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 774 TYR 0.019 0.002 TYR A1309 PHE 0.038 0.002 PHE A1286 TRP 0.031 0.002 TRP A 837 HIS 0.005 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00574 (16567) covalent geometry : angle 0.70727 (22514) SS BOND : bond 0.00562 ( 18) SS BOND : angle 2.71782 ( 36) hydrogen bonds : bond 0.03540 ( 628) hydrogen bonds : angle 5.39214 ( 1758) link_NAG-ASN : bond 0.01119 ( 10) link_NAG-ASN : angle 4.67161 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9000 (pt) REVERT: A 154 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8198 (ptmt) REVERT: A 173 GLU cc_start: 0.8214 (tp30) cc_final: 0.7785 (mm-30) REVERT: A 266 TRP cc_start: 0.6482 (m-10) cc_final: 0.6119 (m-90) REVERT: A 394 ASP cc_start: 0.8207 (p0) cc_final: 0.7969 (p0) REVERT: A 421 MET cc_start: 0.8221 (mmm) cc_final: 0.7884 (mmm) REVERT: A 502 GLU cc_start: 0.7017 (pm20) cc_final: 0.6779 (pm20) REVERT: A 837 TRP cc_start: 0.4482 (m-90) cc_final: 0.4117 (m-90) REVERT: A 953 MET cc_start: 0.5735 (ptt) cc_final: 0.5489 (ptt) REVERT: A 985 LEU cc_start: 0.9122 (mm) cc_final: 0.8862 (mm) REVERT: A 1288 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7509 (mm110) REVERT: B 157 MET cc_start: 0.8507 (ppp) cc_final: 0.7848 (ppp) REVERT: B 387 PHE cc_start: 0.9183 (t80) cc_final: 0.8927 (t80) REVERT: B 501 MET cc_start: 0.8784 (ttp) cc_final: 0.8444 (ttm) REVERT: B 591 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 608 SER cc_start: 0.9255 (t) cc_final: 0.8825 (p) outliers start: 23 outliers final: 13 residues processed: 147 average time/residue: 0.1116 time to fit residues: 27.0747 Evaluate side-chains 136 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 591 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 ASN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.115124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081231 restraints weight = 42490.292| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.90 r_work: 0.3275 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16595 Z= 0.124 Angle : 0.629 16.990 22580 Z= 0.305 Chirality : 0.045 0.514 2553 Planarity : 0.004 0.057 2889 Dihedral : 5.645 55.683 2402 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 1.12 % Allowed : 10.63 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.73 (0.19), residues: 2031 helix: -0.18 (0.34), residues: 214 sheet: -0.09 (0.17), residues: 910 loop : -0.87 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 774 TYR 0.015 0.001 TYR B 491 PHE 0.040 0.001 PHE A1286 TRP 0.026 0.001 TRP A 837 HIS 0.002 0.000 HIS B 854 Details of bonding type rmsd covalent geometry : bond 0.00279 (16567) covalent geometry : angle 0.60490 (22514) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.62776 ( 36) hydrogen bonds : bond 0.02977 ( 628) hydrogen bonds : angle 5.11222 ( 1758) link_NAG-ASN : bond 0.01055 ( 10) link_NAG-ASN : angle 4.47421 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6449 (m-10) cc_final: 0.6189 (m-90) REVERT: A 421 MET cc_start: 0.8242 (mmm) cc_final: 0.7895 (mmm) REVERT: A 619 TRP cc_start: 0.7224 (p90) cc_final: 0.6172 (p-90) REVERT: A 837 TRP cc_start: 0.4362 (m-90) cc_final: 0.3874 (m-90) REVERT: A 985 LEU cc_start: 0.9078 (mm) cc_final: 0.8797 (mm) REVERT: A 1065 TRP cc_start: 0.5915 (m100) cc_final: 0.5238 (m100) REVERT: A 1173 TRP cc_start: 0.6883 (m-90) cc_final: 0.6668 (m-90) REVERT: A 1288 GLN cc_start: 0.7793 (mp-120) cc_final: 0.7561 (mm110) REVERT: B 157 MET cc_start: 0.8390 (ppp) cc_final: 0.7802 (ppp) REVERT: B 387 PHE cc_start: 0.9195 (t80) cc_final: 0.8927 (t80) REVERT: B 501 MET cc_start: 0.8660 (ttp) cc_final: 0.8297 (ttm) outliers start: 20 outliers final: 19 residues processed: 156 average time/residue: 0.1144 time to fit residues: 29.1678 Evaluate side-chains 141 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 106 optimal weight: 30.0000 chunk 180 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.113913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.079806 restraints weight = 42782.892| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.93 r_work: 0.3247 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16595 Z= 0.171 Angle : 0.638 16.977 22580 Z= 0.311 Chirality : 0.045 0.503 2553 Planarity : 0.004 0.056 