Starting phenix.real_space_refine on Thu Jul 2 20:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_42077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_42077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_42077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_42077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub7_42077/07_2026/8ub7_42077.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.74, per 1000 atoms: 0.17 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: 0.85 Conformation dependent library (CDL) restraints added in 228.8 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: 1.22 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: 1.27 Time building geometry restraints manager: 1.07 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 1.534 1.302 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' DCP A 401 " pdb=" C2' DCP A 401 " ideal model delta sigma weight residual 1.534 1.356 0.178 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C4' DCP A 401 " pdb=" O4' DCP A 401 " ideal model delta sigma weight residual 1.420 1.540 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CA ARG A 4 " pdb=" C ARG A 4 " ideal model delta sigma weight residual 1.529 1.474 0.055 9.30e-03 1.16e+04 3.50e+01 bond pdb=" C1' DCP A 401 " pdb=" N1 DCP A 401 " ideal model delta sigma weight residual 1.460 1.572 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 14043 2.55 - 5.09: 1301 5.09 - 7.64: 133 7.64 - 10.18: 17 10.18 - 12.73: 2 Bond angle restraints: 15496 Sorted by residual: 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=" 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 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 110.61 103.22 7.39 1.25e+00 6.40e-01 3.50e+01 angle pdb=" CA GLN F 103 " pdb=" CB GLN F 103 " pdb=" CG GLN F 103 " ideal model delta sigma weight residual 114.10 102.41 11.69 2.00e+00 2.50e-01 3.42e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.15e+01 ... (remaining 15491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5944 35.16 - 70.32: 777 70.32 - 105.48: 74 105.48 - 140.64: 1 140.64 - 175.80: 4 Dihedral angle restraints: 6800 sinusoidal: 4201 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 6797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1492 0.120 - 0.240: 305 0.240 - 0.360: 30 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: 2.290 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 0.232 10931 Z= 0.653 Angle : 1.535 12.729 15496 Z= 0.990 Chirality : 0.098 0.600 1837 Planarity : 0.011 0.106 1403 Dihedral : 25.404 175.798 5124 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.018 0.002 ARG B 22 TYR 0.081 0.008 TYR C 28 PHE 0.057 0.009 PHE A 231 TRP 0.040 0.008 TRP A 33 HIS 0.018 0.004 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.01087 / 0.65 (10931) covalent geometry : angle 1.53487 / 0.99 (15496) hydrogen bonds : bond 0.18109 / 12.00 ( 595) hydrogen bonds : angle 8.70736 / 6.13 ( 1594) *********************** 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 : 0.303 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: 0.7873 (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: 0.6030 (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: 0.7432 (OUTLIER) cc_final: 0.6862 (mt) REVERT: E 52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6770 (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: 0.7619 (tpp) REVERT: E 89 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.6151 (mt0) REVERT: E 90 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6485 (ttmm) REVERT: E 94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (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: 0.6457 (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: 0.4842 (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: 0.1374 time to fit residues: 46.9282 Evaluate side-chains 195 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 89 GLN 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 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN F 13 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.183107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140013 restraints weight = 12799.719| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.43 r_work: 0.3452 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2225 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= 0.211 Angle : 0.738 8.694 15496 Z= 0.411 Chirality : 0.045 0.344 1837 Planarity : 0.008 0.132 1403 Dihedral : 24.460 179.908 3546 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.72 % Favored : 91.37 % Rotamer: Outliers : 8.70 % Allowed : 18.