Starting phenix.real_space_refine on Wed Feb 12 22:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8a_34540/02_2025/8h8a_34540.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 12 5.16 5 C 5317 2.51 5 N 1468 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8454 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7844 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Time building chain proxies: 4.92, per 1000 atoms: 0.58 Number of scatterers: 8454 At special positions: 0 Unit cell: (87.87, 79.17, 113.97, 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 12 16.00 O 1657 8.00 N 1468 7.00 C 5317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 15 sheets defined 2.6% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.073A pdb=" N SER A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 384 " --> pdb=" O GLY A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'B' and resid 1139 through 1148 Processing helix chain 'B' and resid 1154 through 1165 removed outlier: 3.645A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 170 removed outlier: 3.610A pdb=" N LEU A 166 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.438A pdb=" N ARG A 266 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A 279 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 268 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 275 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.463A pdb=" N ILE A 298 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS A 310 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 300 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 311 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 320 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.642A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 403 removed outlier: 5.118A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN A 464 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 469 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 493 removed outlier: 4.038A pdb=" N TYR A 504 " --> pdb=" O TRP A 513 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP A 513 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN A 506 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG A 511 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.545A pdb=" N VAL A 533 " --> pdb=" O TRP A 545 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 555 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 587 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A 596 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR A 599 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A 608 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP A 656 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 661 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N ASN A 660 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N TYR A 676 " --> pdb=" O ASN A 660 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR A 662 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 673 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 685 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP A 675 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 696 through 697 removed outlier: 7.088A pdb=" N LYS A 696 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 715 through 717 removed outlier: 5.530A pdb=" N GLN A 724 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 769 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 781 removed outlier: 3.849A pdb=" N GLU A 780 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.693A pdb=" N THR A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 810 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 821 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 926 through 927 removed outlier: 3.797A pdb=" N LYS A 942 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 941 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A 961 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR A 981 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU A 995 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 999 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 11.680A pdb=" N ARG A 998 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR A1013 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A1000 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE A1008 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A1025 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A1010 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A1023 " --> pdb=" O TRP A1010 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A1012 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A1021 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU A1041 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1054 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N VAL A1051 " --> pdb=" O GLU A1067 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU A1067 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A1053 " --> pdb=" O ASP A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1079 through 1080 Processing sheet with id=AB6, first strand: chain 'A' and resid 1125 through 1126 211 hydrogen bonds defined for protein. 