2889 Dihedral : 5.610 55.300 2402 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 2.29 % Allowed : 11.52 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.67 (0.19), residues: 2031 helix: -0.00 (0.34), residues: 220 sheet: -0.08 (0.17), residues: 908 loop : -0.82 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.016 0.001 TYR B 491 PHE 0.012 0.001 PHE B 209 TRP 0.022 0.001 TRP A 837 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00391 (16567) covalent geometry : angle 0.61624 (22514) SS BOND : bond 0.00399 ( 18) SS BOND : angle 1.46604 ( 36) hydrogen bonds : bond 0.03034 ( 628) hydrogen bonds : angle 5.07771 ( 1758) link_NAG-ASN : bond 0.00985 ( 10) link_NAG-ASN : angle 4.33257 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6453 (m-10) cc_final: 0.6214 (m-90) REVERT: A 985 LEU cc_start: 0.9094 (mm) cc_final: 0.8822 (mm) REVERT: A 1065 TRP cc_start: 0.5912 (m100) cc_final: 0.5255 (m100) REVERT: B 157 MET cc_start: 0.8473 (ppp) cc_final: 0.7858 (ppp) REVERT: B 387 PHE cc_start: 0.9198 (t80) cc_final: 0.8931 (t80) REVERT: B 501 MET cc_start: 0.8684 (ttp) cc_final: 0.8235 (ttm) REVERT: B 591 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 608 SER cc_start: 0.9164 (t) cc_final: 0.8736 (p) REVERT: B 831 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (mp0) outliers start: 41 outliers final: 32 residues processed: 160 average time/residue: 0.1033 time to fit residues: 27.7000 Evaluate side-chains 154 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 831 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 GLN A1288 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.112911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078581 restraints weight = 42847.936| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.90 r_work: 0.3222 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16595 Z= 0.203 Angle : 0.661 16.930 22580 Z= 0.324 Chirality : 0.045 0.491 2553 Planarity : 0.004 0.060 2889 Dihedral : 5.766 55.095 2402 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 2.46 % Allowed : 12.81 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.63 (0.19), residues: 2031 helix: 0.15 (0.35), residues: 220 sheet: -0.10 (0.17), residues: 913 loop : -0.78 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.021 0.001 TYR B 492 PHE 0.042 0.002 PHE A1286 TRP 0.023 0.001 TRP A1036 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00462 (16567) covalent geometry : angle 0.64088 (22514) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.49343 ( 36) hydrogen bonds : bond 0.03117 ( 628) hydrogen bonds : angle 5.12374 ( 1758) link_NAG-ASN : bond 0.00937 ( 10) link_NAG-ASN : angle 4.19199 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 973 GLN cc_start: 0.7762 (pm20) cc_final: 0.7470 (pm20) REVERT: A 985 LEU cc_start: 0.9142 (mm) cc_final: 0.8875 (mm) REVERT: A 1065 TRP cc_start: 0.5890 (m100) cc_final: 0.5184 (m100) REVERT: A 1288 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7640 (mm110) REVERT: B 157 MET cc_start: 0.8518 (ppp) cc_final: 0.7891 (ppp) REVERT: B 387 PHE cc_start: 0.9184 (t80) cc_final: 0.8932 (t80) REVERT: B 501 MET cc_start: 0.8702 (ttp) cc_final: 0.8253 (ttm) REVERT: B 608 SER cc_start: 0.9210 (t) cc_final: 0.8793 (p) REVERT: B 831 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8607 (mp0) outliers start: 44 outliers final: 34 residues processed: 161 average time/residue: 0.1002 time to fit residues: 26.8309 Evaluate side-chains 154 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 831 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.114340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080675 restraints weight = 42253.637| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.86 r_work: 0.3274 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16595 Z= 0.119 Angle : 0.630 16.499 22580 Z= 0.305 Chirality : 0.045 0.515 2553 Planarity : 0.004 0.061 2889 Dihedral : 5.521 55.632 2402 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 2.29 % Allowed : 13.59 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.46 (0.19), residues: 2031 helix: 0.30 (0.36), residues: 220 sheet: 0.05 (0.17), residues: 902 loop : -0.73 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 774 TYR 0.023 0.001 TYR B 492 