Starting phenix.real_space_refine on Fri Nov 15 06:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_34540.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_34540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_34540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_34540.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/11_2024/8h8a_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.16, per 1000 atoms: 0.61 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: 2.15 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: 1.17 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: 3.47 Time building geometry restraints manager: 2.53 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: 0.540 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.990 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- 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 : 0.987 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: 0.2689 time to fit residues: 67.2168 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 : 0.989 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.966 Fit side-chains REVERT: A 200 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6859 (t80) REVERT: A 240 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: A 277 LYS cc_start: 0.6242 (pttt) cc_final: 0.5971 (ptpt) REVERT: A 502 LYS cc_start: 0.7593 (pttt) cc_final: 0.7245 (ptpt) REVERT: A 937 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7776 (mm110) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.2096 time to fit residues: 35.5651 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 : 0.881 ------------------------------------------------------------------------------- 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 51 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 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 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN A 640 GLN A 738 HIS A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3460 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= 0.146 Angle : 0.546 12.169 11704 Z= 0.287 Chirality : 0.043 0.260 1201 Planarity : 0.003 0.049 1544 Dihedral : 4.597 52.170 1179 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.80 % Favored : 90.11 % Rotamer: Outliers : 2.22 % Allowed : 14.32 % Favored : 83.46 % 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: -2.73 (0.23), residues: 1031 helix: -0.11 (1.21), residues: 22 sheet: 1.03 (0.46), residues: 150 loop : -2.68 (0.18), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS A 198 PHE 0.007 0.001 PHE A 390 TYR 0.015 0.001 TYR B1214 ARG 0.002 0.000 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 105 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.974 Fit side-chains REVERT: A 200 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6654 (t80) REVERT: A 240 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: A 502 LYS cc_start: 0.7645 (pttt) cc_final: 0.7304 (ptpt) REVERT: A 937 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7816 (mm110) REVERT: A 1082 GLN cc_start: 0.7966 (tp40) cc_final: 0.7752 (tp-100) outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 0.2377 time to fit residues: 33.7020 Evaluate side-chains 84 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 712 THR 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 1042 ARG 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 92 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8652 Z= 0.242 Angle : 0.610 8.297 11704 Z= 0.324 Chirality : 0.044 0.162 1201 Planarity : 0.004 0.053 1544 Dihedral : 4.906 38.960 1178 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.32 % Favored : 87.58 % Rotamer: Outliers : 2.22 % Allowed : 16.54 % Favored : 81.24 % 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: -2.77 (0.23), residues: 1031 helix: 0.26 (1.20), residues: 22 sheet: 0.26 (0.44), residues: 166 loop : -2.61 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 196 HIS 0.005 0.001 HIS A 198 PHE 0.012 0.002 PHE A1131 TYR 0.014 0.001 TYR B1214 ARG 0.005 0.001 ARG A 952 *********************** 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 99 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.004 Fit side-chains REVERT: A 188 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: A 200 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 240 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: A 502 LYS cc_start: 0.8073 (pttt) cc_final: 0.7617 (ptpt) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.2329 time to fit residues: 29.8100 Evaluate side-chains 87 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL 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 286 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 531 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 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 198 HIS A 481 GLN A 986 GLN A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8652 Z= 0.141 Angle : 0.540 7.461 11704 Z= 0.287 Chirality : 0.043 0.179 1201 Planarity : 0.003 0.048 1544 Dihedral : 4.419 37.701 1176 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.18 % Favored : 89.72 % Rotamer: Outliers : 2.44 % Allowed : 17.09 % Favored : 80.47 % 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: -2.58 (0.24), residues: 1031 helix: 0.50 (1.22), residues: 22 sheet: 0.67 (0.47), residues: 156 loop : -2.51 (0.18), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.003 0.000 HIS A 198 PHE 0.010 0.001 PHE A 249 TYR 0.015 0.001 TYR B1214 ARG 0.004 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 106 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 188 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6894 (mtp180) REVERT: A 200 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.6704 (t80) REVERT: A 240 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: A 337 GLU cc_start: 0.7409 (mp0) cc_final: 0.7156 (mp0) REVERT: A 502 LYS cc_start: 0.8111 (pttt) cc_final: 0.7753 (ptpt) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 0.2287 time to fit residues: 31.2176 Evaluate side-chains 97 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 240 GLN 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 466 GLN 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 842 SER Chi-restraints excluded: chain A residue 893 THR 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 Chi-restraints excluded: chain B residue 1214 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 0.0070 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 481 GLN A 640 GLN A1082 GLN A1087 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8652 Z= 0.282 Angle : 0.640 7.274 11704 Z= 0.343 Chirality : 0.045 0.175 1201 Planarity : 0.004 0.060 1544 Dihedral : 5.029 39.250 1175 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.90 % Favored : 87.00 % Rotamer: Outliers : 3.22 % Allowed : 17.09 % 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: -2.63 (0.23), residues: 1031 helix: 0.73 (1.17), residues: 22 sheet: 0.62 (0.46), residues: 160 loop : -2.56 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 196 HIS 0.004 0.001 HIS A1059 PHE 0.012 0.002 PHE A1131 TYR 0.014 0.001 TYR B1214 ARG 0.004 0.000 ARG A 952 *********************** 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 