Starting phenix.real_space_refine on Wed Sep 17 13:05:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvz_43573/09_2025/8vvz_43573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvz_43573/09_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_43573/09_2025/8vvz_43573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvz_43573/09_2025/8vvz_43573.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvz_43573/09_2025/8vvz_43573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvz_43573/09_2025/8vvz_43573.cif" } resolution = 3.41 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= -0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.09, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 452.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 1.29 Time building geometry restraints manager: 1.04 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: 0.01 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: 15.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.880 Find NCS groups from input model: 0.150 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG E 89 TYR 0.005 0.001 TYR D 87 PHE 0.005 0.001 PHE C 120 TRP 0.007 0.001 TRP A 47 HIS 0.001 0.000 HIS F 116 Details of bonding type rmsd covalent geometry : bond 0.00124 ( 8982) covalent geometry : angle 0.36914 (12096) hydrogen bonds : bond 0.17696 ( 531) hydrogen bonds : angle 4.95811 ( 1512) *********************** 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 : 0.397 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: 0.8034 (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 49 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7960 (tptp) REVERT: D 52 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7068 (ttm110) 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: 0.8107 (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: 0.8484 (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: 0.1155 time to fit residues: 46.9788 Evaluate side-chains 209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0270 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.144301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117479 restraints weight = 12352.857| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.48 r_work: 0.3193 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8982 Z= 0.117 Angle : 0.454 4.469 12096 Z= 0.244 Chirality : 0.037 0.165 1428 Planarity : 0.003 0.036 1512 Dihedral : 3.135 14.924 1176 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 7.32 % Favored : 91.57 % 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 aren not related in a simple way. whole: 2.28 (0.26), residues: 1092 helix: 1.98 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.51 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.012 0.002 TYR E 87 PHE 0.010 0.001 PHE B 20 TRP 0.010 0.001 TRP C 47 HIS 0.002 0.000 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8982) covalent geometry : angle 0.45434 (12096) hydrogen bonds : bond 0.03655 ( 531) hydrogen bonds : angle 3.43516 ( 1512) *********************** 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 : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 61 TYR cc_start: 0.7939 (m-80) cc_final: 0.7282 (m-10) REVERT: B 100 LYS cc_start: 0.7450 (mptt) cc_final: 0.6431 (mmtp) REVERT: C 11 ASP cc_start: 0.8712 (t0) cc_final: 0.8157 (t0) REVERT: C 74 ILE cc_start: 0.8305 (mt) cc_final: 0.8099 (tp) REVERT: C 78 GLN cc_start: 0.8927 (mt0) cc_final: 0.8588 (mm-40) REVERT: C 89 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7686 (ptt-90) REVERT: C 103 LEU cc_start: 0.8852 (mp) cc_final: 0.8437 (mt) REVERT: C 159 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8058 (mt-10) REVERT: C 173 ASN cc_start: 0.8499 (t0) cc_final: 0.8228 (t0) REVERT: C 183 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8547 (tttt) REVERT: D 52 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7281 (ttm110) REVERT: E 6 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7592 (m-40) REVERT: E 11 ASP cc_start: 0.8583 (t0) cc_final: 0.8334 (t0) REVERT: E 77 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8279 (ttm170) REVERT: E 78 GLN cc_start: 0.8984 (mt0) cc_final: 0.8748 (mt0) REVERT: E 138 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: E 173 ASN cc_start: 0.8652 (t0) cc_final: 0.7751 (m110) REVERT: F 30 