Starting phenix.real_space_refine on Mon May 12 06:57:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvz_43573/05_2025/8vvz_43573.cif" } resolution = 3.41 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= -0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 5658 2.51 5 N 1488 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Restraints were copied for chains: C, E, D, F Time building chain proxies: 7.25, per 1000 atoms: 0.82 Number of scatterers: 8856 At special positions: 0 Unit cell: (119.463, 116.779, 92.6177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1680 8.00 N 1488 7.00 C 5658 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.731A pdb=" N LYS A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU A 51 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 70 removed outlier: 4.056A pdb=" N ASN A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.532A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 104 Processing helix chain 'A' and resid 112 through 130 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.840A pdb=" N THR A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 6.305A pdb=" N CYS A 150 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 167 through 184 removed outlier: 4.141A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.886A pdb=" N ALA B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.626A pdb=" N PHE B 69 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 71 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 91 through 104 Processing helix chain 'B' and resid 112 through 130 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.730A pdb=" N LYS C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU C 51 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 70 removed outlier: 4.056A pdb=" N ASN C 68 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 removed outlier: 3.533A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 104 Processing helix chain 'C' and resid 112 through 130 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.840A pdb=" N THR C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 6.305A pdb=" N CYS C 150 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 167 through 184 removed outlier: 4.142A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 29 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.886A pdb=" N ALA D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.627A pdb=" N PHE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 91 through 104 Processing helix chain 'D' and resid 112 through 130 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 167 through 186 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.730A pdb=" N LYS E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU E 51 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 70 removed outlier: 4.056A pdb=" N ASN E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 3.533A pdb=" N LEU E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 112 through 130 Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.840A pdb=" N THR E 146 " --> pdb=" O HIS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 6.304A pdb=" N CYS E 150 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 162 Processing helix chain 'E' and resid 167 through 184 removed outlier: 4.141A pdb=" N ILE E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.886A pdb=" N ALA F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 removed outlier: 3.626A pdb=" N PHE F 69 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR F 71 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 88 Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 112 through 130 Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 167 through 186 531 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2892 1.34 - 1.46: 1784 1.46 - 1.58: 4258 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8982 Sorted by residual: bond pdb=" N GLY E 37 " pdb=" CA GLY E 37 " ideal model delta sigma weight residual 1.443 1.450 -0.007 1.17e-02 7.31e+03 3.61e-01 bond pdb=" N SER C 72 " pdb=" CA SER C 72 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.85e-01 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.443 1.449 -0.006 1.17e-02 7.31e+03 2.85e-01 bond pdb=" N SER A 72 " pdb=" CA SER A 72 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.80e-01 bond pdb=" N GLY C 37 " pdb=" CA GLY C 37 " ideal model delta sigma weight residual 1.443 1.449 -0.006 1.17e-02 7.31e+03 2.69e-01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 11818 0.98 - 1.95: 218 1.95 - 2.93: 45 2.93 - 3.91: 12 3.91 - 4.88: 3 Bond angle restraints: 12096 Sorted by residual: angle pdb=" C THR E 71 " pdb=" N SER E 72 " pdb=" CA SER E 72 