570 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: 3.29 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2841 1.34 - 1.46: 1982 1.46 - 1.58: 3813 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 8652 Sorted by residual: bond pdb=" CA TYR B1214 " pdb=" CB TYR B1214 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.22e-02 2.03e+03 2.21e+00 bond pdb=" CA LEU A 204 " pdb=" C LEU A 204 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.22e-02 6.72e+03 1.47e+00 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.39e+00 bond pdb=" CA ALA A 151 " pdb=" C ALA A 151 " ideal model delta sigma weight residual 1.523 1.509 0.014 1.30e-02 5.92e+03 1.24e+00 bond pdb=" CB ASP A 719 " pdb=" CG ASP A 719 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 8647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11482 1.54 - 3.08: 183 3.08 - 4.63: 34 4.63 - 6.17: 3 6.17 - 7.71: 2 Bond angle restraints: 11704 Sorted by residual: angle pdb=" N GLU A 203 " pdb=" CA GLU A 203 " pdb=" C GLU A 203 " ideal model delta sigma weight residual 107.61 115.32 -7.71 1.74e+00 3.30e-01 1.96e+01 angle pdb=" N VAL A 342 " pdb=" CA VAL A 342 " pdb=" C VAL A 342 " ideal model delta sigma weight residual 113.10 108.88 4.22 9.70e-01 1.06e+00 1.89e+01 angle pdb=" N GLY A 152 " pdb=" CA GLY A 152 " pdb=" C GLY A 152 " ideal model delta sigma weight residual 112.51 106.32 6.19 1.53e+00 4.27e-01 1.64e+01 angle pdb=" N VAL B1179 " pdb=" CA VAL B1179 " pdb=" C VAL B1179 " ideal model delta sigma weight residual 113.47 109.55 3.92 1.01e+00 9.80e-01 1.51e+01 angle pdb=" N VAL A 708 " pdb=" CA VAL A 708 " pdb=" C VAL A 708 " ideal model delta sigma weight residual 110.21 106.90 3.31 1.13e+00 7.83e-01 8.59e+00 ... (remaining 11699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4668 17.63 - 35.26: 304 35.26 - 52.89: 76 52.89 - 70.52: 14 70.52 - 88.15: 9 Dihedral angle restraints: 5071 sinusoidal: 2057 harmonic: 3014 Sorted by residual: dihedral pdb=" CA ASP A 153 " pdb=" C ASP A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP A 935 " pdb=" CB ASP A 935 " pdb=" CG ASP A 935 " pdb=" OD1 ASP A 935 " ideal model delta sinusoidal sigma weight residual -30.00 -88.49 58.49 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASN A 251 " pdb=" C ASN A 251 " pdb=" N PRO A 252 " pdb=" CA PRO A 252 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 772 0.030 - 0.060: 286 0.060 - 0.089: 68 0.089 - 0.119: 67 0.119 - 0.149: 8 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA ASP A 719 " pdb=" N ASP A 719 " pdb=" C ASP A 719 " pdb=" CB ASP A 719 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE A1107 " pdb=" N ILE A1107 " pdb=" C ILE A1107 " pdb=" CB ILE A1107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 726 " pdb=" N ILE A 726 " pdb=" C ILE A 726 " pdb=" CB ILE A 726 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1198 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 153 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 154 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 625 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 626 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 794 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ASP A 794 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP A 794 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS A 795 " -0.007 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2680 2.82 - 3.34: 6382 3.34 - 3.86: 13029 3.86 - 4.38: 14856 4.38 - 4.90: 26999 Nonbonded interactions: 63946 Sorted by model distance: nonbonded pdb=" O LEU A 960 " pdb=" OH TYR A 974 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 715 " pdb=" OE1 GLU B1167 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 393 " pdb=" OG SER A 393 " model vdw 2.331 3.040 nonbonded pdb=" OD1 ASP A 455 " pdb=" OG SER A 457 " model vdw 2.340 3.040 nonbonded pdb=" O SER A 683 " pdb=" OG SER A 683 " model vdw 2.348 3.040 ... (remaining 63941 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=0.00 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: 0.640 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.002 0.033 8652 Z= 0.117 Angle : 0.505 7.711 11704 Z= 0.318 Chirality : 0.040 0.149 1201 Planarity : 0.004 0.115 1544 Dihedral : 12.991 88.149 3165 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.73 % Favored : 91.17 % Rotamer: Outliers : 1.55 % Allowed : 6.55 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.22), residues: 1031 helix: -1.89 (1.07), residues: 21 sheet: 0.31 (0.40), residues: 183 loop : -3.13 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 438 HIS 0.001 0.000 HIS A 198 PHE 0.008 0.000 PHE A 249 TYR 0.010 0.000 TYR A 265 ARG 0.001 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8080 (t80) cc_final: 0.7770 (t80) REVERT: A 284 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: A 775 PHE cc_start: 0.8336 (m-80) cc_final: 0.7904 (m-80) REVERT: A 798 PHE cc_start: 0.6913 (m-10) cc_final: 0.6709 (m-80) REVERT: A 