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 881 helix: -0.38 (0.19), residues: 668 sheet: -3.99 (0.92), residues: 22 loop : -3.40 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 36 TYR 0.021 0.002 TYR C 28 PHE 0.032 0.003 PHE B 80 TRP 0.017 0.002 TRP D 116 HIS 0.006 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (10931) covalent geometry : angle 0.73764 / 0.41 (15496) hydrogen bonds : bond 0.07197 / 4.66 ( 595) hydrogen bonds : angle 4.86268 / 3.37 ( 1594) *********************** 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 204 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8986 (t80) cc_final: 0.8766 (t80) REVERT: A 248 HIS cc_start: 0.7895 (m-70) cc_final: 0.7589 (m90) REVERT: A 256 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7716 (mtp-110) REVERT: A 283 LYS cc_start: 0.8216 (mmtt) cc_final: 0.8002 (mttm) REVERT: C 14 MET cc_start: 0.7465 (tpt) cc_final: 0.7078 (ttt) REVERT: C 33 SER cc_start: 0.8609 (p) cc_final: 0.8408 (m) REVERT: C 90 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6873 (mtpp) REVERT: E 50 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7610 (mt) REVERT: E 52 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7369 (tp40) REVERT: E 67 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: F 14 MET cc_start: 0.5620 (mmp) cc_final: 0.5059 (tmm) REVERT: F 33 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8114 (p) REVERT: F 43 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: F 83 ARG cc_start: 0.8112 (ptp90) cc_final: 0.7820 (ptp90) REVERT: F 122 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4025 (tmm160) outliers start: 65 outliers final: 23 residues processed: 194 average time/residue: 0.1298 time to fit residues: 32.3286 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 256 ARG Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 ASP 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 89 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 90 LYS 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 52 GLN Chi-restraints excluded: chain E residue 67 LYS 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 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 LEU 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 88 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS E 52 GLN E 63 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132505 restraints weight = 12708.657| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.18 r_work: 0.3308 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10931 Z= 0.194 Angle : 0.622 8.061 15496 Z= 0.349 Chirality : 0.041 0.314 1837 Planarity : 0.007 0.136 1403 Dihedral : 23.902 179.342 3438 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.04 % Favored : 92.17 % Rotamer: Outliers : 6.02 % Allowed : 21.95 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.28), residues: 881 helix: 0.08 (0.19), residues: 665 sheet: -3.49 (0.99), residues: 24 loop : -3.15 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.018 0.002 TYR F 28 PHE 0.028 0.002 PHE A 231 TRP 0.022 0.002 TRP A 210 HIS 0.012 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (10931) covalent geometry : angle 0.62163 / 0.35 (15496) hydrogen bonds : bond 0.05986 / 3.83 ( 595) hydrogen bonds : angle 4.50196 / 3.13 ( 1594) *********************** 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 172 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.6715 (ttt180) cc_final: 0.6472 (ttt180) REVERT: A 283 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7991 (mttm) REVERT: B 4 ILE cc_start: 0.8952 (mt) cc_final: 0.8718 (mt) REVERT: C 33 SER cc_start: 0.8510 (p) cc_final: 0.8275 (m) REVERT: C 89 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6477 (pp30) REVERT: E 50 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7659 (mt) REVERT: E 52 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7258 (tp40) REVERT: F 14 MET cc_start: 0.5443 (mmp) cc_final: 0.4553 (ttm) REVERT: F 43 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: F 122 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.3998 (tmm160) outliers start: 45 outliers final: 29 residues processed: 160 average time/residue: 0.1200 time to fit residues: 24.9878 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 135 LEU 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 276 SER Chi-restraints excluded: chain A residue 290 HIS 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 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL 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 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET 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 55 LEU Chi-restraints excluded: chain F residue 65 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 20 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS C 13 GLN C 32 GLN C 121 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132476 restraints weight = 12810.972| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.21 r_work: 0.3321 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3145 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= 0.179 Angle : 0.588 6.999 15496 Z= 0.326 Chirality : 0.040 0.279 1837 Planarity : 0.006 0.126 1403 Dihedral : 23.639 178.775 3421 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.47 % Favored : 92.