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.54e+00 angle pdb=" C THR A 71 " pdb=" N SER A 72 " pdb=" CA SER A 72 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.53e+00 angle pdb=" C THR C 71 " pdb=" N SER C 72 " pdb=" CA SER C 72 " ideal model delta sigma weight residual 121.54 126.35 -4.81 1.91e+00 2.74e-01 6.34e+00 angle pdb=" CA SER A 72 " pdb=" C SER A 72 " pdb=" N ASP A 73 " ideal model delta sigma weight residual 116.84 119.45 -2.61 1.71e+00 3.42e-01 2.32e+00 angle pdb=" CA SER E 72 " pdb=" C SER E 72 " pdb=" N ASP E 73 " ideal model delta sigma weight residual 116.84 119.43 -2.59 1.71e+00 3.42e-01 2.30e+00 ... (remaining 12091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5002 17.57 - 35.14: 470 35.14 - 52.72: 78 52.72 - 70.29: 12 70.29 - 87.86: 12 Dihedral angle restraints: 5574 sinusoidal: 2292 harmonic: 3282 Sorted by residual: dihedral pdb=" CG ARG D 101 " pdb=" CD ARG D 101 " pdb=" NE ARG D 101 " pdb=" CZ ARG D 101 " ideal model delta sinusoidal sigma weight residual 180.00 -135.55 -44.45 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 101 " pdb=" CD ARG B 101 " pdb=" NE ARG B 101 " pdb=" CZ ARG B 101 " ideal model delta sinusoidal sigma weight residual -180.00 -135.57 -44.43 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG F 101 " pdb=" CD ARG F 101 " pdb=" NE ARG F 101 " pdb=" CZ ARG F 101 " ideal model delta sinusoidal sigma weight residual -180.00 -135.64 -44.36 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 918 0.024 - 0.048: 315 0.048 - 0.071: 138 0.071 - 0.095: 34 0.095 - 0.119: 23 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA ILE D 74 " pdb=" N ILE D 74 " pdb=" C ILE D 74 " pdb=" CB ILE D 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA ILE F 74 " pdb=" N ILE F 74 " pdb=" C ILE F 74 " pdb=" CB ILE F 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE C 74 " pdb=" N ILE C 74 " pdb=" C ILE C 74 " pdb=" CB ILE C 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 1425 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 31 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C VAL C 31 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL C 31 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU C 32 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 31 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C VAL E 31 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL E 31 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU E 32 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 31 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C VAL A 31 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL A 31 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A 32 " 0.007 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1884 2.79 - 3.31: 8791 3.31 - 3.84: 13923 3.84 - 4.37: 15987 4.37 - 4.90: 27618 Nonbonded interactions: 68203 Sorted by model distance: nonbonded pdb=" O GLY F 153 " pdb=" OG1 THR F 156 " model vdw 2.257 3.040 nonbonded pdb=" O GLY D 153 " pdb=" OG1 THR D 156 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 153 " pdb=" OG1 THR B 156 " model vdw 2.258 3.040 nonbonded pdb=" O LYS E 4 " pdb=" OH TYR E 61 " model vdw 2.259 3.040 nonbonded pdb=" O LYS A 4 " pdb=" OH TYR A 61 " model vdw 2.259 3.040 ... (remaining 68198 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.090 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.001 0.012 8982 Z= 0.074 Angle : 0.369 4.883 12096 Z= 0.214 Chirality : 0.032 0.119 1428 Planarity : 0.002 0.017 1512 Dihedral : 14.143 87.859 3414 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 1092 helix: 1.93 (0.20), residues: 759 sheet: None (None), residues: 0 loop : 0.46 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.001 0.000 HIS F 116 PHE 0.005 0.001 PHE C 120 TYR 0.005 0.001 TYR D 87 ARG 0.002 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.17696 ( 531) hydrogen bonds : angle 4.95811 ( 1512) covalent geometry : bond 0.00124 ( 8982) covalent geometry : angle 0.36914 (12096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8495 (t0) cc_final: 0.8237 (t0) REVERT: A 36 ASP cc_start: 0.8175 (p0) cc_final: 0.7838 (p0) REVERT: A 100 LYS cc_start: 0.8432 (mttt) cc_final: 0.8093 (mttp) REVERT: A 138 ASP cc_start: 0.8532 (t0) cc_final: 0.7505 (m-30) REVERT: B 51 GLU cc_start: 0.7827 (tp30) cc_final: 0.7549 (tp30) REVERT: B 60 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 61 TYR cc_start: 0.7580 (m-80) cc_final: 0.7120 (m-80) REVERT: B 78 GLN cc_start: 0.8534 (mt0) cc_final: 0.7987 (mp10) REVERT: B 100 LYS cc_start: 0.7056 (mptt) cc_final: 0.6121 (mmtm) REVERT: C 11 ASP cc_start: 0.8830 (t0) cc_final: 0.8241 (t0) REVERT: C 51 GLU cc_start: 0.8631 (tp30) cc_final: 0.8343 (tp30) REVERT: C 78 GLN cc_start: 0.8740 (mt0) cc_final: 0.8035 (mm-40) REVERT: C 89 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7471 (ptt-90) REVERT: C 102 LEU cc_start: 0.7908 (tp) cc_final: 0.7620 (tp) REVERT: C 103 LEU cc_start: 0.8695 (mp) cc_final: 0.8326 (mt) REVERT: C 138 ASP cc_start: 0.8578 (t0) cc_final: 0.7980 (t0) REVERT: C 159 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 6 ASN cc_start: 0.8302 (m-40) cc_final: 0.7901 (t0) REVERT: D 48 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7802 (mmtm) REVERT: D 49 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7917 (tptp) REVERT: D 61 TYR cc_start: 0.7696 (m-80) cc_final: 0.7145 (m-80) REVERT: D 133 LYS cc_start: 0.8591 (mttm) cc_final: 0.8296 (mtmm) REVERT: D 151 TYR cc_start: 0.8631 (m-80) cc_final: 0.8358 (m-80) REVERT: D 183 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7405 (mtpt) REVERT: E 11 ASP cc_start: 0.8648 (t0) cc_final: 0.8446 (t0) REVERT: E 34 VAL cc_start: 0.8372 (t) cc_final: 0.8108 (t) REVERT: E 51 GLU cc_start: 0.8620 (tp30) cc_final: 0.8418 (tp30) REVERT: E 77 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7805 (ttm170) REVERT: E 78 GLN cc_start: 0.8744 (mt0) cc_final: 0.8483 (mt0) REVERT: E 135 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7656 (pm20) REVERT: E 173 ASN cc_start: 0.8467 (t0) cc_final: 0.7231 (m-40) REVERT: E 185 ASP cc_start: 0.8487 (t70) cc_final: 0.8270 (m-30) REVERT: F 11 ASP cc_start: 0.8406 (t0) cc_final: 0.8097 (p0) REVERT: F 32 LEU cc_start: 0.8027 (tt) cc_final: 0.7734 (tt) REVERT: F 48 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8089 (tptp) REVERT: F 59 ILE cc_start: 0.8142 (mt) cc_final: 0.7695 (mm) REVERT: F 111 MET cc_start: 0.8768 (ttp) cc_final: 0.8412 (ttp) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2483 time to fit residues: 100.8109 Evaluate side-chains 210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117113 restraints weight = 12265.013| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.48 r_work: 0.3189 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8982 Z= 0.125 Angle : 0.467 4.443 12096 Z= 0.250 Chirality : 0.037 0.176 1428 Planarity : 0.003 0.038 1512 Dihedral : 3.165 15.211 1176 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.12 % Allowed : 7.42 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1092 helix: 1.97 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.49 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.002 0.000 HIS E 116 PHE 0.011 0.001 PHE E 66 TYR 0.012 0.002 TYR E 87 ARG 0.007 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 531) hydrogen bonds : angle 3.44637 ( 1512) covalent geometry : bond 0.00283 ( 8982) covalent geometry : angle 0.46654 (12096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 61 TYR cc_start: 0.7963 (m-80) cc_final: 0.7337 (m-80) REVERT: B 100 LYS cc_start: 0.7476 (mptt) cc_final: 0.6380 (mmtp) REVERT: C 11 ASP cc_start: 0.8669 (t0) cc_final: 0.8102 (t0) REVERT: C 74 ILE cc_start: 0.8354 (mt) cc_final: 0.8085 (tp) REVERT: C 78 GLN cc_start: 0.8921 (mt0) cc_final: 0.8582 (mm-40) REVERT: C 89 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7677 (ptt-90) REVERT: C 103 LEU cc_start: 0.8850 (mp) cc_final: 0.8428 (mt) REVERT: C 159 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 173 ASN cc_start: 0.8502 (t0) cc_final: 0.8245 (t0) REVERT: C 183 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8557 (tttt) REVERT: D 49 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7715 (tptp) REVERT: D 111 MET cc_start: 0.8743 (ttp) cc_final: 0.8464 (ttm) REVERT: E 6 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: E 11 ASP cc_start: 0.8553 (t0) cc_final: 0.8297 (t0) REVERT: E 77 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8288 (ttm170) REVERT: E 78 GLN cc_start: 0.8964 (mt0) cc_final: 0.8732 (mt0) REVERT: E 138 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: E 173 ASN cc_start: 0.8638 (t0) cc_final: 0.7752 (m110) REVERT: F 30 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: F 59 ILE cc_start: 0.8758 (mt) cc_final: 0.8295 (mm) REVERT: F 64 ASP cc_start: 0.7838 (m-30) cc_final: 0.7572 (m-30) REVERT: F 152 ASP cc_start: 0.7478 (t0) cc_final: 0.7059 (t0) outliers start: 11 outliers final: 4 residues processed: 219 average time/residue: 0.2490 time to fit residues: 71.3520 Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 30 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN C 29 GLN F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112452 restraints weight = 12040.010| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.01 r_work: 0.3104 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8982 Z= 0.113 Angle : 0.445 6.448 12096 Z= 0.235 Chirality : 0.036 0.176 1428 Planarity : 0.003 0.032 1512 