Starting phenix.real_space_refine on Fri Aug 22 22:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8a_34540/08_2025/8h8a_34540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8a_34540/08_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_34540/08_2025/8h8a_34540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8a_34540/08_2025/8h8a_34540.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8a_34540/08_2025/8h8a_34540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8a_34540/08_2025/8h8a_34540.cif" } resolution = 3.25 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'TYR: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: 1.82, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 224.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.29 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: 1.39 Time building geometry restraints manager: 0.98 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- 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= 0.115 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A 511 TYR 0.010 0.000 TYR A 265 PHE 0.008 0.000 PHE A 249 TRP 0.002 0.000 TRP A 438 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 8652) covalent geometry : angle 0.50484 (11704) hydrogen bonds : bond 0.16943 ( 211) hydrogen bonds : angle 6.27911 ( 570) *********************** 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 : 0.318 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: 0.1040 time to fit residues: 25.8311 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 : 0.343 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 551 GLN A 622 GLN A 755 GLN A 772 GLN A1014 GLN A1071 ASN A1082 GLN A1117 GLN B1160 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128794 restraints weight = 10886.112| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.14 r_work: 0.3290 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8652 Z= 0.117 Angle : 0.549 6.992 11704 Z= 0.293 Chirality : 0.042 0.162 1201 Planarity : 0.004 0.047 1544 Dihedral : 4.560 59.220 1184 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.28 % Favored : 89.52 % Rotamer: Outliers : 2.55 % Allowed : 11.32 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.23), residues: 1031 helix: -0.91 (1.12), residues: 22 sheet: 0.96 (0.44), residues: 148 loop : -2.78 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.014 0.001 TYR B1214 PHE 0.010 0.001 PHE A1131 TRP 0.009 0.001 TRP A1010 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8652) covalent geometry : angle 0.54850 (11704) hydrogen bonds : bond 0.03105 ( 211) hydrogen bonds : angle 4.74795 ( 570) *********************** 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 121 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.267 Fit side-chains REVERT: A 200 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6642 (t80) REVERT: A 240 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: A 611 GLU cc_start: 0.8380 (mp0) cc_final: 0.8180 (mp0) REVERT: A 937 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 1033 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8565 (mt-10) outliers start: 23 outliers final: 12 residues processed: 116 average time/residue: 0.0995 time to fit residues: 15.7690 Evaluate side-chains 91 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 893 THR 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 57 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 HIS A1082 GLN A1087 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098771 restraints weight = 11172.351| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.38 r_work: 0.2983 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8652 Z= 0.332 Angle : 0.830 13.105 11704 Z= 0.443 Chirality : 0.051 0.216 1201 Planarity : 0.006 0.064 1544 Dihedral : 6.131 47.692 1178 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.19 % Favored : 86.71 % Rotamer: Outliers : 3.33 % Allowed : 14.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.23), residues: 1031 helix: -0.38 (1.13), residues: 22 sheet: 0.15 (0.42), residues: 184 loop : -2.89 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 952 TYR 0.025 0.002 TYR A 608 PHE 0.021 0.003 PHE A1131 TRP 0.014 0.002 TRP A 196 HIS 0.009 0.002 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 8652) covalent geometry : angle 0.82988 (11704) hydrogen bonds : bond 0.05992 ( 211) hydrogen bonds : angle 5.15442 ( 570) *********************** 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 119 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.351 Fit side-chains REVERT: A 188 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7228 (mtp180) REVERT: A 200 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.6747 (t80) REVERT: A 240 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: A 249 PHE cc_start: 0.8158 (t80) cc_final: 0.7827 (t80) REVERT: A 337 GLU cc_start: 0.8397 (tp30) cc_final: 0.7997 (mp0) REVERT: A 502 LYS cc_start: 0.8687 (pttt) cc_final: 0.8378 (ptpt) REVERT: A 598 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7989 (ttp-110) outliers start: 30 outliers final: 21 residues processed: 113 average time/residue: 0.1014 time to fit residues: 15.4973 Evaluate side-chains 91 