930 VAL cc_start: 0.8552 (t) cc_final: 0.8277 (m) REVERT: A 1033 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 1180 LYS cc_start: 0.7834 (ptmm) cc_final: 0.7632 (tttm) outliers start: 14 outliers final: 8 residues processed: 192 average time/residue: 0.2759 time to fit residues: 68.8126 Evaluate side-chains 107 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 357 GLN A 373 HIS A 456 ASN A 460 GLN A 481 GLN A 510 GLN A 551 GLN A 622 GLN A 755 GLN A 772 GLN A 936 GLN A1014 GLN A1071 ASN A1082 GLN A1117 GLN B1160 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115281 restraints weight = 10816.449| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.19 r_work: 0.3109 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8652 Z= 0.225 Angle : 0.632 7.162 11704 Z= 0.339 Chirality : 0.045 0.164 1201 Planarity : 0.004 0.047 1544 Dihedral : 5.156 58.525 1184 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.83 % Favored : 87.88 % Rotamer: Outliers : 3.33 % Allowed : 11.99 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.23), residues: 1031 helix: -0.92 (1.10), residues: 22 sheet: 0.82 (0.45), residues: 154 loop : -2.86 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1010 HIS 0.005 0.001 HIS A 198 PHE 0.017 0.002 PHE A 823 TYR 0.018 0.002 TYR B1214 ARG 0.004 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.920 Fit side-chains REVERT: A 200 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.6830 (t80) REVERT: A 240 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: A 277 LYS cc_start: 0.6459 (pttt) cc_final: 0.6176 (ptpt) REVERT: A 502 LYS cc_start: 0.7950 (pttt) cc_final: 0.7563 (ptpt) REVERT: A 937 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8159 (mm110) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.2102 time to fit residues: 35.5956 Evaluate side-chains 94 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN A 640 GLN A 738 HIS A1082 GLN A1087 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097103 restraints weight = 11402.923| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.15 r_work: 0.2884 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 8652 Z= 0.444 Angle : 0.782 13.892 11704 Z= 0.416 Chirality : 0.050 0.220 1201 Planarity : 0.006 0.068 1544 Dihedral : 5.985 49.874 1179 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.00 % Favored : 86.91 % Rotamer: Outliers : 3.33 % Allowed : 15.65 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 1031 helix: -0.30 (1.14), residues: 22 sheet: 0.13 (0.42), residues: 179 loop : -2.86 (0.17), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 196 HIS 0.008 0.001 HIS A 198 PHE 0.019 0.002 PHE A1131 TYR 0.022 0.002 TYR A 608 ARG 0.008 0.001 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.908 Fit side-chains REVERT: A 188 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: A 200 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 240 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: A 249 PHE cc_start: 0.8068 (t80) cc_final: 0.7788 (t80) REVERT: A 277 LYS cc_start: 0.6359 (pttt) cc_final: 0.6102 (ptpt) REVERT: A 502 LYS cc_start: 0.8592 (pttt) cc_final: 0.8216 (ptpt) REVERT: A 598 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7918 (ttp-110) REVERT: A 707 ASP cc_start: 0.8575 (t0) cc_final: 0.8197 (t0) outliers start: 30 outliers final: 20 residues processed: 104 average time/residue: 0.2358 time to fit residues: 33.5575 Evaluate side-chains 88 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1207 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117153 restraints weight = 10742.702| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.09 r_work: 0.2992 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8652 Z= 0.148 Angle : 0.569 7.741 11704 Z= 0.302 Chirality : 0.043 0.198 1201 Planarity : 0.004 0.057 1544 Dihedral : 4.879 38.626 1178 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.96 % Favored : 88.94 % Rotamer: Outliers : 2.11 % Allowed : 18.20 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 1031 helix: 0.15 (1.17), residues: 22 sheet: 0.67 (0.47), residues: 145 loop : -2.62 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 177 HIS 0.002 0.001 HIS A1059 PHE 0.008 0.001 PHE A 390 TYR 0.015 0.001 TYR B1214 ARG 0.005 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.900 Fit side-chains REVERT: A 188 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.6900 (mtp180) REVERT: A 200 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 240 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: A 337 GLU cc_start: 0.7968 (mp0) cc_final: 0.7714 (mp0) REVERT: A 406 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7707 (ttpt) REVERT: A 502 LYS cc_start: 0.8556 (pttt) cc_final: 0.8195 (ptpt) REVERT: A 598 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7857 (ttp-110) REVERT: A 707 ASP cc_start: 0.8381 (t0) cc_final: 0.8018 (t0) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.2385 time to fit residues: 32.3152 Evaluate side-chains 84 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.0470 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100086 