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 881 helix: 0.30 (0.19), residues: 666 sheet: -2.68 (1.15), residues: 22 loop : -2.96 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.016 0.002 TYR F 28 PHE 0.027 0.002 PHE A 231 TRP 0.009 0.001 TRP C 81 HIS 0.005 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10931) covalent geometry : angle 0.58823 / 0.33 (15496) hydrogen bonds : bond 0.05612 / 3.53 ( 595) hydrogen bonds : angle 4.29582 / 2.99 ( 1594) *********************** 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 163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.6627 (ttt180) cc_final: 0.6423 (ttt180) REVERT: B 4 ILE cc_start: 0.8922 (mt) cc_final: 0.8697 (mt) REVERT: C 33 SER cc_start: 0.8507 (p) cc_final: 0.8293 (m) REVERT: E 50 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7540 (mt) REVERT: E 52 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7200 (tp40) REVERT: E 103 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8136 (mm-40) REVERT: F 43 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: F 122 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4007 (tmm160) outliers start: 38 outliers final: 23 residues processed: 156 average time/residue: 0.1185 time to fit residues: 24.0750 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain D residue 53 VAL 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 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET 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 55 LEU Chi-restraints excluded: chain F residue 65 VAL 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 47 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 70 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.175005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134827 restraints weight = 12931.797| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.26 r_work: 0.3337 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10931 Z= 0.146 Angle : 0.562 8.949 15496 Z= 0.313 Chirality : 0.039 0.241 1837 Planarity : 0.006 0.124 1403 Dihedral : 23.445 179.917 3411 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.24 % Favored : 92.96 % Rotamer: Outliers : 4.55 % Allowed : 23.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.28), residues: 881 helix: 0.55 (0.20), residues: 664 sheet: -2.55 (1.23), residues: 22 loop : -2.67 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 122 TYR 0.012 0.001 TYR F 28 PHE 0.025 0.002 PHE A 231 TRP 0.010 0.001 TRP F 116 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10931) covalent geometry : angle 0.56163 / 0.31 (15496) hydrogen bonds : bond 0.05287 / 3.30 ( 595) hydrogen bonds : angle 4.15439 / 2.90 ( 1594) *********************** 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 163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.304 Fit side-chains REVERT: A 193 TYR cc_start: 0.8749 (t80) cc_final: 0.8478 (t80) REVERT: A 223 ASP cc_start: 0.7983 (t70) cc_final: 0.7574 (t70) REVERT: B 4 ILE cc_start: 0.8804 (mt) cc_final: 0.8577 (mt) REVERT: C 33 SER cc_start: 0.8399 (p) cc_final: 0.8121 (m) REVERT: C 47 LYS cc_start: 0.8627 (mttm) cc_final: 0.8412 (mtpt) REVERT: E 50 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7432 (mt) REVERT: E 52 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7202 (tp40) REVERT: E 103 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8157 (mm-40) REVERT: E 108 GLU cc_start: 0.8162 (tp30) cc_final: 0.7861 (tp30) REVERT: F 14 MET cc_start: 0.7018 (ttt) cc_final: 0.6723 (ttp) REVERT: F 43 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: F 122 ARG cc_start: 0.4552 (OUTLIER) cc_final: 0.4019 (tmm160) outliers start: 34 outliers final: 20 residues processed: 154 average time/residue: 0.1169 time to fit residues: 23.6142 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 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 95 THR Chi-restraints excluded: chain C residue 11 TYR 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 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET 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 65 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 78 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4006 r_free = 0.4006 target = 0.174553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134175 restraints weight = 13043.942| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.28 r_work: 0.3287 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10931 Z= 0.159 Angle : 0.565 10.070 15496 Z= 0.312 Chirality : 0.039 0.211 1837 Planarity : 0.006 0.122 1403 Dihedral : 23.285 179.302 3407 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.36 % Favored : 92.85 % Rotamer: Outliers : 5.35 % Allowed : 21.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 881 helix: 0.62 (0.19), residues: 667 sheet: -2.37 (1.27), residues: 22 loop : -2.81 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 122 TYR 0.013 0.001 TYR A 35 PHE 0.025 0.002 PHE B 80 TRP 0.007 0.001 TRP A 303 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10931) covalent geometry : angle 0.56504 / 0.31 (15496) hydrogen bonds : bond 0.05259 / 3.28 ( 595) hydrogen bonds : angle 4.10970 / 2.86 ( 1594) *********************** 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 170 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7367 (mtp-110) REVERT: B 4 ILE cc_start: 0.8754 (mt) cc_final: 0.8554 (mt) REVERT: C 33 SER cc_start: 0.8368 (p) cc_final: 0.8121 (m) REVERT: C 47 LYS cc_start: 0.8624 (mttm) cc_final: 0.8404 (mtpt) REVERT: E 52 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7311 (tp40) REVERT: E 108 GLU cc_start: 0.8115 (tp30) cc_final: 0.7545 (tp30) REVERT: F 14 MET cc_start: 0.6947 (ttt) cc_final: 0.6372 (ttp) outliers start: 40 outliers final: 28 residues processed: 156 average time/residue: 0.1106 time to fit residues: 22.3869 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL 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 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 95 THR 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 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 65 VAL 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 18 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4009 r_free = 0.4009 target = 0.174796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135096 restraints weight = 12902.030| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.17 r_work: 0.3311 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3872 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= 0.161 Angle : 0.571 8.735 15496 Z= 0.315 Chirality : 0.038 0.200 1837 Planarity : 0.006 0.119 1403 Dihedral : 23.134 178.516 3398 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.24 % Favored : 92.96 % Rotamer: Outliers : 4.69 % Allowed : 22.