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 GLU 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 204 LEU 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 533 VAL 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 893 THR Chi-restraints excluded: chain A residue 920 MET 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 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 201 GLN A 481 GLN A 986 GLN A1082 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109643 restraints weight = 11162.192| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.24 r_work: 0.2990 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4479 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= 0.106 Angle : 0.575 9.446 11704 Z= 0.304 Chirality : 0.043 0.195 1201 Planarity : 0.004 0.053 1544 Dihedral : 4.779 37.308 1177 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.48 % Favored : 89.43 % Rotamer: Outliers : 2.44 % Allowed : 16.87 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.23), residues: 1031 helix: 0.05 (1.16), residues: 22 sheet: 0.66 (0.47), residues: 145 loop : -2.62 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 290 TYR 0.015 0.001 TYR B1214 PHE 0.009 0.001 PHE A1075 TRP 0.008 0.001 TRP A 438 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8652) covalent geometry : angle 0.57453 (11704) hydrogen bonds : bond 0.03066 ( 211) hydrogen bonds : angle 4.72982 ( 570) *********************** 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 110 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.342 Fit side-chains REVERT: A 188 ARG cc_start: 0.7981 (ptp-110) cc_final: 0.6952 (mtp180) REVERT: A 200 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.6770 (t80) REVERT: A 240 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: A 277 LYS cc_start: 0.6089 (mttt) cc_final: 0.5873 (mttp) REVERT: A 337 GLU cc_start: 0.8311 (tp30) cc_final: 0.8028 (mp0) REVERT: A 502 LYS cc_start: 0.8539 (pttt) cc_final: 0.8202 (ptpt) REVERT: A 707 ASP cc_start: 0.8350 (t0) cc_final: 0.8026 (t0) REVERT: A 916 ASP cc_start: 0.7600 (t70) cc_final: 0.7099 (t0) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.0908 time to fit residues: 13.2218 Evaluate side-chains 88 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL 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 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 834 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 640 GLN A 986 GLN A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114023 restraints weight = 11030.190| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4338 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= 0.096 Angle : 0.537 8.101 11704 Z= 0.284 Chirality : 0.043 0.186 1201 Planarity : 0.003 0.047 1544 Dihedral : 4.279 37.319 1175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.35 % Favored : 88.55 % Rotamer: Outliers : 2.11 % Allowed : 17.76 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.24), residues: 1031 helix: 0.44 (1.20), residues: 22 sheet: 0.38 (0.45), residues: 154 loop : -2.48 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.024 0.001 TYR B1214 PHE 0.006 0.001 PHE A 390 TRP 0.007 0.001 TRP A 417 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 8652) covalent geometry : angle 0.53742 (11704) hydrogen bonds : bond 0.02595 ( 211) hydrogen bonds : angle 4.50632 ( 570) *********************** 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 110 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.336 Fit side-chains REVERT: A 188 ARG cc_start: 0.7989 (ptp-110) cc_final: 0.6926 (mtp180) REVERT: A 200 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 240 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: A 277 LYS cc_start: 0.6087 (mttt) cc_final: 0.5773 (mttp) REVERT: A 337 GLU cc_start: 0.8285 (tp30) cc_final: 0.8012 (mp0) REVERT: A 502 LYS cc_start: 0.8524 (pttt) cc_final: 0.8191 (ptpt) REVERT: A 598 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7822 (ttp-110) REVERT: A 916 ASP cc_start: 0.7671 (t70) cc_final: 0.7161 (t0) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.1049 time to fit residues: 15.2523 Evaluate side-chains 92 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU 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 276 LEU Chi-restraints excluded: chain A residue 331 THR 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 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 22 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 421 HIS A 640 GLN A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097087 restraints weight = 11155.848| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.19 r_work: 0.2939 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 8652 Z= 0.334 Angle : 0.802 9.116 11704 Z= 0.429 Chirality : 0.051 0.209 1201 Planarity : 0.006 0.066 1544 Dihedral : 5.793 41.163 1174 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.65 % Favored : 85.26 % Rotamer: Outliers : 2.89 % Allowed : 18.31 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.23), residues: 1031 helix: 0.12 (1.11), residues: 22 sheet: 0.15 (0.42), residues: 181 loop : -2.67 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 952 