PHE 0.035 0.001 PHE A1286 TRP 0.035 0.002 TRP A1173 HIS 0.003 0.000 HIS B 854 Details of bonding type rmsd covalent geometry : bond 0.00273 (16567) covalent geometry : angle 0.60896 (22514) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.38106 ( 36) hydrogen bonds : bond 0.02858 ( 628) hydrogen bonds : angle 4.95293 ( 1758) link_NAG-ASN : bond 0.00962 ( 10) link_NAG-ASN : angle 4.23908 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6413 (m-90) cc_final: 0.5663 (m-10) REVERT: A 985 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 1065 TRP cc_start: 0.5882 (m100) cc_final: 0.5213 (m100) REVERT: A 1173 TRP cc_start: 0.7115 (m-90) cc_final: 0.6658 (m-90) REVERT: A 1288 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7764 (mm110) REVERT: B 157 MET cc_start: 0.8407 (ppp) cc_final: 0.7812 (ppp) REVERT: B 387 PHE cc_start: 0.9185 (t80) cc_final: 0.8953 (t80) REVERT: B 501 MET cc_start: 0.8604 (ttp) cc_final: 0.8174 (ttm) REVERT: B 608 SER cc_start: 0.9084 (t) cc_final: 0.8666 (p) outliers start: 41 outliers final: 31 residues processed: 157 average time/residue: 0.1005 time to fit residues: 26.1549 Evaluate side-chains 148 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 45 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** 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 = 0.4024 r_free = 0.4024 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079180 restraints weight = 42557.133| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.86 r_work: 0.3229 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16595 Z= 0.192 Angle : 0.675 17.044 22580 Z= 0.328 Chirality : 0.045 0.476 2553 Planarity : 0.004 0.060 2889 Dihedral : 5.679 55.074 2402 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 2.40 % Allowed : 14.09 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.46 (0.19), residues: 2031 helix: 0.35 (0.36), residues: 220 sheet: 0.02 (0.17), residues: 902 loop : -0.70 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.022 0.001 TYR A1142 PHE 0.032 0.001 PHE A1286 TRP 0.026 0.002 TRP A1036 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00445 (16567) covalent geometry : angle 0.65507 (22514) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.46011 ( 36) hydrogen bonds : bond 0.03091 ( 628) hydrogen bonds : angle 5.00973 ( 1758) link_NAG-ASN : bond 0.00960 ( 10) link_NAG-ASN : angle 4.22599 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 735 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 985 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 1065 TRP cc_start: 0.5867 (m100) cc_final: 0.5178 (m100) REVERT: A 1142 TYR cc_start: 0.8886 (t80) cc_final: 0.8605 (t80) REVERT: A 1173 TRP cc_start: 0.7260 (m-90) cc_final: 0.6718 (m-90) REVERT: A 1288 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7748 (mm110) REVERT: B 157 MET cc_start: 0.8477 (ppp) cc_final: 0.7886 (ppp) REVERT: B 387 PHE cc_start: 0.9208 (t80) cc_final: 0.8992 (t80) REVERT: B 501 MET cc_start: 0.8631 (ttp) cc_final: 0.8194 (ttm) REVERT: B 608 SER cc_start: 0.9176 (t) cc_final: 0.8771 (p) outliers start: 43 outliers final: 36 residues processed: 154 average time/residue: 0.1028 time to fit residues: 26.3864 Evaluate side-chains 155 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 0 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.113846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079941 restraints weight = 42651.203| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.90 r_work: 0.3247 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16595 Z= 0.149 Angle : 0.664 16.996 22580 Z= 0.319 Chirality : 0.045 0.504 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.614 55.213 2402 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 2.13 % Allowed : 14.77 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.45 (0.19), residues: 2031 helix: 0.32 (0.35), residues: 222 sheet: 0.04 (0.17), residues: 900 loop : -0.70 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.021 0.001 TYR A1142 PHE 0.032 0.001 PHE A1286 TRP 0.026 0.002 TRP A1036 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00346 (16567) covalent geometry : angle 0.64462 (22514) SS BOND : bond 0.00394 ( 18) SS BOND : angle 1.39128 ( 36) hydrogen bonds : bond 0.02958 ( 