Starting phenix.real_space_refine on Mon Jul 28 09:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2025/8ub7_42077.cif" } resolution = 3.2 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= 0.029 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: 6 Type Number sf(0) Gaussians P 151 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1871 2.21 5 O 2267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10399 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.58, per 1000 atoms: 0.73 Number of scatterers: 10399 At special positions: 0 Unit cell: (81, 105, 134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 151 15.00 Mg 1 11.99 O 2267 8.00 N 1871 7.00 C 6073 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: 2.47 Conformation dependent library (CDL) restraints added in 812.3 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 75.7% alpha, 2.6% beta 48 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.556A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.503A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.617A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 4.200A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.931A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.726A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.537A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 32 removed outlier: 3.754A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.507A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.508A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 32 removed outlier: 3.775A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.529A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.749A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 66 through 86 removed outlier: 3.730A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 4.579A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.557A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.597A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.484A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213 removed outlier: 4.321A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265 474 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1406 1.32 - 1.45: 4069 1.45 - 1.58: 5098 1.58 - 1.71: 297 1.71 - 1.84: 61 Bond restraints: 10931 Sorted by residual: bond pdb=" C3' DCP A 401 " pdb=" C4' DCP A 401 " ideal model delta sigma weight residual 1.527 1.302 0.225 1.10e-02 8.26e+03 4.20e+02 bond pdb=" C1' DCP A 401 " pdb=" C2' DCP A 401 " ideal model delta sigma weight residual 1.521 1.356 0.165 1.20e-02 6.94e+03 1.90e+02 bond pdb=" O3A DCP A 401 " pdb=" PB DCP A 401 " ideal model delta sigma weight residual 1.592 1.698 -0.106 1.10e-02 8.26e+03 9.25e+01 bond pdb=" C4' DCP A 401 " pdb=" O4' DCP A 401 " ideal model delta sigma weight residual 1.444 1.540 -0.096 1.00e-02 1.00e+04 9.21e+01 bond pdb=" C2' DCP A 401 " pdb=" C3' DCP A 401 " ideal model delta sigma weight residual 1.523 1.626 -0.103 1.30e-02 5.92e+03 6.31e+01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13723 2.34 - 4.68: 1555 4.68 - 7.02: 186 7.02 - 9.35: 30 9.35 - 11.69: 2 Bond angle restraints: 15496 Sorted by residual: angle pdb=" PB DCP A 401 " pdb=" O3B DCP A 401 " pdb=" PG DCP A 401 " ideal model delta sigma weight residual 139.87 129.72 10.15 1.00e+00 1.00e+00 1.03e+02 angle pdb=" C ARG A 4 " pdb=" CA ARG A 4 " pdb=" CB ARG A 4 " ideal model delta sigma weight residual 116.54 107.41 9.13 1.15e+00 7.56e-01 6.30e+01 angle pdb=" C1' DCP A 401 " pdb=" O4' DCP A 401 " pdb=" C4' DCP A 401 " ideal model delta sigma weight residual 109.55 100.73 8.82 1.31e+00 5.82e-01 4.52e+01 angle pdb=" PA DCP A 401 " pdb=" O3A DCP A 401 " pdb=" PB DCP A 401 " ideal model delta sigma weight residual 136.83 130.27 6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" N ARG A 6 " pdb=" CA ARG A 6 " pdb=" C ARG A 6 " ideal model delta sigma weight residual 111.55 120.36 -8.81 1.37e+00 5.33e-01 4.13e+01 ... (remaining 15491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5936 35.16 - 70.32: 776 70.32 - 105.48: 76 105.48 - 140.64: 1 140.64 - 175.80: 4 Dihedral angle restraints: 6793 sinusoidal: 4194 harmonic: 2599 Sorted by residual: dihedral pdb=" C5' A I 56 " pdb=" C4' A I 56 " pdb=" C3' A I 56 " pdb=" O3' A I 56 " ideal model delta sinusoidal sigma weight residual 147.00 87.25 59.75 1 8.00e+00 1.56e-02 7.44e+01 dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual -128.00 46.18 -174.18 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 61.10 170.90 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 6790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1492 0.120 - 0.240: 303 0.240 - 0.360: 32 0.360 - 0.480: 6 0.480 - 0.600: 4 Chirality restraints: 1837 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 1834 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " -0.081 2.00e-02 2.50e+03 4.09e-02 3.34e+01 pdb=" CG TYR C 28 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " -0.066 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 U I 7 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U I 7 " 0.021 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U I 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U I 7 " -0.034 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U I 7 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO C 91 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.056 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1821 2.76 - 3.30: 10122 3.30 - 3.83: 21661 3.83 - 4.37: 26817 4.37 - 4.90: 37337 Nonbonded interactions: 97758 Sorted by model distance: nonbonded pdb=" OD2 ASP A 215 " pdb="MG MG A 402 " model vdw 2.230 2.170 nonbonded pdb=" O ILE A 159 " pdb=" N CYS A 161 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP A 138 " pdb="MG MG A 402 " model vdw 2.276 2.170 nonbonded pdb=" O ALA E 118 " pdb=" O ASN E 121 " model vdw 2.300 3.040 nonbonded pdb=" O PHE A 139 " pdb="MG MG A 402 " model vdw 2.345 2.170 ... (remaining 97753 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.99 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.011 0.225 10931 Z= 0.679 Angle : 1.531 11.693 15496 Z= 0.957 Chirality : 0.098 0.600 1837 Planarity : 0.011 0.106 1403 Dihedral : 25.464 175.798 5117 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.08 % Favored : 88.65 % Rotamer: Outliers : 20.48 % Allowed : 13.92 % Favored : 65.60 % 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: -3.80 (0.24), residues: 881 helix: -1.84 (0.17), residues: 663 sheet: -4.83 (0.91), residues: 24 loop : -3.99 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP A 33 HIS 0.018 0.004 HIS A 133 PHE 0.057 0.009 PHE A 231 TYR 0.081 0.008 TYR C 28 ARG 0.018 0.002 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.18109 ( 595) hydrogen bonds : angle 8.70736 ( 1594) covalent geometry : bond 0.01091 (10931) covalent geometry : angle 1.53067 (15496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 154 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (ptm-80) REVERT: A 112 ASP cc_start: 0.8266 (m-30) cc_final: 0.7874 (t70) REVERT: A 222 ASP cc_start: 0.7857 (p0) cc_final: 0.7309 (t0) REVERT: A 223 ASP cc_start: 0.8338 (t70) cc_final: 0.7797 (t0) REVERT: B 75 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 90 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6794 (tppt) REVERT: B 108 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: C 14 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5925 (ttt) REVERT: C 90 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6468 (mtpp) REVERT: C 92 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6862 (m170) REVERT: D 15 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5919 (tp) REVERT: D 19 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7240 (mmp80) REVERT: D 64 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: D 122 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4464 (mmp-170) REVERT: E 19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6777 (mmm160) REVERT: E 50 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6861 (mt) REVERT: E 52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6769 (tp40) REVERT: E 54 GLU cc_start: 0.7082 (tt0) cc_final: 0.6832 (tt0) REVERT: E 63 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6125 (t0) REVERT: E 77 MET cc_start: 0.8196 (tpt) cc_final: 0.7620 (tpp) REVERT: E 90 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6491 (ttmm) REVERT: E 94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: F 13 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3437 (mt0) REVERT: F 14 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.3709 (ttp) REVERT: F 19 ARG cc_start: 0.6747 (tpp80) cc_final: 0.6477 (mmm160) REVERT: F 43 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: F 65 