Starting phenix.real_space_refine on Fri Feb 14 13:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub7_42077/02_2025/8ub7_42077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub7_42077/02_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_42077/02_2025/8ub7_42077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub7_42077/02_2025/8ub7_42077.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub7_42077/02_2025/8ub7_42077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub7_42077/02_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-5592/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: 7.26, per 1000 atoms: 0.70 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: 2.78 Conformation dependent library (CDL) restraints added in 977.0 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: 4.58 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: 3.62 Time building geometry restraints manager: 3.18 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: 2.040 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.590 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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= 0.670 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 *********************** 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 : 0.869 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: 0.3842 time to fit residues: 129.1800 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 : 0.990 ------------------------------------------------------------------------------- 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 = 0.133343 restraints weight = 12343.648| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.20 r_work: 0.3343 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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= 0.261 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 *********************** 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 : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 HIS cc_start: 0.7869 (m-70) cc_final: 0.7624 (m90) REVERT: A 283 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7938 (mttm) REVERT: B 4 ILE cc_start: 0.8889 (mt) cc_final: 0.8662 (mt) REVERT: C 14 MET cc_start: 0.7605 (tpt) cc_final: 0.7250 (ttt) REVERT: C 33 SER cc_start: 0.8489 (p) cc_final: 0.8221 (m) REVERT: D 64 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6679 (mt0) REVERT: E 22 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7446 (mtm-85) REVERT: E 50 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7616 (mt) REVERT: E 54 GLU cc_start: 0.7577 (tt0) cc_final: 0.7252 (tt0) REVERT: E 108 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7845 (tp30) REVERT: F 14 MET cc_start: 0.5267 (mmp) cc_final: 0.4314 (ttm) REVERT: F 43 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: F 77 MET cc_start: 0.8104 (tpt) cc_final: 0.7774 (tpt) REVERT: F 122 ARG cc_start: 0.4705 (OUTLIER) cc_final: 0.3998 (tmm160) outliers start: 52 outliers final: 20 residues processed: 194 average time/residue: 0.3378 time to fit residues: 83.5634 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 : 1.105 ------------------------------------------------------------------------------- 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: 0.0470 chunk 29 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 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: 0.2980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4043 r_free = 0.4043 target = 0.178103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137852 restraints weight = 13012.854| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.17 r_work: 0.3360 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10931 Z= 0.195 Angle : 0.605 8.869 15496 Z= 0.310 Chirality : 0.036 0.186 1837 Planarity : 0.006 0.131 1403 Dihedral : 23.158 178.083 3407 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.47 % Favored : 92.85 % Rotamer: Outliers : 4.82 % Allowed : 22.22 % 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: -0.31 (0.29), residues: 881 helix: 0.64 (0.20), residues: 665 sheet: -3.29 (1.02), residues: 24 loop : -2.66 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 116 HIS 0.006 0.001 HIS D 38 PHE 0.022 0.002 PHE A 231 TYR 0.013 0.001 TYR A 107 ARG 0.008 0.001 ARG B 122 *********************** 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 176 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7572 (t0) cc_final: 0.7309 (t0) REVERT: A 256 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7269 (mtp85) REVERT: C 33 SER cc_start: 0.8238 (p) cc_final: 0.7943 (m) REVERT: D 47 LYS cc_start: 0.8899 (mttm) cc_final: 0.8642 (mttm) REVERT: E 54 GLU cc_start: 0.6889 (tt0) cc_final: 0.6672 (tp30) REVERT: F 77 MET cc_start: 0.7609 (tpt) cc_final: 0.7404 (tpt) REVERT: F 122 ARG cc_start: 0.4413 (OUTLIER) cc_final: 0.4038 (tmm160) outliers start: 36 outliers final: 16 residues processed: 165 average time/residue: 0.3363 time to fit residues: 70.8947 Evaluate side-chains 138 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 99 VAL 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: 3.