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: F 59 ILE cc_start: 0.8725 (mt) cc_final: 0.8245 (mm) REVERT: F 60 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7783 (tp30) REVERT: F 64 ASP cc_start: 0.7834 (m-30) cc_final: 0.7569 (m-30) REVERT: F 152 ASP cc_start: 0.7473 (t0) cc_final: 0.7051 (t0) outliers start: 11 outliers final: 4 residues processed: 219 average time/residue: 0.1194 time to fit residues: 34.3072 Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.0170 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.139120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114242 restraints weight = 11813.555| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.99 r_work: 0.3131 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8982 Z= 0.100 Angle : 0.432 6.584 12096 Z= 0.229 Chirality : 0.036 0.167 1428 Planarity : 0.003 0.032 1512 Dihedral : 3.085 13.901 1176 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.22 % Allowed : 9.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.26), residues: 1092 helix: 2.11 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.51 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 52 TYR 0.012 0.002 TYR B 61 PHE 0.009 0.001 PHE E 66 TRP 0.011 0.001 TRP C 47 HIS 0.001 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8982) covalent geometry : angle 0.43247 (12096) hydrogen bonds : bond 0.03257 ( 531) hydrogen bonds : angle 3.27921 ( 1512) *********************** 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 209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 60 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 61 TYR cc_start: 0.8097 (m-80) cc_final: 0.7363 (m-80) REVERT: B 100 LYS cc_start: 0.7680 (mptt) cc_final: 0.6501 (mmtt) REVERT: C 11 ASP cc_start: 0.8850 (t0) cc_final: 0.8311 (t0) REVERT: C 74 ILE cc_start: 0.8330 (mt) cc_final: 0.8082 (tp) REVERT: C 78 GLN cc_start: 0.9110 (mt0) cc_final: 0.8777 (mm-40) REVERT: C 89 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7537 (ptt-90) REVERT: C 103 LEU cc_start: 0.8864 (mp) cc_final: 0.8476 (mt) REVERT: C 159 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 183 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8632 (tttt) REVERT: D 6 ASN cc_start: 0.8041 (t0) cc_final: 0.7829 (t0) REVERT: E 11 ASP cc_start: 0.8522 (t0) cc_final: 0.8285 (t0) REVERT: E 39 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6695 (tpp) REVERT: E 59 ILE cc_start: 0.9261 (mt) cc_final: 0.8965 (mp) REVERT: E 77 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8228 (ttm170) REVERT: E 78 GLN cc_start: 0.9068 (mt0) cc_final: 0.8839 (mt0) REVERT: E 138 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: E 173 ASN cc_start: 0.8609 (t0) cc_final: 0.7792 (m110) REVERT: F 30 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: F 59 ILE cc_start: 0.8790 (mt) cc_final: 0.8380 (mm) REVERT: F 64 ASP cc_start: 0.8020 (m-30) cc_final: 0.7773 (m-30) REVERT: F 152 ASP cc_start: 0.7602 (t0) cc_final: 0.7304 (t0) outliers start: 12 outliers final: 5 residues processed: 201 average time/residue: 0.1124 time to fit residues: 30.1743 Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 31 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.0070 chunk 43 optimal weight: 0.0270 chunk 21 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118683 restraints weight = 11990.813| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.86 r_work: 0.3208 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8982 Z= 0.084 Angle : 0.410 7.210 12096 Z= 0.218 Chirality : 0.035 0.165 1428 Planarity : 0.003 0.035 1512 Dihedral : 2.982 12.799 1176 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.02 % Allowed : 11.79 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.27), residues: 1092 helix: 2.31 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.59 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 52 TYR 0.011 0.001 TYR C 15 PHE 0.006 0.001 PHE E 66 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 8982) covalent geometry : angle 0.41024 (12096) hydrogen bonds : bond 0.02770 ( 531) hydrogen bonds : angle 3.09339 ( 1512) *********************** 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 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 127 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 60 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 61 TYR cc_start: 0.7933 (m-80) cc_final: 0.7227 (m-80) REVERT: B 78 GLN cc_start: 0.8277 (mt0) cc_final: 0.7606 (mp10) REVERT: B 100 LYS cc_start: 0.7642 (mptt) cc_final: 0.6749 (mmtp) REVERT: C 11 ASP cc_start: 0.8758 (t0) cc_final: 0.8213 (t0) REVERT: C 29 GLN cc_start: 0.8439 (mt0) cc_final: 0.8221 (mt0) REVERT: C 78 GLN cc_start: 0.8954 (mt0) cc_final: 0.8661 (mm-40) REVERT: C 89 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7522 (ptt-90) REVERT: C 103 LEU cc_start: 0.8885 (mp) cc_final: 0.8527 (mt) REVERT: C 159 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 173 ASN cc_start: 0.8509 (t0) cc_final: 0.8269 (t0) REVERT: C 183 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8326 (mmmm) REVERT: E 11 ASP cc_start: 0.8446 (t0) cc_final: 0.8214 (t0) REVERT: E 39 MET cc_start: 0.6998 (tpt) cc_final: 0.6727 (tpp) REVERT: E 59 ILE cc_start: 0.9190 (mt) cc_final: 0.8903 (mp) REVERT: E 60 GLU cc_start: 0.9006 (tp30) cc_final: 0.8659 (tt0) REVERT: E 77 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8181 (ttm170) REVERT: E 78 GLN cc_start: 0.9004 (mt0) cc_final: 0.8729 (mt0) REVERT: E 138 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: E 173 ASN cc_start: 0.8557 (t0) cc_final: 0.7823 (m110) REVERT: F 59 ILE cc_start: 0.8676 (mt) cc_final: 0.8325 (mm) outliers start: 10 outliers final: 4 residues processed: 208 average time/residue: 0.1090 time to fit residues: 30.5945 Evaluate side-chains 189 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN D 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113817 restraints weight = 11868.967| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.99 r_work: 0.3126 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8982 Z= 0.104 Angle : 0.435 6.119 12096 Z= 0.230 Chirality : 0.036 0.175 1428 Planarity : 0.003 0.042 1512 Dihedral : 3.043 13.143 1176 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 13.31 % Favored : 85.16 % 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 aren not related in a simple way. whole: 2.82 (0.26), residues: 1092 helix: 2.52 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.43 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 52 TYR 0.011 0.002 TYR C 15 PHE 0.008 0.001 PHE B 20 TRP 0.011 0.001 TRP C 47 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8982) covalent geometry : angle 0.43469 (12096) hydrogen bonds : bond 0.03075 ( 531) hydrogen bonds : angle 3.14663 ( 1512) *********************** 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 217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.363 Fit side-chains REVERT: A 60 GLU cc_start: 0.8923 (tp30) cc_final: 0.8688 (tp30) REVERT: A 127 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8417 (tt) REVERT: B 61 TYR cc_start: 0.8013 (m-80) cc_final: 0.7248 (m-80) REVERT: B 78 GLN cc_start: 0.8316 (mt0) cc_final: 0.7511 (mp10) REVERT: B 100 LYS cc_start: 0.7658 (mptt) cc_final: 0.6457 (mmtt) REVERT: C 11 ASP cc_start: 0.8856 (t0) cc_final: 0.8288 (t0) REVERT: C 78 GLN cc_start: 0.9040 (mt0) cc_final: 0.8622 (mm-40) REVERT: C 89 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7483 (ptt-90) REVERT: C 103 LEU cc_start: 0.8867 (mp) cc_final: 0.8468 (mt) REVERT: C 159 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 173 ASN cc_start: 0.8554 (t0) cc_final: 0.8317 (t0) REVERT: C 178 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 183 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8380 (mmmm) REVERT: D 51 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7740 (mm-30) REVERT: D 184 ASN cc_start: 0.7918 (m-40) cc_final: 0.7716 (m-40) REVERT: E 11 ASP cc_start: 0.8527 (t0) cc_final: 0.8292 (t0) REVERT: E 39 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6718 (tpp) REVERT: E 59 ILE cc_start: 0.9220 (mt) cc_final: 0.8931 (mp) REVERT: E 60 GLU cc_start: 0.9055 (tp30) cc_final: 0.8707 (tt0) REVERT: E 77 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8156 (ttm170) REVERT: E 78 GLN cc_start: 0.9114 (mt0) cc_final: 0.8854 (mt0) REVERT: E 138 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: E 173 ASN cc_start: 0.8622 (t0) cc_final: 0.7827 (m110) REVERT: F 59 ILE cc_start: 0.8835 (mt) cc_final: 0.8555 (mm) REVERT: F 60 GLU cc_start: 0.8221 (tp30) cc_final: 0.7917 (tp30) outliers start: 15 outliers final: 8 residues processed: 208 average time/residue: 0.1133 time to fit residues: 31.3764 Evaluate side-chains 200 