Starting phenix.real_space_refine on Sat Sep 12 14:41:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q62_13850/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q62_13850/09_2026/7q62_13850.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 chiralities: 5 Time building chain proxies: 3.00, per 1000 atoms: 0.19 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: 1.08 Conformation dependent library (CDL) restraints added in 611.2 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: 0.50 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: 3.60 Time building geometry restraints manager: 1.40 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: 8939 17.69 - 35.38: 717 35.38 - 53.07: 129 53.07 - 70.76: 37 70.76 - 88.45: 34 Dihedral angle restraints: 9856 sinusoidal: 3916 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 9853 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: 13.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.220 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 14.536 88.447 5990 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/Z covalent geometry : bond 0.00570 / 0.27 (16567) covalent geometry : angle 1.13339 / 0.57 (22514) SS BOND : bond 0.01958 / 1.01 ( 18) SS BOND : angle 2.47744 / 1.51 ( 36) hydrogen bonds : bond 0.09654 / 6.69 ( 628) hydrogen bonds : angle 6.67293 / 4.64 ( 1758) link_NAG-ASN : bond 0.01558 / 0.78 ( 10) link_NAG-ASN : angle 6.78288 / 4.37 ( 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 : 0.578 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: 0.1013 time to fit residues: 29.7163 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 : 0.608 ------------------------------------------------------------------------------- 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... A 506 HIS B 22 ASN B 164 ASN ** 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 = 0.4073 r_free = 0.4073 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083206 restraints weight = 42266.932| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.91 r_work: 0.3333 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16595 Z= 0.133 Angle : 0.707 17.835 22580 Z= 0.345 Chirality : 0.047 0.500 2553 Planarity : 0.005 0.057 2889 Dihedral : 5.245 31.983 2192 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 0.56 % Allowed : 6.94 % 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: -1.21 (0.18), residues: 2031 helix: -1.74 (0.29), residues: 217 sheet: -0.09 (0.17), residues: 904 loop : -1.21 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 774 TYR 0.019 0.001 TYR B 435 PHE 0.039 0.001 PHE A1286 TRP 0.040 0.002 TRP A 837 HIS 0.002 0.000 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16567) covalent geometry : angle 0.67132 / 0.33 (22514) SS BOND : bond 0.00477 / 0.29 ( 18) SS BOND : angle 2.95073 / 1.51 ( 36) hydrogen bonds : bond 0.03513 / 2.37 ( 628) hydrogen bonds : angle 5.51810 / 3.85 ( 1758) link_NAG-ASN : bond 0.01506 / 0.78 ( 10) link_NAG-ASN : angle 5.26046 / 3.36 ( 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 162 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6289 (m-10) cc_final: 0.5964 (m-90) REVERT: A 394 ASP cc_start: 0.8046 (p0) cc_final: 0.7745 (p0) REVERT: A 578 GLU cc_start: 0.8543 (tt0) cc_final: 0.7945 (tt0) REVERT: A 619 TRP cc_start: 0.6571 (p90) cc_final: 0.5847 (p-90) REVERT: A 766 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: A 837 TRP cc_start: 0.4269 (m-90) cc_final: 0.3843 (m-90) REVERT: A 985 LEU cc_start: 0.9062 (mm) cc_final: 0.8784 (mm) REVERT: A 1065 TRP cc_start: 0.6004 (m100) cc_final: 0.5335 (m100) REVERT: A 1142 TYR cc_start: 0.8953 (t80) cc_final: 0.8670 (t80) REVERT: B 157 MET cc_start: 0.8264 (ppp) cc_final: 0.7664 (ppp) REVERT: B 298 MET cc_start: 0.7319 (ppp) cc_final: 0.6915 (ppp) REVERT: B 551 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7996 (tp-100) outliers start: 10 outliers final: 5 residues processed: 157 average time/residue: 0.0968 time to fit residues: 24.6218 Evaluate side-chains 143 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 LEU Chi-restraints excluded: chain B residue 398 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: 5.