104 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7104 (mtp180) REVERT: A 200 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.6772 (t80) REVERT: A 240 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: A 502 LYS cc_start: 0.8308 (pttt) cc_final: 0.7927 (ptpt) REVERT: A 677 ASP cc_start: 0.8204 (p0) cc_final: 0.7947 (p0) outliers start: 29 outliers final: 22 residues processed: 96 average time/residue: 0.2385 time to fit residues: 32.3130 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 : 0.908 ------------------------------------------------------------------------------- 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 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 369 THR Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 500 LEU 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 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 96 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.9602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8652 Z= 0.240 Angle : 0.612 6.987 11704 Z= 0.328 Chirality : 0.045 0.194 1201 Planarity : 0.004 0.065 1544 Dihedral : 4.963 38.584 1175 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.45 % Favored : 88.46 % Rotamer: Outliers : 3.22 % Allowed : 17.76 % Favored : 79.02 % 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: -2.51 (0.24), residues: 1031 helix: 0.95 (1.18), residues: 22 sheet: 0.93 (0.46), residues: 159 loop : -2.53 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 438 HIS 0.004 0.001 HIS A1059 PHE 0.010 0.001 PHE A1131 TYR 0.014 0.001 TYR B1214 ARG 0.006 0.000 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 104 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.065 Fit side-chains REVERT: A 188 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7065 (mtp180) REVERT: A 200 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 240 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: A 502 LYS cc_start: 0.8321 (pttt) cc_final: 0.7943 (ptpt) REVERT: A 677 ASP cc_start: 0.8217 (p0) cc_final: 0.7980 (p0) outliers start: 29 outliers final: 24 residues processed: 96 average time/residue: 0.2254 time to fit residues: 30.2315 Evaluate side-chains 95 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 369 THR Chi-restraints excluded: chain A residue 466 GLN 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 1037 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8652 Z= 0.442 Angle : 0.741 8.397 11704 Z= 0.398 Chirality : 0.049 0.202 1201 Planarity : 0.005 0.071 1544 Dihedral : 5.679 39.684 1175 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.45 % Favored : 85.45 % Rotamer: Outliers : 3.22 % Allowed : 18.09 % Favored : 78.69 % 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: -2.79 (0.23), residues: 1031 helix: 0.71 (1.12), residues: 22 sheet: 0.15 (0.43), residues: 164 loop : -2.61 (0.18), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 196 HIS 0.005 0.001 HIS A1059 PHE 0.017 0.002 PHE A1131 TYR 0.016 0.002 TYR A 396 ARG 0.007 0.001 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 103 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.997 Fit side-chains REVERT: A 188 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7097 (mtp180) REVERT: A 200 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.6774 (t80) REVERT: A 240 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: A 502 LYS cc_start: 0.8358 (pttt) cc_final: 0.7963 (ptpt) outliers start: 29 outliers final: 21 residues processed: 93 average time/residue: 0.2437 time to fit residues: 30.7855 Evaluate side-chains 88 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 369 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 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 1037 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 86 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4890 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= 0.156 Angle : 0.579 7.408 11704 Z= 0.310 Chirality : 0.043 0.205 1201 Planarity : 0.004 0.063 1544 Dihedral : 4.849 37.650 1175 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.96 % Favored : 88.94 % Rotamer: Outliers : 2.22 % Allowed : 18.65 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.24), residues: 1031 helix: 0.75 (1.16), residues: 23 sheet: 0.73 (0.47), residues: 143 loop : -2.42 (0.18), residues: 865 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 0.022 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 101 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 1.008 Fit side-chains REVERT: A 188 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7005 (mtp180) REVERT: A 200 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 240 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: A 502 LYS cc_start: 0.8194 (pttt) cc_final: 0.7890 (ptpt) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.2178 time to fit residues: 29.4874 Evaluate side-chains 87 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 369 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 842 SER 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 59 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8652 Z= 0.191 Angle : 0.608 8.291 11704 Z= 0.324 Chirality : 0.044 0.199 1201 Planarity : 0.004 0.067 1544 Dihedral : 4.869 37.910 1175 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.32 % Favored : 87.58 % 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 (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: -2.58 (0.24), residues: 1031 helix: 0.97 (1.18), residues: 23 sheet: 0.22 (0.49), residues: 133 loop : -2.35 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 438 HIS 0.003 0.001 HIS A 198 PHE 0.008 0.001 PHE A 390 TYR 0.023 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 97 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.977 Fit side-chains REVERT: A 188 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7007 (mtp180) REVERT: A 200 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 240 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: A 502 LYS cc_start: 0.8204 (pttt) cc_final: 0.7893 (ptpt) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.2304 time to fit residues: 29.4057 Evaluate side-chains 88 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 25 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3404 r_free = 0.3404 target = 0.124249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098516 restraints weight = 11039.721| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.16 r_work: 0.2879 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8652 Z= 0.465 Angle : 0.770 9.481 11704 Z= 0.413 Chirality : 0.049 0.202 1201 Planarity : 0.005 0.072 1544 Dihedral : 5.801 39.708 1175 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.94 % Favored : 84.97 % Rotamer: Outliers : 2.33 % Allowed : 18.87 % Favored : 78.80 % 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: -2.72 (0.24), residues: 1031 helix: 0.79 (1.11), residues: 22 sheet: -0.05 (0.43), residues: 168 loop : -2.51 (0.18), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 196 HIS 0.012 0.002 HIS A 444 PHE 0.016 0.002 PHE A1131 TYR 0.017 0.002 TYR A 396 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: 1989.61 seconds wall clock time: 36 minutes 49.79 seconds (2209.79 seconds total)