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 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 6 ASN Chi-restraints excluded: chain F residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.135393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.110614 restraints weight = 11906.589| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.98 r_work: 0.3007 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8982 Z= 0.141 Angle : 0.479 6.266 12096 Z= 0.251 Chirality : 0.037 0.191 1428 Planarity : 0.003 0.051 1512 Dihedral : 3.217 13.785 1176 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.73 % Allowed : 14.94 % Favored : 83.33 % 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 aren not related in a simple way. whole: 2.66 (0.26), residues: 1092 helix: 2.40 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.38 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 52 TYR 0.014 0.002 TYR A 87 PHE 0.011 0.001 PHE B 20 TRP 0.016 0.001 TRP C 47 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8982) covalent geometry : angle 0.47882 (12096) hydrogen bonds : bond 0.03459 ( 531) hydrogen bonds : angle 3.27894 ( 1512) *********************** 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 220 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.383 Fit side-chains REVERT: A 60 GLU cc_start: 0.8894 (tp30) cc_final: 0.8611 (tp30) REVERT: A 127 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 134 ILE cc_start: 0.8802 (mt) cc_final: 0.8501 (mt) REVERT: B 61 TYR cc_start: 0.8092 (m-80) cc_final: 0.7260 (m-80) REVERT: B 78 GLN cc_start: 0.8563 (mt0) cc_final: 0.7673 (mp10) REVERT: B 100 LYS cc_start: 0.7608 (mptt) cc_final: 0.6642 (mmtp) REVERT: C 11 ASP cc_start: 0.8866 (t0) cc_final: 0.8312 (t0) REVERT: C 39 MET cc_start: 0.7426 (tpp) cc_final: 0.7107 (tpp) REVERT: C 78 GLN cc_start: 0.9098 (mt0) cc_final: 0.8674 (mm-40) REVERT: C 89 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7493 (ptt-90) REVERT: C 103 LEU cc_start: 0.8948 (mp) cc_final: 0.8640 (mt) REVERT: C 173 ASN cc_start: 0.8586 (t0) cc_final: 0.8312 (t0) REVERT: C 178 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 183 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8437 (mmmm) REVERT: D 51 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7777 (mm-30) REVERT: E 11 ASP cc_start: 0.8497 (t0) cc_final: 0.8282 (t0) REVERT: E 59 ILE cc_start: 0.9284 (mt) cc_final: 0.9036 (mp) REVERT: E 60 GLU cc_start: 0.8997 (tp30) cc_final: 0.8661 (tt0) REVERT: E 77 ARG cc_start: 0.8565 (ttm170) cc_final: 0.8154 (ttm170) REVERT: E 78 GLN cc_start: 0.9105 (mt0) cc_final: 0.8873 (mt0) REVERT: E 138 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: E 173 ASN cc_start: 0.8638 (t0) cc_final: 0.7870 (m110) REVERT: F 30 ASP cc_start: 0.7988 (t0) cc_final: 0.7671 (m-30) REVERT: F 59 ILE cc_start: 0.8841 (mt) cc_final: 0.8624 (mm) REVERT: F 60 GLU cc_start: 0.8294 (tp30) cc_final: 0.8005 (tp30) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 0.1142 time to fit residues: 31.8026 Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 102 LEU 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 73 ASP 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 53 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 0.0030 chunk 90 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 48 optimal weight: 0.0570 chunk 42 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 overall best weight: 0.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN D 6 ASN D 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116752 restraints weight = 11877.005| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.99 r_work: 0.3167 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8982 Z= 0.088 Angle : 0.436 6.121 12096 Z= 0.232 Chirality : 0.036 0.198 1428 Planarity : 0.003 0.049 1512 Dihedral : 3.052 12.827 1176 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.12 % Allowed : 15.35 % Favored : 83.54 % 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 aren not related in a simple way. whole: 2.87 (0.27), residues: 1092 helix: 2.53 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.53 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 52 TYR 0.012 0.001 TYR E 87 PHE 0.005 0.001 PHE E 66 TRP 0.011 0.001 TRP C 47 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 8982) covalent geometry : angle 