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 144 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.5287 > 50:) chunk 152 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 117 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** 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 855 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078612 restraints weight = 43317.042| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.99 r_work: 0.3226 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16595 Z= 0.247 Angle : 0.720 17.216 22580 Z= 0.354 Chirality : 0.047 0.490 2553 Planarity : 0.004 0.058 2889 Dihedral : 5.167 28.556 2192 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 1.17 % Allowed : 9.17 % Favored : 89.65 % 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: -0.96 (0.18), residues: 2031 helix: -0.70 (0.33), residues: 213 sheet: -0.16 (0.17), residues: 912 loop : -1.01 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 774 TYR 0.018 0.001 TYR A1309 PHE 0.040 0.002 PHE A1286 TRP 0.033 0.002 TRP A1173 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (16567) covalent geometry : angle 0.69265 / 0.35 (22514) SS BOND : bond 0.00900 / 0.50 ( 18) SS BOND : angle 2.81971 / 1.40 ( 36) hydrogen bonds : bond 0.03483 / 2.34 ( 628) hydrogen bonds : angle 5.36346 / 3.72 ( 1758) link_NAG-ASN : bond 0.01105 / 0.57 ( 10) link_NAG-ASN : angle 4.58976 / 2.81 ( 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 150 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8958 (pt) REVERT: A 266 TRP cc_start: 0.6441 (m-10) cc_final: 0.6086 (m-90) REVERT: A 394 ASP cc_start: 0.8180 (p0) cc_final: 0.7922 (p0) REVERT: A 837 TRP cc_start: 0.4486 (m-90) cc_final: 0.4120 (m-90) REVERT: A 953 MET cc_start: 0.5673 (ptt) cc_final: 0.5425 (ptt) REVERT: A 985 LEU cc_start: 0.9119 (mm) cc_final: 0.8861 (mm) REVERT: A 1288 GLN cc_start: 0.7761 (mp-120) cc_final: 0.7524 (mm110) REVERT: B 157 MET cc_start: 0.8508 (ppp) cc_final: 0.7861 (ppp) REVERT: B 387 PHE cc_start: 0.9170 (t80) cc_final: 0.8919 (t80) REVERT: B 501 MET cc_start: 0.8743 (ttp) cc_final: 0.8435 (ttm) REVERT: B 608 SER cc_start: 0.9231 (t) cc_final: 0.8788 (p) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.1051 time to fit residues: 25.2112 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 : 0.619 ------------------------------------------------------------------------------- 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 154 LYS 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 A residue 1112 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1133 ASN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.114132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079998 restraints weight = 42719.121| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.94 r_work: 0.3251 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16595 Z= 0.167 Angle : 0.647 16.887 22580 Z= 0.316 Chirality : 0.045 0.494 2553 Planarity : 0.004 0.057 2889 Dihedral : 4.914 26.552 2192 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 1.51 % Allowed : 11.07 % Favored : 87.42 % 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: -0.81 (0.19), residues: 2031 helix: -0.30 (0.34), residues: 220 sheet: -0.13 (0.17), residues: 908 loop : -0.92 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1274 TYR 0.014 0.001 TYR B 491 PHE 0.040 0.001 PHE A1286 TRP 0.026 0.002 TRP A 837 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16567) covalent geometry : angle 0.62435 / 0.31 (22514) SS BOND : bond 0.00394 / 0.26 ( 18) SS BOND : angle 1.63652 / 0.94 ( 36) hydrogen bonds : bond 0.03108 / 2.09 ( 628) hydrogen bonds : angle 5.17441 / 3.60 ( 1758) link_NAG-ASN : bond 0.01010 / 0.52 ( 10) link_NAG-ASN : angle 4.36211 / 2.60 ( 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 158 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6484 (m-10) cc_final: 0.6207 (m-90) REVERT: A 298 MET cc_start: 0.8021 (mpp) cc_final: 0.7806 (ptp) REVERT: A 571 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: A 619 TRP cc_start: 0.7230 (p90) cc_final: 0.6162 (p-90) REVERT: A 837 TRP cc_start: 0.4419 (m-90) cc_final: 0.3895 (m-90) REVERT: A 985 LEU cc_start: 0.9072 (mm) cc_final: 0.8797 (mm) REVERT: A 1065 TRP cc_start: 0.5896 (m100) cc_final: 0.5230 (m100) REVERT: A 1173 TRP