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6451 (t) REVERT: F 77 MET cc_start: 0.7380 (tpt) cc_final: 0.6831 (tpt) REVERT: F 90 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4841 (mtpp) REVERT: F 122 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4648 (mtt-85) REVERT: F 123 LYS cc_start: 0.3481 (OUTLIER) cc_final: 0.3246 (mttm) outliers start: 153 outliers final: 45 residues processed: 272 average time/residue: 0.3689 time to fit residues: 124.4527 Evaluate side-chains 194 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 127 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS C 32 GLN C 64 GLN C 121 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN F 13 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133347 restraints weight = 12343.648| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.20 r_work: 0.3347 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10931 Z= 0.181 Angle : 0.677 8.378 15496 Z= 0.354 Chirality : 0.040 0.301 1837 Planarity : 0.006 0.127 1403 Dihedral : 23.982 176.823 3536 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.58 % Favored : 92.51 % Rotamer: Outliers : 6.96 % Allowed : 19.95 % Favored : 73.09 % 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: -1.28 (0.28), residues: 881 helix: 0.02 (0.19), residues: 665 sheet: -4.49 (0.78), residues: 28 loop : -3.13 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 116 HIS 0.005 0.001 HIS A 121 PHE 0.028 0.002 PHE A 231 TYR 0.016 0.002 TYR C 28 ARG 0.008 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.05475 ( 595) hydrogen bonds : angle 4.43198 ( 1594) covalent geometry : bond 0.00407 (10931) covalent geometry : angle 0.67662 (15496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 HIS cc_start: 0.7873 (m-70) cc_final: 0.7627 (m90) REVERT: A 283 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7930 (mttm) REVERT: B 4 ILE cc_start: 0.8881 (mt) cc_final: 0.8661 (mt) REVERT: C 14 MET cc_start: 0.7574 (tpt) cc_final: 0.7226 (ttt) REVERT: C 33 SER cc_start: 0.8493 (p) cc_final: 0.8225 (m) REVERT: D 64 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: E 22 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7442 (mtm-85) REVERT: E 50 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7611 (mt) REVERT: E 54 GLU cc_start: 0.7559 (tt0) cc_final: 0.7228 (tt0) REVERT: E 108 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7832 (tp30) REVERT: F 14 MET cc_start: 0.5232 (mmp) cc_final: 0.4288 (ttm) REVERT: F 43 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: F 77 MET cc_start: 0.8105 (tpt) cc_final: 0.7759 (tpt) REVERT: F 122 ARG cc_start: 0.4715 (OUTLIER) cc_final: 0.3996 (tmm160) outliers start: 52 outliers final: 20 residues processed: 194 average time/residue: 0.3251 time to fit residues: 80.4403 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 121 HIS A 286 ASN A 290 HIS B 38 HIS C 13 GLN C 92 HIS C 98 GLN C 121 ASN E 32 GLN E 63 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134804 restraints weight = 13000.502| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.25 r_work: 0.3295 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10931 Z= 0.162 Angle : 0.623 9.338 15496 Z= 0.319 Chirality : 0.037 0.177 1837 Planarity : 0.006 0.131 1403 Dihedral : 23.295 179.915 3407 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.36 % Favored : 92.96 % Rotamer: Outliers : 5.09 % Allowed : 21.95 % Favored : 72.96 % 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: -0.53 (0.28), residues: 881 helix: 0.49 (0.20), residues: 666 sheet: -3.36 (1.00), residues: 24 loop : -2.77 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 116 HIS 0.006 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.013 0.002 TYR C 28 ARG 0.008 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 595) hydrogen bonds : angle 4.07531 ( 1594) covalent geometry : bond 0.00368 (10931) covalent geometry : angle 0.62258 (15496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 248 HIS cc_start: 0.7826 (m-70) cc_final: 0.7585 (m-70) REVERT: A 256 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7368 (mtp-110) REVERT: C 33 SER cc_start: 0.8339 (p) cc_final: 0.8057 (m) REVERT: C 92 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6846 (m90) REVERT: D 103 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: E 50 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7159 (mt) REVERT: E 54 GLU