TYR 0.020 0.002 TYR A 608 PHE 0.021 0.003 PHE A1131 TRP 0.014 0.002 TRP A 196 HIS 0.007 0.002 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00814 ( 8652) covalent geometry : angle 0.80234 (11704) hydrogen bonds : bond 0.05734 ( 211) hydrogen bonds : angle 4.95207 ( 570) *********************** 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 103 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.355 Fit side-chains REVERT: A 188 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7236 (mtp180) REVERT: A 200 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.6837 (t80) REVERT: A 240 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: A 337 GLU cc_start: 0.8413 (tp30) cc_final: 0.8112 (mp0) REVERT: A 502 LYS cc_start: 0.8820 (pttt) cc_final: 0.8526 (ptpt) REVERT: A 598 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7915 (ttp-170) outliers start: 26 outliers final: 17 residues processed: 96 average time/residue: 0.1142 time to fit residues: 14.7518 Evaluate side-chains 87 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 161 GLU 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 247 CYS Chi-restraints excluded: chain A residue 251 ASN 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 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 THR 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 B residue 1212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 444 HIS A 481 GLN A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105870 restraints weight = 11213.940| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.25 r_work: 0.2949 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4914 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= 0.111 Angle : 0.579 6.915 11704 Z= 0.311 Chirality : 0.044 0.200 1201 Planarity : 0.004 0.057 1544 Dihedral : 4.801 37.479 1174 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.96 % Favored : 88.94 % Rotamer: Outliers : 2.22 % Allowed : 18.87 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.24), residues: 1031 helix: 0.54 (1.14), residues: 22 sheet: 0.93 (0.49), residues: 131 loop : -2.46 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.022 0.001 TYR B1214 PHE 0.009 0.001 PHE A 249 TRP 0.008 0.001 TRP A 438 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8652) covalent geometry : angle 0.57935 (11704) hydrogen bonds : bond 0.03014 ( 211) hydrogen bonds : angle 4.69648 ( 570) *********************** 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 100 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.364 Fit side-chains REVERT: A 188 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7070 (mtp180) REVERT: A 200 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.6795 (t80) REVERT: A 240 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: A 337 GLU cc_start: 0.8210 (tp30) cc_final: 0.7994 (mp0) REVERT: A 502 LYS cc_start: 0.8585 (pttt) cc_final: 0.8310 (ptpt) REVERT: A 598 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7849 (ttp-110) outliers start: 20 outliers final: 17 residues processed: 96 average time/residue: 0.1104 time to fit residues: 14.4628 Evaluate side-chains 92 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 GLU 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 247 CYS 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 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 712 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108346 restraints weight = 10942.774| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.07 r_work: 0.2905 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.5124 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= 0.186 Angle : 0.649 7.787 11704 Z= 0.348 Chirality : 0.046 0.190 1201 Planarity : 0.004 0.061 1544 Dihedral : 5.149 38.674 1174 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.80 % Favored : 87.10 % Rotamer: Outliers : 2.66 % Allowed : 18.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.24), residues: 1031 helix: 0.86 (1.15), residues: 22 sheet: 0.51 (0.47), residues: 143 loop : -2.52 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 783 TYR 0.018 0.001 TYR B1214 PHE 0.011 0.002 PHE A1131 TRP 0.010 0.001 TRP A 438 HIS 0.005 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8652) covalent geometry : angle 0.64892 (11704) hydrogen bonds : bond 0.04174 ( 211) hydrogen bonds : angle 4.68874 ( 570) *********************** 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 97 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.343 Fit side-chains REVERT: A 188 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7141 (mtp180) REVERT: A 200 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.6841 (t80) REVERT: A 240 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: A 337 GLU cc_start: 0.8230 (tp30) cc_final: 0.8024 (mp0) REVERT: A 502 LYS cc_start: 0.8643 (pttt) cc_final: 0.8352 (ptpt) REVERT: A 598 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7823 (ttp-110) outliers start: 24 outliers final: 20 residues processed: 91 average time/residue: 0.1133 time to fit residues: 13.8174 Evaluate side-chains 89 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 161 GLU 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 