cc_start: 0.7026 (m-90) cc_final: 0.6807 (m-90) REVERT: A 1288 GLN cc_start: 0.7760 (mp-120) cc_final: 0.7472 (mm110) REVERT: B 157 MET cc_start: 0.8454 (ppp) cc_final: 0.7841 (ppp) REVERT: B 173 GLU cc_start: 0.7884 (tp30) cc_final: 0.7662 (tp30) REVERT: B 387 PHE cc_start: 0.9194 (t80) cc_final: 0.8930 (t80) REVERT: B 501 MET cc_start: 0.8704 (ttp) cc_final: 0.8326 (ttm) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.0992 time to fit residues: 25.5912 Evaluate side-chains 145 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 154 LYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 571 GLN 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 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 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 447 SER 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: 10.0000 chunk 180 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1271 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 = 0.4063 r_free = 0.4063 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081633 restraints weight = 42604.777| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.95 r_work: 0.3285 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16595 Z= 0.117 Angle : 0.610 16.489 22580 Z= 0.296 Chirality : 0.044 0.484 2553 Planarity : 0.004 0.059 2889 Dihedral : 4.636 24.814 2192 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 2.01 % Allowed : 12.14 % Favored : 85.85 % 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: -0.57 (0.19), residues: 2031 helix: -0.02 (0.34), residues: 222 sheet: -0.00 (0.17), residues: 907 loop : -0.76 (0.21), residues: 902 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 0.016 0.001 PHE B 552 TRP 0.026 0.001 TRP A 837 HIS 0.002 0.000 HIS B 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16567) covalent geometry : angle 0.58857 / 0.29 (22514) SS BOND : bond 0.00345 / 0.20 ( 18) SS BOND : angle 1.42592 / 0.83 ( 36) hydrogen bonds : bond 0.02865 / 1.94 ( 628) hydrogen bonds : angle 4.96870 / 3.47 ( 1758) link_NAG-ASN : bond 0.01006 / 0.51 ( 10) link_NAG-ASN : angle 4.19008 / 2.48 ( 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 172 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6455 (m-10) cc_final: 0.6234 (m-90) REVERT: A 735 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6935 (mm-30) REVERT: A 985 LEU cc_start: 0.9075 (mm) cc_final: 0.8801 (mm) REVERT: A 1065 TRP cc_start: 0.5912 (m100) cc_final: 0.5246 (m100) REVERT: A 1298 TYR cc_start: 0.7953 (m-80) cc_final: 0.7495 (m-80) REVERT: B 157 MET cc_start: 0.8425 (ppp) cc_final: 0.7833 (ppp) REVERT: B 298 MET cc_start: 0.7273 (ppp) cc_final: 0.6441 (ppp) REVERT: B 387 PHE cc_start: 0.9205 (t80) cc_final: 0.8933 (t80) REVERT: B 501 MET cc_start: 0.8584 (ttp) cc_final: 0.8147 (ttm) REVERT: B 551 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7993 (tp-100) REVERT: B 591 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8228 (tt) outliers start: 36 outliers final: 28 residues processed: 164 average time/residue: 0.0956 time to fit residues: 26.3575 Evaluate side-chains 152 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 151 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 342 MET 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 159 optimal weight: 0.0070 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.113464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079109 restraints weight = 42640.369| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.95 r_work: 0.3242 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2183 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= 0.181 Angle : 0.650 16.644 22580 Z= 0.316 Chirality : 0.045 0.456 2553 Planarity : 0.004 0.059 2889 Dihedral : 4.713 24.915 2192 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 2.74 % Allowed : 12.30 % Favored : 84.96 % 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: -0.55 (0.19), residues: 2031 helix: 0.19 (0.35), residues: 220 sheet: -0.03 (0.17), residues: 908 loop : -0.74 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.016 0.001 TYR B 491 PHE 0.012 0.001 PHE B 209 TRP 0.023 0.001 TRP A1036 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16567) covalent geometry : angle 0.63122 / 0.31 (22514) SS BOND : bond 0.00447 / 0.29 ( 18) SS BOND : angle 1.46847 / 0.89 ( 36) hydrogen bonds : bond 0.03025 / 2.03 ( 628) hydrogen bonds : angle 5.00829 / 3.49 ( 1758) link_NAG-ASN : bond 0.00957 / 0.49 ( 10) link_NAG-ASN : angle 4.08871 / 2.39 ( 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 171 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6435 (m-10) cc_final: 0.6226 (m-90) REVERT: A 973 GLN cc_start: 0.7765 (pm20) cc_final: 0.7504 (pm20) REVERT: A 985 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8843 (mm) REVERT: A 1065 TRP cc_start: 0.5890 (m100) cc_final: 0.5215 (m100) REVERT: B 157 MET cc_start: 0.8487 (ppp) cc_final: 0.7874 (ppp) REVERT: B 387 PHE cc_start: 0.9202 (t80) cc_final: 0.8937 (t80) REVERT: B 501 MET cc_start: 0.8675 (ttp) cc_final: 0.8280 (ttm) REVERT: B 551 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7974 (tp-100) REVERT: B 591 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 608 SER cc_start: 0.9181 (t) cc_final: 0.8749 (p) REVERT: B 619 TRP cc_start: 0.7052 (p90) cc_final: 0.6796 (p90) outliers start: 49 outliers final: 33 residues processed: 163 average time/residue: 0.1014 time to fit residues: 27.3285 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 : 0.646 ------------------------------------------------------------------------------- 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 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 619 TRP 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 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 594 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4041 r_free = 0.4041 target = 0.114211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080256 restraints weight = 42388.087| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.90 r_work: 0.3265 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16595 Z= 0.138 Angle : 0.637 16.516 22580 Z= 0.309 Chirality : 0.045 0.474 2553 Planarity : 0.004 0.058 2889 Dihedral : 4.616 24.275 2192 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 2.24 % Allowed : 13.48 % Favored : 84.28 % 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: -0.47 (0.19), residues: 2031 helix: 0.29 (0.35), residues: 220 sheet: 0.02 (0.17), residues: 908 loop : -0.70 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.017 0.001 TYR A1142 PHE 0.015 0.001 PHE B 887 TRP 0.031 0.001 TRP A1173 HIS 0.002 0.000 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16567) covalent geometry : angle 0.61703 / 0.30 (22514) SS BOND : bond 0.00408 / 0.25 ( 18) SS BOND : angle 1.39840 / 0.82 ( 36) hydrogen bonds : bond 0.02920 / 1.95 ( 628) hydrogen bonds : angle 4.93327 / 3.43 ( 1758) link_NAG-ASN : bond 0.00949 / 0.49 ( 10) link_NAG-ASN : angle 4.11844 / 2.41 ( 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 161 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8443 (tp30) cc_final: 0.8233 (tm-30) REVERT: A 266 TRP cc_start: 0.6466 (m-10) cc_final: 0.6257 (m-90) REVERT: A 985 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 1065 TRP cc_start: 0.5875 (m100) cc_final: 0.5188 (m100) REVERT: A 1173 TRP cc_start: 0.7164 (m-90) cc_final: 0.6682 (m-90) REVERT: B 157 MET cc_start: 0.8458 (ppp) cc_final: 0.7866 (ppp) REVERT: B 387 PHE cc_start: 0.9200 (t80) cc_final: 0.8940 (t80) REVERT: B 501 MET cc_start: 0.8650 (ttp) cc_final: 0.8243 (ttm) REVERT: B 591 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 608 SER cc_start: 0.9120 (t) cc_final: 0.8698 (p) outliers start: 40 outliers final: 33 residues processed: 154 average time/residue: 0.0945 time to fit residues: 24.6383 Evaluate side-chains 150 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 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 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 591 LEU Chi-restraints excluded: chain B residue 594 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: 2.9990 chunk 39 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 76 optimal weight: 0.0060 chunk 199 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.115981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081958 restraints weight = 42567.738| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.98 r_work: 0.3293 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2313 