Starting phenix.real_space_refine on Fri Aug 22 15:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1z_18829/08_2025/8r1z_18829.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 64 5.16 5 C 3152 2.51 5 N 842 2.21 5 O 968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2513 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 21, 'TRANS': 307} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.53, per 1000 atoms: 0.30 Number of scatterers: 5028 At special positions: 0 Unit cell: (78.7152, 107.493, 71.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 64 16.00 O 968 8.00 N 842 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 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: 0.42 Conformation dependent library (CDL) restraints added in 192.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 22.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 934 through 936 No H-bonds generated for 'chain 'A' and resid 934 through 936' Processing helix chain 'A' and resid 1025 through 1029 Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1148 removed outlier: 3.819A pdb=" N CYS A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 936 No H-bonds generated for 'chain 'B' and resid 934 through 936' Processing helix chain 'B' and resid 1025 through 1029 Processing helix chain 'B' and resid 1057 through 1064 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1096 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1103 through 1108 Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1148 removed outlier: 3.819A pdb=" N CYS B1134 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 905 removed outlier: 3.505A pdb=" N ASN A1023 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A1011 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 910 through 912 removed outlier: 3.534A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 979 through 983 removed outlier: 3.522A pdb=" N SER A 976 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 972 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 964 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A1033 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1176 through 1178 removed outlier: 3.742A pdb=" N HIS A1177 " --> pdb=" O TYR A1207 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A1207 " --> pdb=" O HIS A1177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 903 through 905 removed outlier: 3.506A pdb=" N ASN B1023 " --> pdb=" O VAL B1011 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B1011 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.534A pdb=" N TYR B 911 " --> pdb=" O TYR B 919 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.522A pdb=" N SER B 976 " --> pdb=" O LYS B 979 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 972 " --> pdb=" O ILE B 983 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 964 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS B1033 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1176 through 1178 removed outlier: 3.742A pdb=" N HIS B1177 " --> pdb=" O TYR B1207 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B1207 " --> pdb=" O HIS B1177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 150 hydrogen bonds defined for protein. 402 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: 0.54 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1664 1.35 - 1.46: 1240 1.46 - 1.58: 2190 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 5162 Sorted by residual: bond pdb=" CA CYS B1161 " pdb=" C CYS B1161 " ideal model delta sigma weight residual 1.534 1.525 0.010 9.50e-03 1.11e+04 1.02e+00 bond pdb=" CA ILE A1000 " pdb=" C ILE A1000 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.12e-02 7.97e+03 7.84e-01 bond pdb=" CA CYS A1161 " pdb=" C CYS A1161 " ideal model delta sigma weight residual 1.534 1.526 0.008 9.50e-03 1.11e+04 7.84e-01 bond pdb=" CA ILE B1000 " pdb=" C ILE B1000 " ideal model delta sigma weight residual 1.530 1.521 0.010 1.12e-02 7.97e+03 7.45e-01 bond pdb=" CA LEU B 968 " pdb=" C LEU B 968 " ideal model delta sigma weight residual 1.526 1.518 0.009 1.03e-02 9.43e+03 7.41e-01 ... (remaining 5157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 6653 0.92 - 1.83: 295 1.83 - 2.75: 48 2.75 - 3.66: 28 3.66 - 4.58: 8 Bond angle restraints: 7032 Sorted by residual: angle pdb=" N ILE B1000 " pdb=" CA ILE B1000 " pdb=" C ILE B1000 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N ILE A1000 " pdb=" CA ILE A1000 " pdb=" C ILE A1000 " ideal model delta sigma weight residual 111.91 108.71 3.20 8.90e-01 1.26e+00 1.29e+01 angle pdb=" C THR B 940 " pdb=" N GLN B 941 " pdb=" CA GLN B 941 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.18e+00 angle pdb=" C THR A 940 " pdb=" N GLN A 941 " pdb=" CA GLN A 941 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.11e+00 angle pdb=" C CYS A1161 " pdb=" CA CYS A1161 " pdb=" CB CYS A1161 " ideal model delta sigma weight residual 111.20 109.63 1.57 7.10e-01 1.98e+00 4.88e+00 ... (remaining 7027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 2737 15.36 - 30.72: 271 30.72 - 46.07: 80 46.07 - 61.43: 22 61.43 - 76.79: 12 Dihedral angle restraints: 3122 sinusoidal: 1236 harmonic: 1886 Sorted by residual: dihedral pdb=" CB CYS A 953 " pdb=" SG CYS A 953 " pdb=" SG CYS A 960 " pdb=" CB CYS A 960 " ideal model delta sinusoidal sigma weight residual 93.00 167.88 -74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B 953 " pdb=" SG CYS B 953 " pdb=" SG CYS B 960 " pdb=" CB CYS B 960 " ideal model delta sinusoidal sigma weight residual 93.00 167.88 -74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 903 " pdb=" SG CYS A 903 " pdb=" SG CYS A1036 " pdb=" CB CYS A1036 " ideal model delta sinusoidal sigma weight residual -86.00 -123.83 37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 3119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 425 0.024 - 0.048: 148 0.048 - 0.072: 91 0.072 - 0.096: 58 0.096 - 0.120: 32 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA PRO A1026 " pdb=" N PRO A1026 " pdb=" C PRO A1026 " pdb=" CB PRO A1026 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA PRO B1026 " pdb=" N PRO B1026 " pdb=" C PRO B1026 " pdb=" CB PRO B1026 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ILE A 964 " pdb=" N ILE A 964 " pdb=" C ILE A 964 " pdb=" CB ILE A 964 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 751 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B1025 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B1026 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B1026 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B1026 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1025 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A1026 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B1071 " -0.012 5.00e-02 4.00e+02 1.79e-02 5.13e-01 pdb=" N PRO B1072 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO B1072 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO B1072 " -0.010 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1641 2.81 - 3.34: 4924 3.34 - 3.86: 8710 3.86 - 4.38: 9485 4.38 - 4.90: 15706 Nonbonded interactions: 40466 Sorted by model distance: nonbonded pdb=" OD1 ASN B1038 " pdb="CA CA B1401 " model vdw 2.292 2.510 nonbonded pdb=" OD1 ASN A1038 " pdb="CA CA A1401 " model vdw 2.293 2.510 nonbonded pdb=" ND2 ASN B1191 " pdb=" O ASP B1195 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN A1191 " pdb=" O ASP A1195 " model vdw 2.296 3.120 nonbonded pdb=" OD2 ASP A1079 " pdb=" OG1 THR A1082 " model vdw 2.301 3.040 ... (remaining 40461 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' } 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: 1.120 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.003 0.030 5190 Z= 0.130 Angle : 0.486 4.577 7088 Z= 0.274 Chirality : 0.042 0.120 754 Planarity : 0.003 0.032 930 Dihedral : 14.163 76.791 1834 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 16.01 % Favored : 83.81 % 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: -0.23 (0.34), residues: 654 helix: 0.69 (0.44), residues: 130 