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.28), residues: 881 helix: 0.66 (0.19), residues: 666 sheet: -2.72 (1.18), residues: 24 loop : -2.79 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 122 TYR 0.016 0.001 TYR B 26 PHE 0.025 0.002 PHE B 80 TRP 0.007 0.001 TRP A 303 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10931) covalent geometry : angle 0.57117 / 0.31 (15496) hydrogen bonds : bond 0.05203 / 3.24 ( 595) hydrogen bonds : angle 4.08017 / 2.84 ( 1594) *********************** 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 168 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7937 (t70) cc_final: 0.7479 (t70) REVERT: A 256 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7359 (mtp-110) REVERT: B 4 ILE cc_start: 0.8718 (mt) cc_final: 0.8511 (mt) REVERT: B 77 MET cc_start: 0.8927 (tpt) cc_final: 0.8578 (tpt) REVERT: C 33 SER cc_start: 0.8406 (p) cc_final: 0.8124 (m) REVERT: C 47 LYS cc_start: 0.8623 (mttm) cc_final: 0.8400 (mtpt) REVERT: D 19 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7643 (mmt-90) REVERT: E 19 ARG cc_start: 0.7071 (mmm160) cc_final: 0.6776 (mmm160) REVERT: E 50 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7398 (mt) REVERT: E 52 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7401 (tp40) REVERT: E 108 GLU cc_start: 0.8061 (tp30) cc_final: 0.7833 (tp30) outliers start: 35 outliers final: 24 residues processed: 155 average time/residue: 0.1255 time to fit residues: 25.1683 Evaluate side-chains 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL 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 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 95 THR 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 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 27 LEU 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 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.4013 r_free = 0.4013 target = 0.175131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135906 restraints weight = 12880.077| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.21 r_work: 0.3337 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10931 Z= 0.158 Angle : 0.557 9.460 15496 Z= 0.308 Chirality : 0.038 0.197 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.994 177.973 3393 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.79 % Favored : 93.42 % Rotamer: Outliers : 4.69 % Allowed : 23.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 881 helix: 0.77 (0.19), residues: 664 sheet: -2.45 (1.22), residues: 22 loop : -2.76 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 19 TYR 0.013 0.001 TYR F 20 PHE 0.025 0.002 PHE B 80 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10931) covalent geometry : angle 0.55669 / 0.31 (15496) hydrogen bonds : bond 0.05202 / 3.23 ( 595) hydrogen bonds : angle 4.03743 / 2.81 ( 1594) *********************** 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 167 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7957 (t70) cc_final: 0.7500 (t70) REVERT: A 256 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7329 (mtp-110) REVERT: B 4 ILE cc_start: 0.8723 (mt) cc_final: 0.8496 (mt) REVERT: B 64 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6936 (tt0) REVERT: B 77 MET cc_start: 0.8903 (tpt) cc_final: 0.8513 (tpt) REVERT: C 33 SER cc_start: 0.8409 (p) cc_final: 0.8123 (m) REVERT: C 47 LYS cc_start: 0.8641 (mttm) cc_final: 0.8413 (mtpt) REVERT: E 50 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7434 (mt) REVERT: E 52 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7386 (tp40) REVERT: E 54 GLU cc_start: 0.7334 (tt0) cc_final: 0.7030 (tt0) REVERT: F 43 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7540 (tt0) outliers start: 35 outliers final: 22 residues processed: 155 average time/residue: 0.1229 time to fit residues: 24.7278 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL 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 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR 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 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET 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 87 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 19 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.4021 r_free = 0.4021 target = 0.175849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134718 restraints weight = 12899.227| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.24 r_work: 0.3320 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4146 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= 0.150 Angle : 0.561 9.458 15496 Z= 0.308 Chirality : 0.038 0.217 1837 Planarity : 0.006 0.117 1403 Dihedral : 22.876 177.876 3391 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.02 % Favored : 93.30 % Rotamer: Outliers : 4.28 % Allowed : 24.