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= 0.113 Angle : 0.635 16.631 22580 Z= 0.304 Chirality : 0.045 0.471 2553 Planarity : 0.004 0.058 2889 Dihedral : 4.449 22.998 2192 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 2.13 % Allowed : 13.81 % Favored : 84.06 % 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: -0.38 (0.19), residues: 2031 helix: 0.35 (0.35), residues: 222 sheet: 0.09 (0.17), residues: 906 loop : -0.66 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 774 TYR 0.016 0.001 TYR B 491 PHE 0.013 0.001 PHE B 887 TRP 0.027 0.001 TRP A1036 HIS 0.002 0.000 HIS B 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (16567) covalent geometry : angle 0.61563 / 0.30 (22514) SS BOND : bond 0.00341 / 0.19 ( 18) SS BOND : angle 1.37619 / 0.79 ( 36) hydrogen bonds : bond 0.02803 / 1.88 ( 628) hydrogen bonds : angle 4.79405 / 3.34 ( 1758) link_NAG-ASN : bond 0.00981 / 0.50 ( 10) link_NAG-ASN : angle 4.11792 / 2.41 ( 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 170 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6474 (m-10) cc_final: 0.6247 (m-90) REVERT: A 985 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 1065 TRP cc_start: 0.5844 (m100) cc_final: 0.5187 (m100) REVERT: A 1142 TYR cc_start: 0.8910 (t80) cc_final: 0.8673 (t80) REVERT: A 1173 TRP cc_start: 0.7140 (m-90) cc_final: 0.6661 (m-90) REVERT: B 157 MET cc_start: 0.8431 (ppp) cc_final: 0.7826 (ppp) REVERT: B 387 PHE cc_start: 0.9205 (t80) cc_final: 0.8966 (t80) REVERT: B 501 MET cc_start: 0.8609 (ttp) cc_final: 0.8206 (ttm) REVERT: B 591 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 608 SER cc_start: 0.9067 (t) cc_final: 0.8638 (p) REVERT: B 766 MET cc_start: 0.8520 (ppp) cc_final: 0.8301 (tmm) outliers start: 38 outliers final: 33 residues processed: 161 average time/residue: 0.0957 time to fit residues: 25.5596 Evaluate side-chains 153 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain B residue 56 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 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 591 LEU 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: 7.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 187 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4056 r_free = 0.4056 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081276 restraints weight = 42387.505| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.90 r_work: 0.3287 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16595 Z= 0.127 Angle : 0.643 16.497 22580 Z= 0.309 Chirality : 0.045 0.453 2553 Planarity : 0.004 0.057 2889 Dihedral : 4.418 22.853 2192 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 2.24 % Allowed : 14.26 % 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: -0.31 (0.19), residues: 2031 helix: 0.41 (0.36), residues: 220 sheet: 0.15 (0.17), residues: 900 loop : -0.63 (0.22), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.017 0.001 TYR A1142 PHE 0.031 0.001 PHE A1286 TRP 0.026 0.001 TRP A1036 HIS 0.002 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16567) covalent geometry : angle 0.62430 / 0.30 (22514) SS BOND : bond 0.00371 / 0.22 ( 18) SS BOND : angle 1.39130 / 0.80 ( 36) hydrogen bonds : bond 0.02830 / 1.89 ( 628) hydrogen bonds : angle 4.76591 / 3.32 ( 1758) link_NAG-ASN : bond 0.00947 / 0.48 ( 10) link_NAG-ASN : angle 4.07319 / 2.38 ( 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 161 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 266 TRP cc_start: 0.6450 (m-10) cc_final: 0.6243 (m-90) REVERT: A 735 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7067 (mm-30) REVERT: A 985 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8832 (mm) REVERT: A 1065 TRP cc_start: 0.5854 (m100) cc_final: 0.5177 (m100) REVERT: A 1142 TYR cc_start: 0.8894 (t80) cc_final: 0.8672 (t80) REVERT: A 1173 TRP cc_start: 0.7092 (m-90) cc_final: 0.6588 (m-90) REVERT: B 157 MET cc_start: 0.8399 (ppp) cc_final: 0.7817 (ppp) REVERT: B 387 PHE cc_start: 0.9213 (t80) cc_final: 0.8989 (t80) REVERT: B 501 MET cc_start: 0.8638 (ttp) cc_final: 0.8243 (ttm) REVERT: B 591 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8171 (tt) REVERT: B 608 SER cc_start: 0.9081 (t) cc_final: 0.8677 (p) outliers start: 40 