Dihedral : 3.152 14.178 1176 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 9.55 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.26), residues: 1092 helix: 2.22 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.37 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE E 66 TYR 0.011 0.002 TYR B 61 ARG 0.008 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 531) hydrogen bonds : angle 3.32948 ( 1512) covalent geometry : bond 0.00258 ( 8982) covalent geometry : angle 0.44474 (12096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8652 (t0) cc_final: 0.8408 (t0) REVERT: A 60 GLU cc_start: 0.8904 (tp30) cc_final: 0.8698 (tp30) REVERT: B 60 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 61 TYR cc_start: 0.8054 (m-80) cc_final: 0.7190 (m-80) REVERT: B 100 LYS cc_start: 0.7692 (mptt) cc_final: 0.6521 (mmtt) REVERT: C 11 ASP cc_start: 0.8849 (t0) cc_final: 0.8296 (t0) REVERT: C 74 ILE cc_start: 0.8369 (mt) cc_final: 0.8100 (tp) REVERT: C 78 GLN cc_start: 0.9102 (mt0) cc_final: 0.8768 (mm-40) REVERT: C 89 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7524 (ptt-90) REVERT: C 102 LEU cc_start: 0.8786 (tp) cc_final: 0.8461 (tp) REVERT: C 103 LEU cc_start: 0.8883 (mp) cc_final: 0.8483 (mt) REVERT: C 159 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 173 ASN cc_start: 0.8515 (t0) cc_final: 0.8287 (t0) REVERT: C 183 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8629 (tttt) REVERT: D 6 ASN cc_start: 0.8075 (t0) cc_final: 0.7844 (t0) REVERT: D 51 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 11 ASP cc_start: 0.8510 (t0) cc_final: 0.8281 (t0) REVERT: E 39 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6805 (tpp) REVERT: E 59 ILE cc_start: 0.9234 (mt) cc_final: 0.8975 (mp) REVERT: E 77 ARG cc_start: 0.8567 (ttm170) cc_final: 0.8197 (ttm170) REVERT: E 78 GLN cc_start: 0.9093 (mt0) cc_final: 0.8859 (mt0) REVERT: E 138 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: E 173 ASN cc_start: 0.8621 (t0) cc_final: 0.7800 (m110) REVERT: F 30 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: F 59 ILE cc_start: 0.8906 (mt) cc_final: 0.8511 (mm) REVERT: F 60 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: F 88 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8528 (mt-10) REVERT: F 152 ASP cc_start: 0.7634 (t0) cc_final: 0.7345 (t0) outliers start: 13 outliers final: 6 residues processed: 199 average time/residue: 0.2565 time to fit residues: 67.8576 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 60 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.0980 chunk 100 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111887 restraints weight = 11950.647| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.02 r_work: 0.3061 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8982 Z= 0.116 Angle : 0.440 6.827 12096 Z= 0.232 Chirality : 0.036 0.170 1428 Planarity : 0.003 0.037 1512 Dihedral : 3.130 14.279 1176 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.42 % Allowed : 11.79 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.26), residues: 1092 helix: 2.30 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.42 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 20 TYR 0.013 0.002 TYR A 87 ARG 0.009 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 531) hydrogen bonds : angle 3.27040 ( 1512) covalent geometry : bond 0.00269 ( 8982) covalent geometry : angle 0.43960 (12096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8716 (t0) cc_final: 0.8421 (t0) REVERT: A 60 GLU cc_start: 0.8919 (tp30) cc_final: 0.8636 (tp30) REVERT: A 87 TYR cc_start: 0.8473 (m-80) cc_final: 0.8041 (m-80) REVERT: A 127 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8400 (tt) REVERT: B 60 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 61 TYR cc_start: 0.8000 (m-80) cc_final: 0.7094 (m-80) REVERT: B 78 GLN cc_start: 0.8566 (mt0) cc_final: 0.7730 (mp10) REVERT: B 100 LYS cc_start: 0.7691 (mptt) cc_final: 0.6505 (mmtt) REVERT: C 11 ASP cc_start: 0.8855 (t0) cc_final: 0.8317 (t0) REVERT: C 74 ILE cc_start: 0.8216 (mt) cc_final: 0.7989 (tp) REVERT: C 78 GLN cc_start: 0.9088 (mt0) cc_final: 0.8763 (mm-40) REVERT: C 89 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7511 (ptt-90) REVERT: C 102 LEU cc_start: 0.8801 (tp) cc_final: 0.8523 (tp) REVERT: C 103 LEU cc_start: 0.8877 (mp) cc_final: 0.8419 (mt) REVERT: C 138 ASP cc_start: 0.8591 (t0) cc_final: 0.8384 (t0) REVERT: C 159 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 183 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8415 (mmmm) REVERT: D 51 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7735 (mm-30) REVERT: E 11 ASP cc_start: 0.8510 (t0) cc_final: 0.8280 (t0) REVERT: E 39 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6836 (tpp) REVERT: E 59 ILE cc_start: 0.9219 (mt) cc_final: 0.8964 (mp) REVERT: E 77 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8172 (ttm170) REVERT: E 78 GLN cc_start: 0.9086 (mt0) cc_final: 0.8850 (mt0) REVERT: E 138 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: E 155 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8625 (mt) REVERT: E 173 ASN cc_start: 0.8643 (t0) cc_final: 0.7825 (m110) REVERT: F 59 ILE cc_start: 0.8881 (mt) cc_final: 0.8470 (mm) REVERT: F 60 GLU cc_start: 0.8224 (tp30) cc_final: 0.7927 (tp30) outliers start: 14 outliers final: 6 residues processed: 203 average time/residue: 0.2286 time to fit residues: 61.7864 Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0170 chunk 91 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111831 restraints weight = 11814.343| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.99 r_work: 0.3045 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8982 Z= 0.109 Angle : 0.434 6.166 12096 Z= 0.230 Chirality : 0.036 0.176 1428 Planarity : 0.003 0.042 1512 Dihedral : 3.119 13.702 1176 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 12.91 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.26), residues: 1092 helix: 2.39 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.47 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.002 0.001 HIS A 116 PHE 0.008 0.001 PHE B 20 TYR 0.011 0.002 TYR C 15 ARG 0.009 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 531) hydrogen bonds : angle 3.20224 ( 1512) covalent geometry : bond 0.00251 ( 8982) covalent geometry : angle 0.43393 (12096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8848 (tp30) cc_final: 0.8542 (tp30) REVERT: A 87 TYR cc_start: 0.8340 (m-80) cc_final: 0.8057 (m-80) REVERT: A 127 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 134 ILE cc_start: 0.8773 (mt) cc_final: 0.8479 (mt) REVERT: B 60 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8231 (tp30) REVERT: B 61 TYR cc_start: 0.8008 (m-80) cc_final: 0.7140 (m-80) REVERT: B 78 GLN cc_start: 0.8578 (mt0) cc_final: 0.7721 (mp10) REVERT: B 100 LYS cc_start: 0.7601 (mptt) cc_final: 0.6539 (mmtt) REVERT: C 11 ASP cc_start: 0.8853 (t0) cc_final: 0.8318 (t0) REVERT: C 74 ILE cc_start: 0.8354 (mt) cc_final: 0.8153 (tp) REVERT: C 78 GLN cc_start: 0.9007 (mt0) cc_final: 0.8655 (mm-40) REVERT: C 89 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7493 (ptt-90) REVERT: C 102 LEU cc_start: 0.8755 (tp) cc_final: 0.8521 (tp) REVERT: C 103 LEU cc_start: 0.8887 (mp) cc_final: 0.8491 (mt) REVERT: C 173 ASN cc_start: 0.8556 (t0) cc_final: 0.8300 (t0) REVERT: C 178 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8278 (tm-30) REVERT: C 183 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8449 (mmmm) REVERT: D 51 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7826 (mm-30) REVERT: E 11 ASP cc_start: 0.8514 (t0) cc_final: 0.8288 (t0) REVERT: E 39 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6728 (tpp) REVERT: E 59 ILE cc_start: 0.9252 (mt) cc_final: 0.8963 (mp) REVERT: E 77 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8164 (ttm170) REVERT: E 78 GLN cc_start: 0.9056 (mt0) cc_final: 0.8794 (mt0) REVERT: E 138 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: E 173 ASN cc_start: 0.8640 (t0) cc_final: 0.7847 (m110) REVERT: E 185 ASP cc_start: 0.8005 (m-30) cc_final: 0.7740 (m-30) REVERT: F 59 ILE cc_start: 0.8857 (mt) cc_final: 0.8641 (mm) REVERT: F 60 GLU cc_start: 0.8218 (tp30) cc_final: 0.7865 (tp30) outliers start: 14 outliers final: 6 residues processed: 209 average time/residue: 0.2187 time to fit residues: 61.3512 Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN C 29 GLN F 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107660 restraints weight = 11973.024| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.01 r_work: 0.2950 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8982 Z= 0.189 Angle : 0.516 6.696 12096 Z= 0.270 Chirality : 0.038 0.185 1428 Planarity : 0.003 0.053 1512 Dihedral : 3.373 15.154 1176 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.52 % Allowed : 15.55 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.26), residues: 1092 helix: 2.18 (0.19), residues: 747 sheet: None (None), residues: 0 loop : 0.39 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 47 HIS 0.003 0.001 HIS C 142 PHE 0.013 0.001 PHE B 20 TYR 0.018 0.002 TYR A 87 ARG 0.011 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 531) hydrogen bonds : angle 3.44837 ( 1512) covalent geometry : bond 0.00456 ( 8982) covalent geometry : angle 0.51552 (12096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8862 (tp30) cc_final: 0.8536 (tp30) REVERT: A 127 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 