cc_start: 0.7072 (tt0) cc_final: 0.6637 (tt0) REVERT: F 54 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: F 77 MET cc_start: 0.7740 (tpt) cc_final: 0.7514 (tpt) REVERT: F 122 ARG cc_start: 0.4502 (OUTLIER) cc_final: 0.4027 (tmm160) outliers start: 38 outliers final: 17 residues processed: 162 average time/residue: 0.3322 time to fit residues: 69.7041 Evaluate side-chains 143 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136757 restraints weight = 12789.345| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.13 r_work: 0.3328 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10931 Z= 0.156 Angle : 0.612 8.945 15496 Z= 0.313 Chirality : 0.037 0.201 1837 Planarity : 0.006 0.125 1403 Dihedral : 22.922 177.646 3391 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.79 % Favored : 93.64 % Rotamer: Outliers : 4.82 % Allowed : 21.95 % Favored : 73.23 % 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: -0.19 (0.29), residues: 881 helix: 0.72 (0.20), residues: 664 sheet: -3.39 (0.97), residues: 28 loop : -2.50 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.020 0.001 HIS C 92 PHE 0.025 0.002 PHE B 80 TYR 0.012 0.001 TYR C 28 ARG 0.010 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 595) hydrogen bonds : angle 3.99300 ( 1594) covalent geometry : bond 0.00354 (10931) covalent geometry : angle 0.61152 (15496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7224 (p0) cc_final: 0.7016 (p0) REVERT: A 296 LEU cc_start: 0.7070 (tt) cc_final: 0.6822 (tt) REVERT: C 33 SER cc_start: 0.8446 (p) cc_final: 0.8159 (m) REVERT: D 103 GLN cc_start: 0.8073 (mt0) cc_final: 0.7865 (mm-40) REVERT: F 43 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: F 77 MET cc_start: 0.7957 (tpt) cc_final: 0.7639 (tpt) REVERT: F 122 ARG cc_start: 0.4399 (OUTLIER) cc_final: 0.4144 (tmm160) outliers start: 36 outliers final: 21 residues processed: 163 average time/residue: 0.3255 time to fit residues: 68.3687 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 56 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137414 restraints weight = 12824.096| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.13 r_work: 0.3375 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10931 Z= 0.145 Angle : 0.598 8.102 15496 Z= 0.304 Chirality : 0.036 0.175 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.761 177.516 3387 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.24 % Favored : 93.08 % Rotamer: Outliers : 4.02 % Allowed : 22.49 % Favored : 73.49 % 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: -0.02 (0.28), residues: 881 helix: 0.82 (0.20), residues: 664 sheet: -2.73 (1.16), residues: 24 loop : -2.48 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.005 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.013 0.001 TYR F 20 ARG 0.010 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 595) hydrogen bonds : angle 3.91049 ( 1594) covalent geometry : bond 0.00332 (10931) covalent geometry : angle 0.59756 (15496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7836 (t70) cc_final: 0.7406 (t70) REVERT: A 290 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6461 (m-70) REVERT: A 296 LEU cc_start: 0.7029 (tt) cc_final: 0.6818 (tt) REVERT: B 26 TYR cc_start: 0.8653 (t80) cc_final: 0.8390 (t80) REVERT: C 33 SER cc_start: 0.8423 (p) cc_final: 0.8034 (m) REVERT: E 54 GLU cc_start: 0.7104 (tt0) cc_final: 0.6531 (tt0) REVERT: F 43 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: F 77 MET cc_start: 0.7928 (tpt) cc_final: 0.7617 (tpt) outliers start: 30 outliers final: 18 residues processed: 152 average time/residue: 0.3538 time to fit residues: 68.8204 Evaluate side-chains 143 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 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 87 GLN D 92 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.175339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135512 restraints weight = 12893.707| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.13 r_work: 0.3340 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10931 Z= 0.177 Angle : 0.615 9.080 15496 Z= 0.314 Chirality : 0.036 0.166 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.629 176.996 3381 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.56 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 23.56 % Favored : 72.42 % 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: -0.01 (0.28), residues: 881 helix: 0.80 (0.20), residues: 666 sheet: -3.14 (1.05), residues: 28 loop : -2.25 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 81 HIS 0.005 0.001 HIS D 38 PHE 0.027 0.002 PHE B 80 TYR 0.015 0.002 TYR F 20 ARG 0.011 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 595) hydrogen bonds : angle 3.97612 ( 1594) covalent geometry : bond 0.00409 (10931) covalent geometry : angle 0.61499 (15496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7786 (mtt-85) REVERT: A 290 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6518 (m-70) REVERT: B 26 TYR cc_start: 0.8751 (t80) cc_final: 0.8417 (t80) REVERT: C 33 SER cc_start: 0.8397 (p) cc_final: 0.8018 (m) REVERT: F 43 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: F 77 MET cc_start: 0.7982 (tpt) cc_final: 0.7667 (tpt) outliers start: 30 outliers final: 20 residues processed: 151 average time/residue: 0.3228 time to fit residues: 63.5268 Evaluate side-chains 148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135108 restraints weight = 13001.558| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.22 r_work: 0.3289 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10931 Z= 0.163 Angle : 0.606 7.597 15496 Z= 0.309 Chirality : 0.036 0.169 1837 Planarity : 0.006 0.117 1403 Dihedral : 22.596 176.936 3381 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.56 % Favored : 93.87 % Rotamer: Outliers : 3.75 % Allowed : 23.43 % Favored : 72.82 % 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: 0.06 (0.28), residues: 881 helix: 0.86 (0.19), residues: 663 sheet: -3.12 (1.05), residues: 28 loop : -2.25 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.004 0.001 HIS D 38 PHE 0.027 0.002 PHE B 80 TYR 0.012 0.001 TYR F 20 ARG 0.012 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 595) hydrogen bonds : angle 3.99651 ( 1594) covalent geometry : bond 0.00376 (10931) covalent geometry : angle 0.60635 (15496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8771 (t80) cc_final: 0.8442 (t80) REVERT: A 223 ASP cc_start: 0.7615 (t70) cc_final: 0.7172 (t70) REVERT: A 290 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6418 (m-70) REVERT: B 26 TYR cc_start: 0.8689 (t80) cc_final: 0.8395 (t80) REVERT: C 33 SER cc_start: 0.8345 (p) cc_final: 0.7981 (m) REVERT: E 50 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 43 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: F 77 MET cc_start: 0.7786 (tpt) cc_final: 0.7445 (tpt) outliers start: 28 outliers final: 23 residues processed: 147 average time/residue: 0.3142 time to fit residues: 59.9164 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS F 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136568 restraints weight = 12917.396| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.23 r_work: 0.3317 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10931 Z= 0.144 Angle : 0.591 7.098 15496 Z= 0.302 Chirality : 0.035 0.175 1837 Planarity : 0.006 0.116 1403 Dihedral : 22.470 177.592 3381 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.68 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 22.76 % Favored : 73.23 % 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: 0.22 (0.28), residues: 881 helix: 0.97 (0.20), residues: 663 sheet: -3.07 (1.04), residues: 28 loop : -2.16 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.004 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.018 0.001 TYR F 20 ARG 0.012 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 595) hydrogen bonds : angle 3.93844 ( 1594) covalent geometry : bond 0.00327 (10931) covalent geometry : angle 0.59138 (15496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8709 (t0) cc_final: 0.8485 (t0) REVERT: A 193 TYR cc_start: 0.8758 (t80) cc_final: 0.8520 (t80) REVERT: A 223 ASP cc_start: 0.7582 (t70) cc_final: 0.7157 (t70) REVERT: A 290 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6437 (m-70) REVERT: C 33 SER cc_start: 0.8345 (p) cc_final: 0.8002 (m) REVERT: E 50 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7280 (mt) REVERT: F 43 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: F 77 MET cc_start: 0.7785 (tpt) cc_final: 0.7442 (tpt) outliers start: 30 outliers final: 20 residues processed: 154 average time/residue: 0.3029 time to fit residues: 61.5885 Evaluate side-chains 148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.0040 