outliers final: 34 residues processed: 152 average time/residue: 0.0972 time to fit residues: 24.5789 Evaluate side-chains 153 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 591 LEU 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: 4.9990 chunk 190 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4031 r_free = 0.4031 target = 0.113622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079253 restraints weight = 42737.741| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.90 r_work: 0.3236 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 16595 Z= 0.203 Angle : 0.693 16.961 22580 Z= 0.334 Chirality : 0.046 0.460 2553 Planarity : 0.004 0.056 2889 Dihedral : 4.627 24.906 2192 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 2.13 % Allowed : 14.26 % Favored : 83.61 % 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: -0.39 (0.19), residues: 2031 helix: 0.40 (0.36), residues: 221 sheet: 0.07 (0.17), residues: 905 loop : -0.66 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.019 0.001 TYR A1142 PHE 0.025 0.001 PHE A1286 TRP 0.029 0.002 TRP A1036 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (16567) covalent geometry : angle 0.67557 / 0.33 (22514) SS BOND : bond 0.00463 / 0.30 ( 18) SS BOND : angle 1.46210 / 0.89 ( 36) hydrogen bonds : bond 0.03078 / 2.06 ( 628) hydrogen bonds : angle 4.92144 / 3.42 ( 1758) link_NAG-ASN : bond 0.00941 / 0.48 ( 10) link_NAG-ASN : angle 4.10088 / 2.39 ( 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 156 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.8531 (ppp) cc_final: 0.7621 (ppp) REVERT: A 190 GLU cc_start: 0.8559 (tp30) cc_final: 0.8356 (tm-30) REVERT: A 266 TRP cc_start: 0.6494 (m-10) cc_final: 0.6294 (m-90) REVERT: A 985 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 1065 TRP cc_start: 0.5807 (m100) cc_final: 0.5132 (m100) REVERT: A 1142 TYR cc_start: 0.8890 (t80) cc_final: 0.8664 (t80) REVERT: A 1173 TRP cc_start: 0.7233 (m-90) cc_final: 0.6617 (m-90) REVERT: B 157 MET cc_start: 0.8511 (ppp) cc_final: 0.7913 (ppp) REVERT: B 387 PHE cc_start: 0.9201 (t80) cc_final: 0.8986 (t80) REVERT: B 501 MET cc_start: 0.8783 (ttp) cc_final: 0.8379 (ttm) REVERT: B 591 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 608 SER cc_start: 0.9178 (t) cc_final: 0.8778 (p) outliers start: 38 outliers final: 33 residues processed: 150 average time/residue: 0.0956 time to fit residues: 24.0696 Evaluate side-chains 150 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 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 398 LEU Chi-restraints excluded: chain B residue 447 SER 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 591 LEU 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: 0.5980 chunk 177 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 185 optimal weight: 0.0370 chunk 127 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A1137 GLN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.115660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082105 restraints weight = 42788.451| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.91 r_work: 0.3297 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2491 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= 0.115 Angle : 0.656 16.469 22580 Z= 0.315 Chirality : 0.046 0.467 2553 Planarity : 0.004 0.056 2889 Dihedral : 4.453 23.132 2192 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.90 % Allowed : 14.65 % Favored : 83.45 % 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: -0.27 (0.19), residues: 2031 helix: 0.42 (0.36), residues: 220 sheet: 0.18 (0.17), residues: 902 loop : -0.60 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.016 0.001 TYR A1142 PHE 0.030 0.001 PHE A1286 TRP 0.029 0.001 TRP A1036 HIS 0.002 0.000 HIS B 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (16567) covalent geometry : angle 0.63816 / 0.31 (22514) SS BOND : bond 0.00360 / 0.20 ( 18) SS BOND : angle 1.37142 / 0.78 ( 36) hydrogen bonds : bond 0.02820 / 1.89 ( 628) hydrogen bonds : angle 4.82103 / 3.36 ( 1758) link_NAG-ASN : bond 0.00983 / 0.50 ( 10) link_NAG-ASN : angle 4.05626 / 2.36 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4105.48 seconds wall clock time: 71 minutes 11.64 seconds (4271.64 seconds total)