134 ILE cc_start: 0.8810 (mt) cc_final: 0.8524 (mt) REVERT: B 60 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8370 (tp30) REVERT: B 61 TYR cc_start: 0.8172 (m-80) cc_final: 0.7024 (m-80) REVERT: B 100 LYS cc_start: 0.7663 (mptt) cc_final: 0.6619 (mmtt) REVERT: C 5 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6906 (mtm-85) REVERT: C 11 ASP cc_start: 0.8875 (t0) cc_final: 0.8337 (t0) REVERT: C 74 ILE cc_start: 0.8373 (mt) cc_final: 0.8092 (tp) REVERT: C 78 GLN cc_start: 0.9106 (mt0) cc_final: 0.8695 (mm-40) REVERT: C 103 LEU cc_start: 0.8938 (mp) cc_final: 0.8503 (mt) REVERT: C 173 ASN cc_start: 0.8635 (t0) cc_final: 0.8328 (t0) REVERT: C 178 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 182 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.7991 (mp) REVERT: C 183 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8455 (mmmm) REVERT: D 51 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7834 (mm-30) REVERT: E 6 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: E 11 ASP cc_start: 0.8532 (t0) cc_final: 0.8311 (t0) REVERT: E 77 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8265 (ttm170) REVERT: E 78 GLN cc_start: 0.9172 (mt0) cc_final: 0.8940 (mt0) REVERT: E 138 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: E 173 ASN cc_start: 0.8665 (t0) cc_final: 0.7854 (m110) REVERT: E 185 ASP cc_start: 0.8095 (m-30) cc_final: 0.7815 (m-30) REVERT: F 59 ILE cc_start: 0.8945 (mt) cc_final: 0.8700 (mm) REVERT: F 60 GLU cc_start: 0.8325 (tp30) cc_final: 0.7993 (tp30) outliers start: 15 outliers final: 8 residues processed: 204 average time/residue: 0.2433 time to fit residues: 65.3820 Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.3980 chunk 62 optimal weight: 0.0060 chunk 73 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 ASN D 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113282 restraints weight = 11933.302| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.01 r_work: 0.3066 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8982 Z= 0.090 Angle : 0.438 6.202 12096 Z= 0.233 Chirality : 0.035 0.197 1428 Planarity : 0.003 0.050 1512 Dihedral : 3.170 12.723 1176 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.02 % Allowed : 16.57 % Favored : 82.42 % 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: 2.73 (0.26), residues: 1092 helix: 2.45 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.43 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.001 0.000 HIS C 142 PHE 0.006 0.001 PHE E 66 TYR 0.011 0.002 TYR C 15 ARG 0.012 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 531) hydrogen bonds : angle 3.11923 ( 1512) covalent geometry : bond 0.00195 ( 8982) covalent geometry : angle 0.43819 (12096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.065 Fit side-chains REVERT: A 60 GLU cc_start: 0.8830 (tp30) cc_final: 0.8507 (tp30) REVERT: A 87 TYR cc_start: 0.8232 (m-80) cc_final: 0.7984 (m-80) REVERT: A 123 LEU cc_start: 0.8782 (mt) cc_final: 0.8575 (mt) REVERT: A 127 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8391 (tt) REVERT: A 134 ILE cc_start: 0.8791 (mt) cc_final: 0.8516 (mt) REVERT: B 6 ASN cc_start: 0.7969 (t0) cc_final: 0.7747 (t0) REVERT: B 60 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8218 (tp30) REVERT: B 61 TYR cc_start: 0.7937 (m-80) cc_final: 0.7032 (m-80) REVERT: B 78 GLN cc_start: 0.8791 (mt0) cc_final: 0.7822 (mp10) REVERT: B 100 LYS cc_start: 0.7646 (mptt) cc_final: 0.6523 (mmtp) REVERT: C 11 ASP cc_start: 0.8862 (t0) cc_final: 0.8327 (t0) REVERT: C 39 MET cc_start: 0.7380 (tpp) cc_final: 0.7107 (tpp) REVERT: C 78 GLN cc_start: 0.9038 (mt0) cc_final: 0.8556 (mm-40) REVERT: C 89 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7486 (ptt-90) REVERT: C 103 LEU cc_start: 0.8967 (mp) cc_final: 0.8541 (mt) REVERT: C 173 ASN cc_start: 0.8553 (t0) cc_final: 0.8285 (t0) REVERT: C 178 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8237 (tm-30) REVERT: C 183 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8443 (mmmm) REVERT: D 51 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 11 ASP cc_start: 0.8520 (t0) cc_final: 0.8287 (t0) REVERT: E 52 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7874 (ptt90) REVERT: E 77 ARG cc_start: 0.8612 (ttm170) cc_final: 0.8170 (ttm170) REVERT: E 78 GLN cc_start: 0.9105 (mt0) cc_final: 0.8865 (mt0) REVERT: E 138 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: E 173 ASN cc_start: 0.8607 (t0) cc_final: 0.7845 (m110) REVERT: F 59 ILE cc_start: 0.8811 (mt) cc_final: 0.8588 (mm) REVERT: F 60 GLU cc_start: 0.8274 (tp30) cc_final: 0.7883 (tp30) outliers start: 10 outliers final: 6 residues processed: 207 average time/residue: 0.2232 time to fit residues: 62.2303 Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109624 restraints weight = 12100.146| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.04 r_work: 0.2980 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8982 Z= 0.143 Angle : 0.491 6.384 12096 Z= 0.258 Chirality : 0.038 0.199 1428 Planarity : 0.003 0.053 1512 Dihedral : 3.243 13.438 1176 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.63 % Allowed : 17.17 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.26), residues: 1092 helix: 2.33 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.36 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.003 0.001 HIS C 142 PHE 0.010 0.001 PHE B 20 TYR 0.014 0.002 TYR C 87 ARG 0.011 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 531) hydrogen bonds : angle 3.29441 ( 1512) covalent geometry : bond 0.00341 ( 8982) covalent geometry : angle 0.49132 (12096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.003 Fit side-chains REVERT: A 60 GLU cc_start: 0.8902 (tp30) cc_final: 0.8549 (tp30) REVERT: A 127 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 134 ILE cc_start: 0.8776 (mt) cc_final: 0.8484 (mt) REVERT: B 30 ASP cc_start: 0.7909 (t0) cc_final: 0.7664 (p0) REVERT: B 60 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8222 (tp30) REVERT: B 61 TYR cc_start: 0.8066 (m-80) cc_final: 0.7044 (m-80) REVERT: B 78 GLN cc_start: 0.8774 (mt0) cc_final: 0.7733 (mp10) REVERT: B 100 LYS cc_start: 0.7649 (mptt) cc_final: 0.6579 (mmtt) REVERT: C 11 ASP cc_start: 0.8869 (t0) cc_final: 0.8304 (t0) REVERT: C 39 MET cc_start: 0.7520 (tpp) cc_final: 0.7293 (tpp) REVERT: C 78 GLN cc_start: 0.9099 (mt0) cc_final: 0.8542 (mm-40) REVERT: C 89 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.7616 (ptt-90) REVERT: C 103 LEU cc_start: 0.8976 (mp) cc_final: 0.8646 (mt) REVERT: C 173 ASN cc_start: 0.8589 (t0) cc_final: 0.8323 (t0) REVERT: C 178 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 183 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8427 (mmmm) REVERT: D 6 ASN cc_start: 0.8233 (t160) cc_final: 0.8001 (t0) REVERT: D 51 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7856 (mm-30) REVERT: E 11 ASP cc_start: 0.8531 (t0) cc_final: 0.8303 (t0) REVERT: E 77 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8207 (ttm170) REVERT: E 78 GLN cc_start: 0.9112 (mt0) cc_final: 0.8870 (mt0) REVERT: E 127 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8398 (tt) REVERT: E 138 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: E 173 ASN cc_start: 0.8652 (t0) cc_final: 0.7854 (m110) REVERT: F 59 ILE cc_start: 0.8872 (mt) cc_final: 0.8643 (mm) REVERT: F 60 GLU cc_start: 0.8308 (tp30) cc_final: 0.8026 (tp30) outliers start: 16 outliers final: 11 residues processed: 193 average time/residue: 0.2304 time to fit residues: 59.3018 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN D 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111384 restraints weight = 11991.521| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3067 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8982 Z= 0.116 Angle : 0.475 6.815 12096 Z= 0.250 Chirality : 0.037 0.214 1428 Planarity : 0.003 0.054 1512 Dihedral : 3.220 12.860 1176 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.32 % Allowed : 17.68 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1092 helix: 2.36 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.41 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.002 0.001 HIS C 142 PHE 0.008 0.001 PHE B 20 TYR 0.012 0.002 TYR C 87 ARG 0.013 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 531) hydrogen bonds : angle 3.21628 ( 1512) covalent geometry : bond 0.00274 ( 8982) covalent geometry : angle 0.47470 (12096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 1.148 Fit side-chains REVERT: A 60 GLU cc_start: 0.8851 (tp30) cc_final: 0.8483 (tp30) REVERT: A 127 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 134 ILE cc_start: 0.8738 (mt) cc_final: 0.8441 (mt) REVERT: B 30 ASP cc_start: 0.8145 (t0) cc_final: 0.7787 (p0) REVERT: B 60 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8138 (tp30) REVERT: B 61 TYR cc_start: 0.8028 (m-80) cc_final: 0.7021 (m-80) REVERT: B 78 GLN cc_start: 0.8788 (mt0) cc_final: 0.7728 (mp10) REVERT: B 100 LYS cc_start: 0.7669 (mptt) cc_final: 0.6552 (mmtt) REVERT: C 11 ASP cc_start: 0.8880 (t0) cc_final: 0.8122 (t0) REVERT: C 39 MET cc_start: 0.7440 (tpp) cc_final: 0.7202 (tpp) REVERT: C 78 GLN cc_start: 0.9093 (mt0) cc_final: 0.8567 (mm-40) REVERT: C 89 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.7509 (ptt-90) REVERT: C 103 LEU cc_start: 0.9063 (mp) cc_final: 0.8743 (mt) REVERT: C 173 ASN cc_start: 0.8545 (t0) cc_final: 0.8285 (t0) REVERT: C 178 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 