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN D 121 ASN ** 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 = 0.4038 r_free = 0.4038 target = 0.177754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137513 restraints weight = 12783.167| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.19 r_work: 0.3349 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10931 Z= 0.204 Angle : 0.595 8.749 15496 Z= 0.304 Chirality : 0.036 0.180 1837 Planarity : 0.006 0.123 1403 Dihedral : 22.805 177.102 3387 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.56 % Favored : 93.87 % Rotamer: Outliers : 4.15 % Allowed : 21.95 % Favored : 73.90 % 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: 0.00 (0.29), residues: 881 helix: 0.86 (0.20), residues: 665 sheet: -3.42 (0.97), residues: 28 loop : -2.45 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.005 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.012 0.001 TYR F 20 ARG 0.009 0.001 ARG E 22 *********************** 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 164 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6368 (m-70) REVERT: C 33 SER cc_start: 0.8293 (p) cc_final: 0.8011 (m) REVERT: E 54 GLU cc_start: 0.6990 (tt0) cc_final: 0.6586 (tt0) REVERT: F 43 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: F 54 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: F 77 MET cc_start: 0.7691 (tpt) cc_final: 0.7457 (tpt) outliers start: 31 outliers final: 16 residues processed: 156 average time/residue: 0.3379 time to fit residues: 66.9363 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 : 0.851 ------------------------------------------------------------------------------- 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 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 43 GLU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 113 LEU 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: 0.5980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.177288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137059 restraints weight = 12823.447| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.18 r_work: 0.3348 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10931 Z= 0.224 Angle : 0.603 8.954 15496 Z= 0.306 Chirality : 0.036 0.239 1837 Planarity : 0.006 0.122 1403 Dihedral : 22.663 176.966 3381 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.02 % Favored : 93.30 % Rotamer: Outliers : 4.28 % Allowed : 23.03 % Favored : 72.69 % 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: 0.01 (0.28), residues: 881 helix: 0.85 (0.20), residues: 665 sheet: -3.27 (1.02), residues: 28 loop : -2.37 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 116 HIS 0.005 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.014 0.001 TYR F 20 ARG 0.009 0.001 ARG B 122 *********************** 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 168 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7515 (t70) cc_final: 0.7087 (t70) REVERT: A 256 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7182 (mtp-110) REVERT: A 290 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6348 (m-70) REVERT: A 296 LEU cc_start: 0.6998 (tt) cc_final: 0.6773 (tt) REVERT: C 33 SER cc_start: 0.8330 (p) cc_final: 0.7950 (m) REVERT: E 54 GLU cc_start: 0.6915 (tt0) cc_final: 0.6460 (tt0) REVERT: F 43 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: F 77 MET cc_start: 0.7703 (tpt) cc_final: 0.7450 (tpt) outliers start: 32 outliers final: 19 residues processed: 159 average time/residue: 0.3343 time to fit residues: 67.6861 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 VAL 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 30 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 94 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 41 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137840 restraints weight = 12926.380| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.22 r_work: 0.3340 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10931 Z= 0.199 Angle : 0.592 9.230 15496 Z= 0.300 Chirality : 0.035 0.167 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.573 176.918 3381 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.99 % Favored : 94.44 % 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: 0.16 (0.28), residues: 881 helix: 0.94 (0.20), residues: 666 sheet: -3.18 (1.02), residues: 28 loop : -2.25 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.005 0.001 HIS D 38 PHE 0.024 0.002 PHE B 80 TYR 0.017 0.001 TYR F 20 ARG 0.012 0.001 ARG B 122 *********************** 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 162 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8642 (t0) cc_final: 0.8429 (t0) REVERT: A 193 TYR cc_start: 0.8692 (t80) cc_final: 0.8435 (t80) REVERT: A 223 ASP cc_start: 0.7605 (t70) cc_final: 0.7211 (t70) REVERT: A 290 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6334 (m-70) REVERT: C 33 SER cc_start: 0.8349 (p) cc_final: 0.7987 (m) REVERT: E 54 GLU cc_start: 0.6886 (tt0) cc_final: 0.6380 (tt0) REVERT: F 43 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: F 77 MET cc_start: 0.7726 (tpt) cc_final: 0.7458 (tpt) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.3387 time to fit residues: 65.2830 Evaluate side-chains 153 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 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 68 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 181 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 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 D residue 18 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 94 MET 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 123 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 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 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136806 restraints weight = 12960.218| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.14 r_work: 0.3364 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10931 Z= 0.231 Angle : 0.597 8.819 15496 Z= 0.304 Chirality : 0.035 0.169 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.468 176.808 3380 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.68 % Favored : 93.76 % Rotamer: Outliers : 3.75 % Allowed : 23.96 % Favored : 72.29 % 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: 0.25 (0.28), residues: 881 helix: 0.98 (0.19), residues: 665 sheet: -2.95 (1.08), residues: 26 loop : -2.20 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 116 HIS 0.004 0.001 HIS D 38 PHE 0.025 0.002 PHE B 80 TYR 0.014 0.001 TYR F 20 ARG 0.011 0.001 ARG B 122 *********************** 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 : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8726 (t0) cc_final: 0.8522 (t0) REVERT: A 193 TYR cc_start: 0.8762 (t80) cc_final: 0.8490 (t80) REVERT: C 33 SER cc_start: 0.8505 (p) cc_final: 0.8195 (p) REVERT: E 54 GLU cc_start: 0.7064 (tt0) cc_final: 0.6513 (tt0) REVERT: F 43 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: F 77 MET cc_start: 0.7962 (tpt) cc_final: 0.7629 (tpt) outliers start: 28 outliers final: 21 residues processed: 145 average time/residue: 0.3231 time to fit residues: 60.8103 Evaluate side-chains 145 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 68 VAL 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 259 ASN 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 C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 94 MET 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: 0.0870 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.176763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136351 restraints weight = 12883.863| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.16 r_work: 0.3313 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10931 Z= 0.252 Angle : 0.605 8.525 15496 Z= 0.309 Chirality : 0.036 0.172 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.415 177.769 3378 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.90 % Favored : 93.53 % Rotamer: Outliers : 4.28 % Allowed : 23.83 % Favored : 71.89 % 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: 0.18 (0.28), residues: 881 helix: 0.93 (0.19), residues: 662 sheet: -3.19 (1.03), residues: 28 loop : -2.09 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 116 HIS 0.005 0.001 HIS B 38 PHE 0.026 0.002 PHE B 80 TYR 0.016 0.001 TYR F 20 ARG 0.012 0.001 ARG B 122 *********************** 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: 32 poor density : 131 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8683 (t0) cc_final: 0.8468 (t0) REVERT: A 193 TYR cc_start: 0.8739 (t80) cc_final: 0.8498 (t80) REVERT: A 290 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6451 (m-70) REVERT: C 33 SER cc_start: 0.8437 (p) cc_final: 0.8075 (m) REVERT: E 19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6810 (mmm160) REVERT: F 14 MET cc_start: 0.7141 (ttp) cc_final: 0.6557 (tpt) REVERT: F 43 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: F 77 MET cc_start: 0.7709 (tpt) cc_final: 0.7422 (tpt) outliers start: 32 outliers final: 24 residues processed: 150 average time/residue: 0.3103 time to fit residues: 60.7587 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 68 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 ASP 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 275 SER 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 C residue 11 TYR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET 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: 0.6980 chunk 14 