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.28), residues: 881 helix: 0.76 (0.19), residues: 665 sheet: -2.54 (1.19), residues: 22 loop : -2.69 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 122 TYR 0.015 0.001 TYR F 20 PHE 0.025 0.002 PHE B 80 TRP 0.007 0.001 TRP A 249 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10931) covalent geometry : angle 0.56130 / 0.31 (15496) hydrogen bonds : bond 0.05152 / 3.19 ( 595) hydrogen bonds : angle 4.04535 / 2.82 ( 1594) *********************** 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 164 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7962 (t70) cc_final: 0.7525 (t70) REVERT: B 4 ILE cc_start: 0.8663 (mt) cc_final: 0.8455 (mt) REVERT: C 33 SER cc_start: 0.8433 (p) cc_final: 0.8131 (m) REVERT: C 47 LYS cc_start: 0.8651 (mttm) cc_final: 0.8417 (mtpt) REVERT: E 50 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7487 (mt) REVERT: E 52 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7249 (tp40) REVERT: E 54 GLU cc_start: 0.7291 (tt0) cc_final: 0.6980 (tt0) REVERT: F 43 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7560 (tt0) outliers start: 32 outliers final: 25 residues processed: 153 average time/residue: 0.1179 time to fit residues: 23.5195 Evaluate side-chains 155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL 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 B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR 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 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU 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 65 VAL 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 95 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3985 r_free = 0.3985 target = 0.172285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133291 restraints weight = 12842.557| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.11 r_work: 0.3290 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 10931 Z= 0.264 Angle : 0.632 9.810 15496 Z= 0.344 Chirality : 0.041 0.204 1837 Planarity : 0.006 0.120 1403 Dihedral : 22.831 177.612 3391 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.58 % Favored : 92.85 % Rotamer: Outliers : 4.28 % Allowed : 23.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.28), residues: 881 helix: 0.53 (0.19), residues: 665 sheet: -2.83 (1.16), residues: 24 loop : -2.91 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.019 0.002 TYR F 20 PHE 0.031 0.003 PHE B 80 TRP 0.010 0.002 TRP C 81 HIS 0.006 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (10931) covalent geometry : angle 0.63163 / 0.34 (15496) hydrogen bonds : bond 0.05562 / 3.48 ( 595) hydrogen bonds : angle 4.27843 / 2.98 ( 1594) ********************** 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 162 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 SER cc_start: 0.8390 (p) cc_final: 0.8153 (m) REVERT: C 47 LYS cc_start: 0.8589 (mttm) cc_final: 0.8377 (mtpt) REVERT: C 108 GLU cc_start: 0.7944 (tp30) cc_final: 0.7706 (tp30) REVERT: D 18 GLU cc_start: 0.7321 (mp0) cc_final: 0.6959 (mp0) REVERT: E 50 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7552 (mt) REVERT: E 52 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: F 43 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7487 (tt0) outliers start: 32 outliers final: 26 residues processed: 150 average time/residue: 0.1076 time to fit residues: 20.9334 Evaluate side-chains 156 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 138 ASP 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 197 VAL 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 B residue 95 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 95 THR 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 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 VAL 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 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.4013 r_free = 0.4013 target = 0.175025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135401 restraints weight = 12931.462| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.19 r_work: 0.3303 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4234 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= 0.164 Angle : 0.576 9.434 15496 Z= 0.315 Chirality : 0.038 0.191 1837 Planarity : 0.006 0.118 1403 Dihedral : 22.827 177.156 3391 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.68 % Favored : 93.76 % Rotamer: Outliers : 3.75 % Allowed : 24.63 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.28), residues: 881 helix: 0.66 (0.19), residues: 665 sheet: -2.58 (1.18), residues: 22 loop : -2.74 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 122 TYR 0.018 0.001 TYR F 20 PHE 0.027 0.002 PHE B 80 TRP 0.007 0.001 TRP A 210 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (10931) covalent geometry : angle 0.57588 / 0.32 (15496) hydrogen bonds : bond 0.05257 / 3.23 ( 595) hydrogen bonds : angle 4.12795 / 2.88 ( 1594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.68 seconds wall clock time: 38 minutes 20.01 seconds (2300.01 seconds total)