restraints weight = 11152.368| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.09 r_work: 0.2923 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8652 Z= 0.270 Angle : 0.632 7.731 11704 Z= 0.337 Chirality : 0.045 0.185 1201 Planarity : 0.004 0.062 1544 Dihedral : 5.170 38.640 1177 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.80 % Favored : 87.10 % Rotamer: Outliers : 3.22 % Allowed : 18.42 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1031 helix: 0.36 (1.16), residues: 22 sheet: 0.54 (0.44), residues: 167 loop : -2.63 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 438 HIS 0.004 0.001 HIS A1059 PHE 0.010 0.002 PHE A 775 TYR 0.021 0.001 TYR B1214 ARG 0.005 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.000 Fit side-chains REVERT: A 150 LYS cc_start: 0.8482 (mptm) cc_final: 0.8217 (mmtm) REVERT: A 188 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7054 (mtp180) REVERT: A 200 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6820 (t80) REVERT: A 240 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: A 406 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7713 (ttpt) REVERT: A 502 LYS cc_start: 0.8663 (pttt) cc_final: 0.8322 (ptpt) REVERT: A 598 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7883 (ttp-110) REVERT: A 707 ASP cc_start: 0.8560 (t0) cc_final: 0.8254 (t0) outliers start: 29 outliers final: 20 residues processed: 97 average time/residue: 0.2564 time to fit residues: 33.6858 Evaluate side-chains 94 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101468 restraints weight = 11039.552| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.23 r_work: 0.2914 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8652 Z= 0.278 Angle : 0.640 7.790 11704 Z= 0.342 Chirality : 0.046 0.192 1201 Planarity : 0.004 0.065 1544 Dihedral : 5.214 38.586 1175 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.00 % Favored : 86.91 % Rotamer: Outliers : 2.89 % Allowed : 18.76 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1031 helix: 0.56 (1.13), residues: 22 sheet: 0.77 (0.46), residues: 157 loop : -2.58 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 438 HIS 0.004 0.001 HIS A 198 PHE 0.011 0.002 PHE A 249 TYR 0.022 0.001 TYR B1214 ARG 0.006 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.087 Fit side-chains REVERT: A 188 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7067 (mtp180) REVERT: A 200 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6764 (t80) REVERT: A 240 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 406 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: A 502 LYS cc_start: 0.8650 (pttt) cc_final: 0.8305 (ptpt) REVERT: A 598 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7812 (ttp-110) REVERT: A 677 ASP cc_start: 0.8657 (p0) cc_final: 0.8448 (p0) REVERT: A 707 ASP cc_start: 0.8525 (t0) cc_final: 0.8181 (t0) outliers start: 26 outliers final: 17 residues processed: 99 average time/residue: 0.2491 time to fit residues: 33.2731 Evaluate side-chains 89 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.094826 restraints weight = 11276.821| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.26 r_work: 0.2847 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 8652 Z= 0.511 Angle : 0.788 9.818 11704 Z= 0.421 Chirality : 0.051 0.200 1201 Planarity : 0.006 0.070 1544 Dihedral : 5.956 39.365 1175 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.74 % Favored : 85.16 % Rotamer: Outliers : 3.77 % Allowed : 18.20 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1031 helix: 0.30 (1.08), residues: 22 sheet: -0.09 (0.42), residues: 182 loop : -2.62 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 196 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.002 PHE A1131 TYR 0.018 0.002 TYR B1214 ARG 0.006 0.001 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.004 Fit side-chains REVERT: A 188 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7191 (mtp180) REVERT: A 200 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.6886 (t80) REVERT: A 240 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: A 406 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7906 (ttpt) REVERT: A 502 LYS cc_start: 0.8822 (pttt) cc_final: 0.8542 (ptpt) REVERT: A 598 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7853 (ttp-170) REVERT: A 677 ASP cc_start: 0.8704 (p0) cc_final: 0.8452 (p0) REVERT: A 707 ASP cc_start: 0.8711 (t0) cc_final: 0.8422 (t0) REVERT: A 710 ASP cc_start: 0.8134 (t0) cc_final: 0.7760 (t0) outliers start: 34 outliers final: 27 residues processed: 102 average time/residue: 0.2453 time to fit residues: 33.6897 Evaluate side-chains 95 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.105172 restraints weight = 11165.577| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.21 r_work: 0.2973 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8652 Z= 0.160 Angle : 0.582 7.697 11704 Z= 0.312 Chirality : 0.044 0.204 1201 Planarity : 0.004 0.061 1544 Dihedral : 4.989 37.347 1175 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.64 % Favored : 88.26 % Rotamer: Outliers : 2.44 % Allowed : 19.87 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1031 helix: 0.58 (1.13), residues: 23 sheet: 0.91 (0.48), residues: 140 loop : -2.48 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 513 HIS 0.003 0.001 HIS A 198 PHE 0.008 0.001 PHE A1075 TYR 0.023 0.001 TYR B1214 ARG 0.006 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.962 Fit side-chains REVERT: A 188 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7151 (mtp180) REVERT: A 200 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6764 (t80) REVERT: A 240 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 406 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7749 (ttpt) REVERT: A 502 LYS cc_start: 0.8637 (pttt) cc_final: 0.8370 (ptpt) REVERT: A 598 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7764 (ttp-110) REVERT: A 707 ASP cc_start: 0.8523 (t0) cc_final: 0.8198 (t0) REVERT: A 710 ASP cc_start: 0.7887 (t0) cc_final: 0.7503 (t0) outliers start: 22 outliers final: 16 residues processed: 100 average time/residue: 0.2330 time to fit residues: 31.7777 Evaluate side-chains 89 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.099814 restraints weight = 11308.132| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.27 r_work: 0.2886 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8652 Z= 0.244 Angle : 0.630 8.237 11704 Z= 0.337 Chirality : 0.045 0.196 1201 Planarity : 0.004 0.063 1544 Dihedral : 5.155 38.002 1175 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.51 % Favored : 87.39 % Rotamer: Outliers : 2.55 % Allowed : 19.87 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1031 helix: 1.03 (1.16), residues: 22 sheet: 0.48 (0.47), residues: 147 loop : -2.46 (0.18), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 438 HIS 0.003 0.001 HIS A 198 PHE 0.009 0.001 PHE A 390 TYR 0.020 0.001 TYR B1214 ARG 0.007 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.961 Fit side-chains REVERT: A 188 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7053 (mtp180) REVERT: A 200 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 240 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: A 406 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: A 502 LYS cc_start: 0.8612 (pttt) cc_final: 0.8305 (ptpt) REVERT: A 598 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7730 (ttp-110) REVERT: A 707 ASP cc_start: 0.8590 (t0) cc_final: 0.8237 (t0) REVERT: A 710 ASP cc_start: 0.8022 (t0) cc_final: 0.7613 (t0) outliers start: 23 outliers final: 18 residues processed: 90 average time/residue: 0.2430 time to fit residues: 29.9372 Evaluate side-chains 90 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098181 restraints weight = 11261.527| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.16 r_work: 0.3024 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8652 Z= 0.285 Angle : 0.661 8.646 11704 Z= 0.354 Chirality : 0.046 0.197 1201 Planarity : 0.004 0.064 1544 Dihedral : 5.355 38.452 1175 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.09 % Favored : 86.81 % Rotamer: Outliers : 2.77 % Allowed : 19.53 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1031 helix: 0.72 (1.14), residues: 23 sheet: 0.36 (0.45), residues: 157 loop : -2.53 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 438 HIS 0.003 0.001 HIS A 198 PHE 0.010 0.002 PHE A 839 TYR 0.019 0.001 TYR B1214 ARG 0.007 0.000 ARG A 783 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.995 Fit side-chains REVERT: A 188 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: A 200 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 240 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: A 406 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7883 (ttpt) REVERT: A 502 LYS cc_start: 0.8738 (pttt) cc_final: 0.8506 (ptpt) REVERT: A 598 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7808 (ttp-170) REVERT: A 710 ASP cc_start: 0.7991 (t0) cc_final: 0.7583 (t0) outliers start: 25 outliers final: 21 residues processed: 89 average time/residue: 0.2348 time to fit residues: 28.6103 Evaluate side-chains 91 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain B residue 1180 LYS Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 0.0670 chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.095356 restraints weight = 11429.041| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.26 r_work: 0.2866 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8652 Z= 0.373 Angle : 0.715 9.520 11704 Z= 0.383 Chirality : 0.048 0.200 1201 Planarity : 0.005 0.066 1544 Dihedral : 5.664 38.453 1175 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.06 % Favored : 85.84 % Rotamer: Outliers : 3.22 % Allowed : 18.98 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.24), residues: 1031 helix: 0.57 (1.11), residues: 23 sheet: 0.32 (0.46), residues: 153 loop : -2.57 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 196 HIS 0.003 0.001 HIS A 198 PHE 0.012 0.002 PHE A1131 TYR 0.017 0.002 TYR B1214 ARG 0.007 0.001 ARG A 783 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.33 seconds wall clock time: 78 minutes 33.55 seconds (4713.55 seconds total)