0.43648 (12096) hydrogen bonds : bond 0.02694 ( 531) hydrogen bonds : angle 3.07511 ( 1512) *********************** 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 225 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.390 Fit side-chains REVERT: A 60 GLU cc_start: 0.8927 (tp30) cc_final: 0.8642 (tp30) REVERT: A 123 LEU cc_start: 0.8757 (mt) cc_final: 0.8539 (mt) REVERT: A 127 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 134 ILE cc_start: 0.8763 (mt) cc_final: 0.8477 (mt) REVERT: B 60 GLU cc_start: 0.8748 (tp30) cc_final: 0.8524 (tp30) REVERT: B 61 TYR cc_start: 0.7861 (m-80) cc_final: 0.7138 (m-10) REVERT: B 78 GLN cc_start: 0.8304 (mt0) cc_final: 0.7459 (mp10) REVERT: B 100 LYS cc_start: 0.7604 (mptt) cc_final: 0.6614 (mmtp) REVERT: C 11 ASP cc_start: 0.8854 (t0) cc_final: 0.8305 (t0) REVERT: C 29 GLN cc_start: 0.8306 (mt0) cc_final: 0.7913 (mt0) REVERT: C 78 GLN cc_start: 0.8997 (mt0) cc_final: 0.8492 (mm-40) REVERT: C 89 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7400 (ptt-90) REVERT: C 103 LEU cc_start: 0.9040 (mp) cc_final: 0.8678 (mt) REVERT: C 173 ASN cc_start: 0.8495 (t0) cc_final: 0.8244 (t0) REVERT: C 178 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 183 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8349 (mmmm) REVERT: D 6 ASN cc_start: 0.7995 (t160) cc_final: 0.7758 (t160) REVERT: D 51 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7766 (mm-30) REVERT: D 184 ASN cc_start: 0.7923 (m-40) cc_final: 0.7711 (m-40) REVERT: E 11 ASP cc_start: 0.8498 (t0) cc_final: 0.8283 (t0) REVERT: E 59 ILE cc_start: 0.9184 (mt) cc_final: 0.8876 (mp) REVERT: E 60 GLU cc_start: 0.8900 (tp30) cc_final: 0.8636 (tt0) REVERT: E 77 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8076 (ttm170) REVERT: E 78 GLN cc_start: 0.9117 (mt0) cc_final: 0.8859 (mt0) REVERT: E 138 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: E 173 ASN cc_start: 0.8569 (t0) cc_final: 0.7849 (m110) REVERT: F 59 ILE cc_start: 0.8790 (mt) cc_final: 0.8510 (mm) REVERT: F 60 GLU cc_start: 0.8149 (tp30) cc_final: 0.7725 (tp30) REVERT: F 77 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7715 (ttm110) outliers start: 11 outliers final: 8 residues processed: 217 average time/residue: 0.1132 time to fit residues: 32.7236 Evaluate side-chains 218 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain F residue 6 ASN 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 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 54 optimal weight: 0.0050 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.1584 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.142208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117730 restraints weight = 11878.030| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.98 r_work: 0.3157 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 0.035 8982 Z= 0.086 Angle : 0.441 6.152 12096 Z= 0.233 Chirality : 0.036 0.193 1428 Planarity : 0.003 0.055 1512 Dihedral : 2.967 12.891 1176 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.02 % Allowed : 16.16 % Favored : 82.83 % 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 aren not related in a simple way. whole: 2.94 (0.27), residues: 1092 helix: 2.60 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.53 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.013 0.001 TYR C 15 PHE 0.005 0.000 PHE E 66 TRP 0.009 0.000 TRP C 47 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 8982) covalent geometry : angle 0.44144 (12096) hydrogen bonds : bond 0.02619 ( 531) hydrogen bonds : angle 3.00414 ( 1512) *********************** 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 222 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8884 (tp30) cc_final: 0.8540 (tp30) REVERT: A 123 LEU cc_start: 0.8650 (mt) cc_final: 0.8406 (mt) REVERT: A 127 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 134 ILE cc_start: 0.8757 (mt) cc_final: 0.8486 (mt) REVERT: A 159 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 30 ASP cc_start: 0.7287 (m-30) cc_final: 0.7061 (t0) REVERT: B 61 TYR cc_start: 0.7890 (m-80) cc_final: 0.7359 (m-10) REVERT: B 78 GLN cc_start: 0.8318 (mt0) cc_final: 0.7432 (mp10) REVERT: B 100 LYS cc_start: 0.7884 (mptt) cc_final: 0.7120 (mmtp) REVERT: C 11 ASP cc_start: 0.8841 (t0) cc_final: 0.8282 (t0) REVERT: C 29 GLN cc_start: 0.8204 (mt0) cc_final: 0.7729 (mt0) REVERT: C 30 ASP cc_start: 0.8395 (t70) cc_final: 0.8145 (t0) REVERT: C 78 GLN cc_start: 0.9002 (mt0) cc_final: 0.8550 (mm-40) REVERT: C 89 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7337 (ptm-80) REVERT: C 103 LEU cc_start: 0.8992 (mp) cc_final: 0.8660 (mt) REVERT: C 159 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 178 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 183 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8327 (mmmm) REVERT: D 51 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7736 (mm-30) REVERT: D 184 ASN cc_start: 0.7920 (m-40) cc_final: 0.7705 (m-40) REVERT: E 11 ASP cc_start: 0.8484 (t0) cc_final: 0.8253 (t0) REVERT: E 59 ILE cc_start: 0.9162 (mt) cc_final: 0.8872 (mp) REVERT: E 60 GLU cc_start: 0.8924 (tp30) cc_final: 0.8649 (tt0) REVERT: E 77 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8120 (ttm170) REVERT: E 78 GLN cc_start: 0.9055 (mt0) cc_final: 0.8789 (mt0) REVERT: E 138 ASP cc_start: 0.8335 (t70) cc_final: 0.8004 (m-30) REVERT: E 173 ASN cc_start: 0.8579 (t0) cc_final: 0.7866 (m110) REVERT: F 59 ILE cc_start: 0.8702 (mt) cc_final: 0.8455 (mm) REVERT: F 60 GLU cc_start: 0.8019 (tp30) cc_final: 0.7580 (tp30) outliers start: 10 outliers final: 6 residues processed: 215 average time/residue: 0.1168 time to fit residues: 33.1831 Evaluate side-chains 209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 100 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN D 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116012 restraints weight = 11870.622| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.99 r_work: 0.3105 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8982 Z= 0.099 Angle : 0.462 6.787 12096 Z= 0.242 Chirality : 0.036 0.201 1428 Planarity : 0.003 0.055 1512 Dihedral : 3.006 14.081 1176 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.02 % Allowed : 17.28 % Favored : 81.71 % 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 aren not related in a simple way. whole: 2.89 (0.27), residues: 1092 helix: 2.57 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.48 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.013 0.002 TYR E 87 PHE 0.006 0.001 PHE F 20 TRP 0.010 0.001 TRP C 47 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8982) covalent geometry : angle 0.46234 (12096) hydrogen bonds : bond 0.02755 ( 531) hydrogen bonds : angle 3.05866 ( 1512) *********************** 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 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8874 (tp30) cc_final: 0.8547 (tp30) REVERT: A 89 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.8347 (ptm-80) REVERT: A 127 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 134 ILE cc_start: 0.8786 (mt) cc_final: 0.8510 (mt) REVERT: B 30 ASP cc_start: 0.7224 (m-30) cc_final: 0.6949 (m-30) REVERT: B 61 TYR cc_start: 0.7962 (m-80) cc_final: 0.7333 (m-10) REVERT: B 78 GLN cc_start: 0.8330 (mt0) cc_final: 0.7443 (mp10) REVERT: B 100 LYS cc_start: 0.7895 (mptt) cc_final: 0.6784 (mmtt) REVERT: C 11 ASP cc_start: 0.8866 (t0) cc_final: 0.8298 (t0) REVERT: C 29 GLN cc_start: 0.8222 (mt0) cc_final: 0.7736 (mt0) REVERT: C 78 GLN cc_start: 0.8932 (mt0) cc_final: 0.8519 (mm-40) REVERT: C 89 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7332 (ptm-80) REVERT: C 103 LEU cc_start: 0.8969 (mp) cc_final: 0.8615 (mt) REVERT: C 173 ASN cc_start: 0.8541 (t0) cc_final: 0.8260 (t0) REVERT: C 178 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 183 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8336 (mmmm) REVERT: D 51 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 184 ASN cc_start: 0.7943 (m-40) cc_final: 0.7737 (m-40) REVERT: E 11 ASP cc_start: 0.8484 (t0) cc_final: 0.8247 (t0) REVERT: E 59 ILE cc_start: 0.9143 (mt) cc_final: 0.8882 (mp) REVERT: E 60 GLU cc_start: 0.8919 (tp30) cc_final: 0.8664 (tt0) REVERT: E 77 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8106 (ttm170) REVERT: E 78 GLN cc_start: 0.9064 (mt0) cc_final: 0.8814 (mt0) REVERT: E 138 ASP cc_start: 0.8326 (t70) cc_final: 0.7998 (m-30) REVERT: E 173 ASN cc_start: 0.8585 (t0) cc_final: 0.7860 (m110) REVERT: F 59 ILE cc_start: 0.8727 (mt) cc_final: 0.8454 (mm) REVERT: F 60 GLU cc_start: 0.8050 (tp30) cc_final: 0.7619 (tp30) outliers start: 10 outliers final: 8 residues processed: 206 average time/residue: 0.1190 time to fit residues: 