183 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8454 (mmmm) REVERT: D 6 ASN cc_start: 0.8198 (t160) cc_final: 0.7946 (t0) REVERT: D 51 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7819 (mm-30) REVERT: E 11 ASP cc_start: 0.8520 (t0) cc_final: 0.8279 (t0) REVERT: E 77 ARG cc_start: 0.8629 (ttm170) cc_final: 0.8167 (ttm170) REVERT: E 78 GLN cc_start: 0.9091 (mt0) cc_final: 0.8847 (mt0) REVERT: E 138 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: E 173 ASN cc_start: 0.8632 (t0) cc_final: 0.7847 (m110) REVERT: F 59 ILE cc_start: 0.8850 (mt) cc_final: 0.8623 (mm) REVERT: F 60 GLU cc_start: 0.8245 (tp30) cc_final: 0.7863 (tp30) outliers start: 13 outliers final: 9 residues processed: 192 average time/residue: 0.2398 time to fit residues: 61.3997 Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111602 restraints weight = 11901.250| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.92 r_work: 0.3015 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8982 Z= 0.128 Angle : 0.496 7.114 12096 Z= 0.259 Chirality : 0.037 0.206 1428 Planarity : 0.003 0.058 1512 Dihedral : 3.266 13.856 1176 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.32 % Allowed : 17.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.26), residues: 1092 helix: 2.33 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.41 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.002 0.001 HIS C 142 PHE 0.009 0.001 PHE B 20 TYR 0.013 0.002 TYR C 87 ARG 0.013 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 531) hydrogen bonds : angle 3.25359 ( 1512) covalent geometry : bond 0.00307 ( 8982) covalent geometry : angle 0.49586 (12096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.091 Fit side-chains REVERT: A 60 GLU cc_start: 0.8850 (tp30) cc_final: 0.8478 (tp30) REVERT: A 127 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 134 ILE cc_start: 0.8806 (mt) cc_final: 0.8512 (mt) REVERT: B 30 ASP cc_start: 0.8080 (t0) cc_final: 0.7713 (p0) REVERT: B 60 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8154 (tp30) REVERT: B 61 TYR cc_start: 0.8030 (m-80) cc_final: 0.7019 (m-80) REVERT: B 78 GLN cc_start: 0.8750 (mt0) cc_final: 0.7678 (mp10) REVERT: B 100 LYS cc_start: 0.7703 (mptt) cc_final: 0.6616 (mmtt) REVERT: C 11 ASP cc_start: 0.8836 (t0) cc_final: 0.8068 (t0) REVERT: C 39 MET cc_start: 0.7430 (tpp) cc_final: 0.7217 (tpp) REVERT: C 78 GLN cc_start: 0.8982 (mt0) cc_final: 0.8461 (mm-40) REVERT: C 89 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.7595 (ptt-90) REVERT: C 103 LEU cc_start: 0.8849 (mp) cc_final: 0.8524 (mt) REVERT: C 173 ASN cc_start: 0.8560 (t0) cc_final: 0.8285 (t0) REVERT: C 178 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 183 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8454 (mmmm) REVERT: D 6 ASN cc_start: 0.8184 (t160) cc_final: 0.7917 (t0) REVERT: D 51 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 11 ASP cc_start: 0.8462 (t0) cc_final: 0.8226 (t0) REVERT: E 77 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8216 (ttm170) REVERT: E 78 GLN cc_start: 0.9076 (mt0) cc_final: 0.8837 (mt0) REVERT: E 127 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8424 (tt) REVERT: E 138 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: E 173 ASN cc_start: 0.8659 (t0) cc_final: 0.7882 (m110) REVERT: F 59 ILE cc_start: 0.8862 (mt) cc_final: 0.8636 (mm) REVERT: F 60 GLU cc_start: 0.8261 (tp30) cc_final: 0.7890 (tp30) REVERT: F 77 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7731 (ttm110) REVERT: F 163 GLU cc_start: 0.7923 (pm20) cc_final: 0.7548 (mp0) outliers start: 13 outliers final: 9 residues processed: 196 average time/residue: 0.2408 time to fit residues: 62.0368 Evaluate side-chains 190 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113641 restraints weight = 11824.686| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.96 r_work: 0.3037 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8982 Z= 0.105 Angle : 0.480 7.257 12096 Z= 0.253 Chirality : 0.037 0.209 1428 Planarity : 0.003 0.057 1512 Dihedral : 3.192 14.794 1176 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.42 % Allowed : 17.99 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.26), residues: 1092 helix: 2.42 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.48 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.002 0.000 HIS C 142 PHE 0.007 0.001 PHE E 66 TYR 0.013 0.002 TYR D 87 ARG 0.013 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 531) hydrogen bonds : angle 3.20256 ( 1512) covalent geometry : bond 0.00243 ( 8982) covalent geometry : angle 0.48047 (12096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4862.30 seconds wall clock time: 85 minutes 48.85 seconds (5148.85 seconds total)