628) hydrogen bonds : angle 4.95170 ( 1758) link_NAG-ASN : bond 0.00970 ( 10) link_NAG-ASN : angle 4.25270 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 1065 TRP cc_start: 0.5857 (m100) cc_final: 0.5176 (m100) REVERT: A 1142 TYR cc_start: 0.8883 (t80) cc_final: 0.8592 (t80) REVERT: A 1173 TRP cc_start: 0.7223 (m-90) cc_final: 0.6690 (m-90) REVERT: A 1288 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7761 (mm110) REVERT: A 1298 TYR cc_start: 0.8010 (m-80) cc_final: 0.7587 (m-80) REVERT: B 157 MET cc_start: 0.8438 (ppp) cc_final: 0.7854 (ppp) REVERT: B 387 PHE cc_start: 0.9211 (t80) cc_final: 0.9001 (t80) REVERT: B 501 MET cc_start: 0.8590 (ttp) cc_final: 0.8145 (ttm) REVERT: B 608 SER cc_start: 0.9120 (t) cc_final: 0.8711 (p) outliers start: 38 outliers final: 36 residues processed: 153 average time/residue: 0.1049 time to fit residues: 26.4654 Evaluate side-chains 155 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 0.2980 chunk 190 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.077872 restraints weight = 43036.804| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.89 r_work: 0.3213 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 16595 Z= 0.252 Angle : 0.720 17.370 22580 Z= 0.351 Chirality : 0.047 0.491 2553 Planarity : 0.004 0.059 2889 Dihedral : 5.980 54.846 2402 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 2.40 % Allowed : 14.88 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.60 (0.19), residues: 2031 helix: 0.26 (0.35), residues: 220 sheet: -0.10 (0.17), residues: 908 loop : -0.76 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.027 0.002 TYR B 68 PHE 0.032 0.002 PHE A1286 TRP 0.026 0.002 TRP A1036 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00582 (16567) covalent geometry : angle 0.70090 (22514) SS BOND : bond 0.00521 ( 18) SS BOND : angle 1.55631 ( 36) hydrogen bonds : bond 0.03291 ( 628) hydrogen bonds : angle 5.17364 ( 1758) link_NAG-ASN : bond 0.00972 ( 10) link_NAG-ASN : angle 4.25950 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 985 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 1065 TRP cc_start: 0.5854 (m100) cc_final: 0.5194 (m100) REVERT: A 1142 TYR cc_start: 0.8851 (t80) cc_final: 0.8570 (t80) REVERT: A 1173 TRP cc_start: 0.7302 (m-90) cc_final: 0.6647 (m-90) REVERT: A 1288 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7800 (mm110) REVERT: B 157 MET cc_start: 0.8586 (ppp) cc_final: 0.8343 (pmm) REVERT: B 387 PHE cc_start: 0.9157 (t80) cc_final: 0.8956 (t80) REVERT: B 501 MET cc_start: 0.8809 (ttp) cc_final: 0.8377 (ttm) REVERT: B 608 SER cc_start: 0.9240 (t) cc_final: 0.8829 (p) outliers start: 43 outliers final: 37 residues processed: 158 average time/residue: 0.1065 time to fit residues: 27.7630 Evaluate side-chains 156 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 0.2980 chunk 177 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 195 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 HIS ** 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 = 0.4037 r_free = 0.4037 target = 0.114231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080374 restraints weight = 42757.857| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.90 r_work: 0.3257 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16595 Z= 0.126 Angle : 0.678 16.816 22580 Z= 0.326 Chirality : 0.046 0.498 2553 Planarity : 0.004 0.055 2889 Dihedral : 5.687 55.724 2402 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.90 % Allowed : 15.49 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -0.48 (0.19), residues: 2031 helix: 0.20 (0.35), residues: 222 sheet: 0.04 (0.17), residues: 901 loop : -0.71 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 774 TYR 0.020 0.001 TYR A1142 PHE 0.031 0.001 PHE A1286 TRP 0.026 0.002 TRP A1036 HIS 0.002 0.000 HIS B 854 Details of bonding type rmsd covalent geometry : bond 0.00296 (16567) covalent geometry : angle 0.65873 (22514) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.36546 ( 36) hydrogen bonds : bond 0.02935 ( 628) hydrogen bonds : angle 5.00314 ( 1758) link_NAG-ASN : bond 0.01001 ( 10) link_NAG-ASN : angle 4.21349 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.10 seconds wall clock time: 81 minutes 24.76 seconds (4884.76 seconds total)