247 CYS 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 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 797 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102646 restraints weight = 11118.948| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.26 r_work: 0.2942 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.5128 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= 0.157 Angle : 0.623 7.543 11704 Z= 0.335 Chirality : 0.045 0.192 1201 Planarity : 0.004 0.060 1544 Dihedral : 5.061 38.173 1174 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.83 % Favored : 88.07 % Rotamer: Outliers : 2.33 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.24), residues: 1031 helix: 0.73 (1.14), residues: 23 sheet: 0.96 (0.50), residues: 130 loop : -2.47 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 783 TYR 0.023 0.001 TYR B1214 PHE 0.009 0.001 PHE A 390 TRP 0.009 0.001 TRP A 438 HIS 0.006 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8652) covalent geometry : angle 0.62311 (11704) hydrogen bonds : bond 0.03785 ( 211) hydrogen bonds : angle 4.65524 ( 570) *********************** 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: 21 poor density : 74 time to evaluate : 0.402 Fit side-chains REVERT: A 188 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: A 200 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.6850 (t80) REVERT: A 240 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: A 337 GLU cc_start: 0.8232 (tp30) cc_final: 0.8032 (mp0) REVERT: A 502 LYS cc_start: 0.8653 (pttt) cc_final: 0.8385 (ptpt) REVERT: A 598 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7840 (ttp-110) outliers start: 21 outliers final: 18 residues processed: 90 average time/residue: 0.1081 time to fit residues: 13.3683 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 GLU 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 247 CYS 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 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 712 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 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 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103019 restraints weight = 10945.672| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.22 r_work: 0.2947 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5170 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= 0.162 Angle : 0.632 7.634 11704 Z= 0.340 Chirality : 0.045 0.193 1201 Planarity : 0.004 0.060 1544 Dihedral : 5.083 38.319 1174 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.80 % Favored : 87.10 % Rotamer: Outliers : 2.55 % Allowed : 19.20 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.24), residues: 1031 helix: 0.82 (1.15), residues: 23 sheet: 0.65 (0.48), residues: 140 loop : -2.46 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 783 TYR 0.023 0.001 TYR B1214 PHE 0.009 0.002 PHE A1131 TRP 0.009 0.001 TRP A 438 HIS 0.006 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8652) covalent geometry : angle 0.63235 (11704) hydrogen bonds : bond 0.03851 ( 211) hydrogen bonds : angle 4.63757 ( 570) ********************** 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 96 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.345 Fit side-chains REVERT: A 188 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7178 (mtp180) REVERT: A 200 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.6873 (t80) REVERT: A 240 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: A 502 LYS cc_start: 0.8687 (pttt) cc_final: 0.8434 (ptpt) REVERT: A 598 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7857 (ttp-110) outliers start: 23 outliers final: 20 residues processed: 91 average time/residue: 0.1019 time to fit residues: 12.7341 Evaluate side-chains 91 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 GLU 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 247 CYS 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 470 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 797 SER 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 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 481 GLN A1082 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109455 restraints weight = 10961.844| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.3013 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8652 Z= 0.106 Angle : 0.568 8.661 11704 Z= 0.303 Chirality : 0.043 0.198 1201 Planarity : 0.004 0.056 1544 Dihedral : 4.590 37.605 1174 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.25 % Favored : 88.65 % Rotamer: Outliers : 2.33 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.24), residues: 1031 helix: 0.91 (1.17), residues: 23 sheet: 1.08 (0.52), residues: 117 loop : -2.33 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 783 TYR 0.026 0.001 TYR B1214 PHE 0.007 0.001 PHE A 390 TRP 0.008 0.001 TRP A 438 HIS 0.006 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8652) covalent geometry : angle 0.56826 (11704) hydrogen bonds : bond 0.02724 ( 211) hydrogen bonds : angle 4.53420 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.32 seconds wall clock time: 36 minutes 44.62 seconds (2204.62 seconds total)