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 92 HIS F 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139979 restraints weight = 12923.471| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.12 r_work: 0.3410 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10931 Z= 0.195 Angle : 0.583 7.901 15496 Z= 0.297 Chirality : 0.035 0.183 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.336 179.118 3378 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.22 % Favored : 94.21 % Rotamer: Outliers : 3.75 % Allowed : 24.36 % Favored : 71.89 % 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: 0.35 (0.28), residues: 881 helix: 1.05 (0.19), residues: 664 sheet: -3.15 (1.02), residues: 28 loop : -2.07 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 116 HIS 0.004 0.001 HIS B 38 PHE 0.023 0.002 PHE B 80 TYR 0.018 0.001 TYR F 20 ARG 0.014 0.001 ARG B 122 *********************** 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 163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8654 (t0) cc_final: 0.8447 (t0) REVERT: A 193 TYR cc_start: 0.8770 (t80) cc_final: 0.8528 (t80) REVERT: C 33 SER cc_start: 0.8494 (p) cc_final: 0.8201 (p) REVERT: C 99 VAL cc_start: 0.9168 (t) cc_final: 0.8962 (t) REVERT: E 54 GLU cc_start: 0.7074 (tt0) cc_final: 0.6525 (tt0) REVERT: F 14 MET cc_start: 0.7294 (ttp) cc_final: 0.6745 (tpt) REVERT: F 43 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: F 77 MET cc_start: 0.7873 (tpt) cc_final: 0.7568 (tpt) REVERT: F 113 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8068 (mt) outliers start: 28 outliers final: 22 residues processed: 152 average time/residue: 0.3191 time to fit residues: 63.1128 Evaluate side-chains 150 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 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 68 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 ASP 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 275 SER 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 C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137897 restraints weight = 12789.424| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.11 r_work: 0.3351 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10931 Z= 0.246 Angle : 0.605 9.223 15496 Z= 0.308 Chirality : 0.036 0.229 1837 Planarity : 0.006 0.119 1403 Dihedral : 22.273 179.203 3378 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.24 % Favored : 93.19 % Rotamer: Outliers : 4.02 % Allowed : 24.10 % Favored : 71.89 % 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: 0.26 (0.28), residues: 881 helix: 0.97 (0.19), residues: 666 sheet: -3.14 (1.01), residues: 28 loop : -2.08 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.005 0.001 HIS B 38 PHE 0.026 0.002 PHE B 80 TYR 0.018 0.001 TYR F 20 ARG 0.013 0.001 ARG B 122 ********************** 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 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8813 (t80) cc_final: 0.8480 (t80) REVERT: C 33 SER cc_start: 0.8426 (p) cc_final: 0.8072 (m) REVERT: E 19 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6824 (mmm160) REVERT: F 14 MET cc_start: 0.7389 (ttp) cc_final: 0.6703 (tpt) REVERT: F 43 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: F 77 MET cc_start: 0.7954 (tpt) cc_final: 0.7591 (tpt) outliers start: 30 outliers final: 25 residues processed: 143 average time/residue: 0.3050 time to fit residues: 57.3899 Evaluate side-chains 148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 68 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 ASP 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 259 ASN Chi-restraints excluded: chain A residue 275 SER 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 C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 94 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 chunk 84 optimal weight: 0.0980 chunk 10 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.1654 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.184458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146175 restraints weight = 12825.758| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.17 r_work: 0.3483 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10931 Z= 0.159 Angle : 0.576 9.322 15496 Z= 0.293 Chirality : 0.035 0.229 1837 Planarity : 0.006 0.117 1403 Dihedral : 22.066 179.113 3378 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.45 % Favored : 93.98 % Rotamer: Outliers : 2.54 % Allowed : 25.97 % Favored : 71.49 % 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: 0.71 (0.29), residues: 881 helix: 1.29 (0.20), residues: 661 sheet: -2.38 (1.18), residues: 24 loop : -1.91 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.004 0.001 HIS D 38 PHE 0.020 0.002 PHE B 80 TYR 0.023 0.001 TYR F 20 ARG 0.014 0.001 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.05 seconds wall clock time: 89 minutes 47.01 seconds (5387.01 seconds total)