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152267 restraints weight = 13131.195| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.20 r_work: 0.3582 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.003 0.083 10931 Z= 0.131 Angle : 0.594 8.919 15496 Z= 0.306 Chirality : 0.035 0.232 1837 Planarity : 0.006 0.116 1403 Dihedral : 22.340 179.108 3381 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.22 % Favored : 94.21 % Rotamer: Outliers : 3.08 % Allowed : 23.69 % Favored : 73.23 % 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: 0.38 (0.29), residues: 881 helix: 1.06 (0.20), residues: 667 sheet: -2.66 (1.12), residues: 26 loop : -2.14 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.004 0.001 HIS D 38 PHE 0.022 0.002 PHE B 80 TYR 0.018 0.001 TYR F 20 ARG 0.013 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 595) hydrogen bonds : angle 3.90675 ( 1594) covalent geometry : bond 0.00290 (10931) covalent geometry : angle 0.59368 (15496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8778 (t80) cc_final: 0.8328 (t80) REVERT: A 223 ASP cc_start: 0.7891 (t70) cc_final: 0.7542 (t70) REVERT: C 33 SER cc_start: 0.8566 (p) cc_final: 0.8321 (p) REVERT: E 50 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7394 (mt) REVERT: E 54 GLU cc_start: 0.7334 (tt0) cc_final: 0.6682 (tt0) REVERT: F 43 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: F 77 MET cc_start: 0.7882 (tpt) cc_final: 0.7534 (tpt) outliers start: 23 outliers final: 17 residues processed: 147 average time/residue: 0.3068 time to fit residues: 58.9402 Evaluate side-chains 145 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151160 restraints weight = 13025.507| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.19 r_work: 0.3574 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10931 Z= 0.152 Angle : 0.604 8.830 15496 Z= 0.309 Chirality : 0.036 0.220 1837 Planarity : 0.006 0.117 1403 Dihedral : 22.265 179.183 3379 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.47 % Favored : 92.96 % Rotamer: Outliers : 2.68 % Allowed : 24.10 % Favored : 73.23 % 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: 0.41 (0.29), residues: 881 helix: 1.07 (0.20), residues: 668 sheet: -2.76 (1.10), residues: 26 loop : -2.09 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.004 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.020 0.001 TYR F 20 ARG 0.013 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 595) hydrogen bonds : angle 3.94688 ( 1594) covalent geometry : bond 0.00349 (10931) covalent geometry : angle 0.60376 (15496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8752 (t80) cc_final: 0.8321 (t80) REVERT: A 223 ASP cc_start: 0.7838 (t70) cc_final: 0.7484 (t70) REVERT: C 33 SER cc_start: 0.8536 (p) cc_final: 0.8203 (m) REVERT: D 18 GLU cc_start: 0.7175 (mp0) cc_final: 0.6909 (mp0) REVERT: E 50 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7452 (mt) REVERT: F 43 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: F 77 MET cc_start: 0.7887 (tpt) cc_final: 0.7556 (tpt) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.3161 time to fit residues: 57.4366 Evaluate side-chains 142 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 6.9990 chunk 44 optimal weight: 0.0000 chunk 84 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.193665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155875 restraints weight = 13043.204| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.16 r_work: 0.3636 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10931 Z= 0.123 Angle : 0.586 8.797 15496 Z= 0.299 Chirality : 0.035 0.206 1837 Planarity : 0.006 0.116 1403 Dihedral : 22.149 179.997 3378 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.33 % Favored : 94.10 % Rotamer: Outliers : 2.68 % Allowed : 24.23 % Favored : 73.09 % 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: 0.61 (0.29), residues: 881 helix: 1.19 (0.20), residues: 669 sheet: -2.03 (1.24), residues: 22 loop : -2.07 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.007 0.001 HIS B 38 PHE 0.021 0.002 PHE A 231 TYR 0.020 0.001 TYR F 20 ARG 0.013 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 595) hydrogen bonds : angle 3.83816 ( 1594) covalent geometry : bond 0.00268 (10931) covalent geometry : angle 0.58641 (15496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.01 seconds wall clock time: 99 minutes 34.86 seconds (5974.86 seconds total)