32.4508 Evaluate side-chains 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain B residue 161 LEU 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 F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 72 optimal weight: 0.4980 chunk 22 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114572 restraints weight = 11908.509| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.98 r_work: 0.3072 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8982 Z= 0.108 Angle : 0.475 7.115 12096 Z= 0.248 Chirality : 0.037 0.203 1428 Planarity : 0.003 0.057 1512 Dihedral : 3.044 13.744 1176 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.91 % Allowed : 17.17 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.27), residues: 1092 helix: 2.55 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.47 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.014 0.002 TYR E 87 PHE 0.008 0.001 PHE B 20 TRP 0.012 0.001 TRP C 47 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8982) covalent geometry : angle 0.47472 (12096) hydrogen bonds : bond 0.02910 ( 531) hydrogen bonds : angle 3.09612 ( 1512) ********************** 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 214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.305 Fit side-chains REVERT: A 60 GLU cc_start: 0.8874 (tp30) cc_final: 0.8529 (tp30) REVERT: A 127 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 134 ILE cc_start: 0.8746 (mt) cc_final: 0.8443 (mt) REVERT: B 61 TYR cc_start: 0.8057 (m-80) cc_final: 0.7368 (m-80) REVERT: B 78 GLN cc_start: 0.8344 (mt0) cc_final: 0.7453 (mp10) REVERT: B 100 LYS cc_start: 0.7903 (mptt) cc_final: 0.6785 (mmtt) REVERT: C 11 ASP cc_start: 0.8851 (t0) cc_final: 0.8295 (t0) REVERT: C 78 GLN cc_start: 0.8909 (mt0) cc_final: 0.8530 (mm-40) REVERT: C 89 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7325 (ptm-80) REVERT: C 103 LEU cc_start: 0.8998 (mp) cc_final: 0.8678 (mt) REVERT: C 173 ASN cc_start: 0.8554 (t0) cc_final: 0.8279 (t0) REVERT: C 178 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 183 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8405 (mmmm) REVERT: D 51 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7786 (mm-30) REVERT: D 184 ASN cc_start: 0.7964 (m-40) cc_final: 0.7752 (m-40) REVERT: E 11 ASP cc_start: 0.8437 (t0) cc_final: 0.8210 (t0) REVERT: E 59 ILE cc_start: 0.9161 (mt) cc_final: 0.8898 (mp) REVERT: E 60 GLU cc_start: 0.9011 (tp30) cc_final: 0.8716 (tt0) REVERT: E 77 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8150 (ttm170) REVERT: E 78 GLN cc_start: 0.9088 (mt0) cc_final: 0.8835 (mt0) REVERT: E 138 ASP cc_start: 0.8356 (t70) cc_final: 0.8011 (m-30) REVERT: E 173 ASN cc_start: 0.8590 (t0) cc_final: 0.7877 (m110) REVERT: F 59 ILE cc_start: 0.8836 (mt) cc_final: 0.8570 (mm) REVERT: F 60 GLU cc_start: 0.8049 (tp30) cc_final: 0.7632 (tp30) REVERT: F 77 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7745 (ttm110) outliers start: 9 outliers final: 8 residues processed: 209 average time/residue: 0.1146 time to fit residues: 31.6392 Evaluate side-chains 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain B residue 161 LEU 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 F residue 6 ASN Chi-restraints excluded: chain F residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.138641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113760 restraints weight = 11794.198| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.00 r_work: 0.3062 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8982 Z= 0.115 Angle : 0.485 7.122 12096 Z= 0.253 Chirality : 0.037 0.204 1428 Planarity : 0.003 0.058 1512 Dihedral : 3.096 13.594 1176 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.12 % Allowed : 17.38 % Favored : 81.50 % 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 aren not related in a simple way. whole: 2.80 (0.26), residues: 1092 helix: 2.52 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.42 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.014 0.002 TYR E 87 PHE 0.008 0.001 PHE B 20 TRP 0.013 0.001 TRP C 47 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8982) covalent geometry : angle 0.48504 (12096) hydrogen bonds : bond 0.03027 ( 531) hydrogen bonds : angle 3.13285 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.07 seconds wall clock time: 44 minutes 23.02 seconds (2663.02 seconds total)