sheet: 1.39 (0.56), residues: 92 loop : -0.80 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1190 TYR 0.006 0.001 TYR A1207 PHE 0.007 0.001 PHE A 944 TRP 0.003 0.001 TRP A1065 HIS 0.002 0.001 HIS B1147 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5162) covalent geometry : angle 0.48450 ( 7032) SS BOND : bond 0.00256 ( 28) SS BOND : angle 0.64891 ( 56) hydrogen bonds : bond 0.19432 ( 150) hydrogen bonds : angle 7.16373 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 927 TYR cc_start: 0.8183 (m-80) cc_final: 0.7913 (m-80) REVERT: A 1109 HIS cc_start: 0.8992 (t-90) cc_final: 0.8766 (t-90) REVERT: A 1122 ASP cc_start: 0.8656 (t0) cc_final: 0.8214 (t0) REVERT: A 1187 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.7980 (tpt-90) REVERT: A 1199 ASP cc_start: 0.8550 (p0) cc_final: 0.8109 (p0) REVERT: B 1109 HIS cc_start: 0.8973 (t-90) cc_final: 0.8761 (t-90) REVERT: B 1122 ASP cc_start: 0.8639 (t0) cc_final: 0.8198 (t0) REVERT: B 1199 ASP cc_start: 0.8583 (p0) cc_final: 0.8212 (p0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1077 time to fit residues: 6.9954 Evaluate side-chains 34 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0470 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.075697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.057965 restraints weight = 22198.556| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 6.72 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5190 Z= 0.130 Angle : 0.541 5.557 7088 Z= 0.284 Chirality : 0.045 0.139 754 Planarity : 0.004 0.052 930 Dihedral : 3.584 14.467 704 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.16 % Allowed : 19.06 % Favored : 78.78 % 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: -0.28 (0.34), residues: 654 helix: 0.51 (0.45), residues: 130 sheet: 1.43 (0.54), residues: 92 loop : -0.81 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1198 TYR 0.007 0.001 TYR B1116 PHE 0.018 0.002 PHE B1061 TRP 0.002 0.001 TRP A1090 HIS 0.004 0.001 HIS B1107 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5162) covalent geometry : angle 0.54102 ( 7032) SS BOND : bond 0.00288 ( 28) SS BOND : angle 0.55830 ( 56) hydrogen bonds : bond 0.03970 ( 150) hydrogen bonds : angle 5.27573 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8875 (t-90) cc_final: 0.8664 (t-90) REVERT: A 1122 ASP cc_start: 0.8576 (t0) cc_final: 0.8139 (t0) REVERT: A 1187 ARG cc_start: 0.8253 (ptp-170) cc_final: 0.7909 (tpp-160) REVERT: B 1109 HIS cc_start: 0.8914 (t-90) cc_final: 0.8703 (t-90) REVERT: B 1122 ASP cc_start: 0.8640 (t0) cc_final: 0.8245 (t0) outliers start: 12 outliers final: 9 residues processed: 41 average time/residue: 0.1283 time to fit residues: 6.2042 Evaluate side-chains 45 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 0.0060 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.076687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.058953 restraints weight = 22030.734| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 6.77 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5190 Z= 0.093 Angle : 0.513 5.689 7088 Z= 0.263 Chirality : 0.045 0.200 754 Planarity : 0.003 0.024 930 Dihedral : 3.438 13.574 704 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.98 % Allowed : 19.96 % Favored : 78.06 % 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: -0.23 (0.34), residues: 654 helix: 0.81 (0.46), residues: 126 sheet: 1.60 (0.55), residues: 92 loop : -0.89 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1187 TYR 0.005 0.001 TYR A1116 PHE 0.021 0.001 PHE A1061 TRP 0.004 0.001 TRP B1014 HIS 0.002 0.001 HIS B1107 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 5162) covalent geometry : angle 0.51308 ( 7032) SS BOND : bond 0.00230 ( 28) SS BOND : angle 0.49979 ( 56) hydrogen bonds : bond 0.03235 ( 150) hydrogen bonds : angle 4.83428 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8851 (t-90) cc_final: 0.8642 (t-90) REVERT: A 1122 ASP cc_start: 0.8576 (t0) cc_final: 0.8138 (t0) REVERT: A 1187 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7797 (tpp-160) REVERT: B 1109 HIS cc_start: 0.8886 (t-90) cc_final: 0.8678 (t-90) REVERT: B 1122 ASP cc_start: 0.8616 (t0) cc_final: 0.8212 (t0) REVERT: B 1198 ARG cc_start: 0.8981 (tpt170) cc_final: 0.8702 (tpm170) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.1550 time to fit residues: 8.2296 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.077051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059236 restraints weight = 21873.063| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 6.74 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5190 Z= 0.091 Angle : 0.500 5.731 7088 Z= 0.257 Chirality : 0.044 0.184 754 Planarity : 0.003 0.032 930 Dihedral : 3.355 13.421 704 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.98 % Allowed : 20.50 % Favored : 77.52 % 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: -0.18 (0.34), residues: 654 helix: 0.93 (0.46), residues: 126 sheet: 1.63 (0.55), residues: 92 loop : -0.88 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1052 TYR 0.004 0.001 TYR B1116 PHE 0.027 0.002 PHE B1061 TRP 0.004 0.001 TRP B1014 HIS 0.002 0.001 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5162) covalent geometry : angle 0.49917 ( 7032) SS BOND : bond 0.00211 ( 28) SS BOND : angle 0.55652 ( 56) hydrogen bonds : bond 0.02958 ( 150) hydrogen bonds : angle 4.56834 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8876 (t-90) cc_final: 0.8665 (t-90) REVERT: A 1122 ASP cc_start: 0.8569 (t0) cc_final: 0.8129 (t0) REVERT: A 1187 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7821 (tpp-160) REVERT: B 1109 HIS cc_start: 0.8900 (t-90) cc_final: 0.8695 (t-90) REVERT: B 1122 ASP cc_start: 0.8584 (t0) cc_final: 0.8136 (t0) REVERT: B 1198 ARG cc_start: 0.8985 (tpt170) cc_final: 0.8702 (tpm170) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1437 time to fit residues: 7.0545 Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.077343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059369 restraints weight = 22071.412| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 6.79 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5190 Z= 0.087 Angle : 0.491 5.228 7088 Z= 0.251 Chirality : 0.044 0.177 754 Planarity : 0.003 0.024 930 Dihedral : 3.295 13.255 704 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.80 % Allowed : 20.32 % Favored : 77.88 % 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: -0.29 (0.34), residues: 654 helix: 1.04 (0.46), residues: 126 sheet: 1.44 (0.54), residues: 96 loop : -1.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1052 TYR 0.021 0.001 TYR A 927 PHE 0.020 0.001 PHE B1061 TRP 0.004 0.001 TRP B1014 HIS 0.002 0.000 HIS B1107 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 5162) covalent geometry : angle 0.49136 ( 7032) SS BOND : bond 0.00205 ( 28) SS BOND : angle 0.49717 ( 56) hydrogen bonds : bond 0.02848 ( 150) hydrogen bonds : angle 4.39497 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8874 (t-90) cc_final: 0.8660 (t-90) REVERT: A 1122 ASP cc_start: 0.8556 (t0) cc_final: 0.8129 (t0) REVERT: A 1187 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7994 (tpt170) REVERT: B 1109 HIS cc_start: 0.8878 (t-90) cc_final: 0.8673 (t-90) REVERT: B 1122 ASP cc_start: 0.8582 (t0) cc_final: 0.8151 (t0) REVERT: B 1198 ARG cc_start: 0.9018 (tpt170) cc_final: 0.8788 (tpm170) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1511 time to fit residues: 7.3438 Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.076615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.058540 restraints weight = 22408.272| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 6.80 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5190 Z= 0.104 Angle : 0.497 5.296 7088 Z= 0.255 Chirality : 0.044 0.168 754 Planarity : 0.003 0.028 930 Dihedral : 3.306 13.273 704 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.34 % Allowed : 20.32 % Favored : 77.34 % 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: -0.29 (0.34), residues: 654 helix: 1.08 (0.46), residues: 126 sheet: 1.40 (0.53), residues: 96 loop : -1.02 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1052 TYR 0.014 0.001 TYR A 927 PHE 0.015 0.001 PHE B1061 TRP 0.004 0.001 TRP B1014 HIS 0.002 0.001 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5162) covalent geometry : angle 0.49641 ( 7032) SS BOND : bond 0.00224 ( 28) SS BOND : angle 0.56463 ( 56) hydrogen bonds : bond 0.03020 ( 150) hydrogen bonds : angle 4.29312 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8866 (t-90) cc_final: 0.8639 (t-90) REVERT: A 1122 ASP cc_start: 0.8566 (t0) cc_final: 0.8140 (t0) REVERT: A 1187 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.8092 (tpp-160) REVERT: B 1109 HIS cc_start: 0.8874 (t-90) cc_final: 0.8661 (t-90) REVERT: B 1122 ASP cc_start: 0.8597 (t0) cc_final: 0.8153 (t0) REVERT: B 1198 ARG cc_start: 0.9022 (tpt170) cc_final: 0.8784 (tpm170) outliers start: 13 outliers final: 11 residues processed: 42 average time/residue: 0.1333 time to fit residues: 6.5563 Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.0170 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.077396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.059474 restraints weight = 22127.531| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 6.83 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5190 Z= 0.088 Angle : 0.512 7.884 7088 Z= 0.261 Chirality : 0.044 0.170 754 Planarity : 0.003 0.026 930 Dihedral : 3.267 13.060 704 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 20.50 % Favored : 77.88 % 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: -0.28 (0.34), residues: 654 helix: 1.13 (0.46), residues: 126 sheet: 1.48 (0.54), residues: 96 loop : -1.05 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1052 TYR 0.019 0.001 TYR A 927 PHE 0.016 0.001 PHE B1061 TRP 0.004 0.001 TRP B1014 HIS 0.001 0.000 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 5162) covalent geometry : angle 0.51212 ( 7032) SS BOND : bond 0.00204 ( 28) SS BOND : angle 0.50753 ( 56) hydrogen bonds : bond 0.02710 ( 150) hydrogen bonds : angle 4.17982 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8856 (t-90) cc_final: 0.8632 (t-90) REVERT: A 1122 ASP cc_start: 0.8546 (t0) cc_final: 0.8112 (t0) REVERT: A 1198 ARG cc_start: 0.8992 (tpt170) cc_final: 0.8734 (tpm170) REVERT: B 1109 HIS cc_start: 0.8857 (t-90) cc_final: 0.8635 (t-90) REVERT: B 1122 ASP cc_start: 0.8570 (t0) cc_final: 0.8147 (t0) outliers start: 9 outliers final: 9 residues processed: 38 average time/residue: 0.1185 time to fit residues: 5.3507 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.075940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058217 restraints weight = 22567.352| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 6.79 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5190 Z= 0.113 Angle : 0.511 6.762 7088 Z= 0.262 Chirality : 0.044 0.161 754 Planarity : 0.003 0.031 930 Dihedral : 3.303 13.259 704 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.98 % Allowed : 20.32 % Favored : 77.70 % 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: -0.33 (0.34), residues: 654 helix: 0.91 (0.45), residues: 130 sheet: 1.44 (0.53), residues: 96 loop : -1.03 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.016 0.001 TYR A 927 PHE 0.012 0.001 PHE B1061 TRP 0.005 0.001 TRP B1014 HIS 0.002 0.001 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5162) covalent geometry : angle 0.51024 ( 7032) SS BOND : bond 0.00228 ( 28) SS BOND : angle 0.57807 ( 56) hydrogen bonds : bond 0.03006 ( 150) hydrogen bonds : angle 4.18195 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8866 (t-90) cc_final: 0.8622 (t-90) REVERT: A 1122 ASP cc_start: 0.8563 (t0) cc_final: 0.8139 (t0) REVERT: A 1187 ARG cc_start: 0.4573 (tpt170) cc_final: 0.4245 (tpp-160) REVERT: A 1198 ARG cc_start: 0.8972 (tpt170) cc_final: 0.8681 (tpm170) REVERT: B 1109 HIS cc_start: 0.8875 (t-90) cc_final: 0.8645 (t-90) REVERT: B 1122 ASP cc_start: 0.8558 (t0) cc_final: 0.8110 (t0) REVERT: B 1190 ARG cc_start: 0.8285 (ttt180) cc_final: 0.7164 (tmm-80) outliers start: 11 outliers final: 10 residues processed: 37 average time/residue: 0.1048 time to fit residues: 4.7601 Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.075773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.058119 restraints weight = 22313.293| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 6.68 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5190 Z= 0.108 Angle : 0.505 5.989 7088 Z= 0.258 Chirality : 0.044 0.162 754 Planarity : 0.003 0.031 930 Dihedral : 3.355 13.382 704 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.44 % Allowed : 21.22 % Favored : 77.34 % 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: -0.37 (0.34), residues: 654 helix: 0.84 (0.45), residues: 130 sheet: 1.43 (0.53), residues: 96 loop : -1.05 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1193 TYR 0.017 0.001 TYR B 927 PHE 0.012 0.001 PHE B1061 TRP 0.004 0.001 TRP B1014 HIS 0.002 0.000 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5162) covalent geometry : angle 0.50433 ( 7032) SS BOND : bond 0.00227 ( 28) SS BOND : angle 0.56436 ( 56) hydrogen bonds : bond 0.03028 ( 150) hydrogen bonds : angle 4.16349 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8872 (t-90) cc_final: 0.8623 (t-90) REVERT: A 1122 ASP cc_start: 0.8563 (t0) cc_final: 0.8140 (t0) REVERT: A 1198 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8786 (tpm170) REVERT: B 1109 HIS cc_start: 0.8876 (t-90) cc_final: 0.8632 (t-90) REVERT: B 1122 ASP cc_start: 0.8564 (t0) cc_final: 0.8122 (t0) outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 0.1145 time to fit residues: 4.8044 Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.073226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.055627 restraints weight = 22797.893| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 6.67 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5190 Z= 0.207 Angle : 0.582 5.740 7088 Z= 0.303 Chirality : 0.044 0.147 754 Planarity : 0.004 0.030 930 Dihedral : 3.758 14.083 704 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.26 % Allowed : 21.58 % Favored : 77.16 % 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: -0.60 (0.33), residues: 654 helix: 0.47 (0.45), residues: 130 sheet: 1.30 (0.54), residues: 92 loop : -1.13 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1193 TYR 0.017 0.002 TYR A 911 PHE 0.009 0.001 PHE A1039 TRP 0.008 0.002 TRP A1155 HIS 0.003 0.001 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5162) covalent geometry : angle 0.57903 ( 7032) SS BOND : bond 0.00315 ( 28) SS BOND : angle 0.86464 ( 56) hydrogen bonds : bond 0.04044 ( 150) hydrogen bonds : angle 4.50946 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8867 (t-90) cc_final: 0.8596 (t-90) REVERT: A 1122 ASP cc_start: 0.8593 (t0) cc_final: 0.8156 (t0) REVERT: B 1109 HIS cc_start: 0.8865 (t-90) cc_final: 0.8597 (t-90) REVERT: B 1122 ASP cc_start: 0.8592 (t0) cc_final: 0.8142 (t0) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.0936 time to fit residues: 3.7949 Evaluate side-chains 30 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 0.0040 chunk 48 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.075111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.057442 restraints weight = 22885.369| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 6.79 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5190 Z= 0.098 Angle : 0.511 6.224 7088 Z= 0.262 Chirality : 0.044 0.167 754 Planarity : 0.003 0.031 930 Dihedral : 3.497 13.689 704 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.72 % Allowed : 22.12 % Favored : 77.16 % 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: -0.38 (0.34), residues: 654 helix: 0.64 (0.46), residues: 130 sheet: 1.57 (0.55), residues: 92 loop : -1.01 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1193 TYR 0.019 0.001 TYR B 927 PHE 0.026 0.001 PHE A1061 TRP 0.004 0.001 TRP A1176 HIS 0.002 0.000 HIS B 933 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5162) covalent geometry : angle 0.50999 ( 7032) SS BOND : bond 0.00248 ( 28) SS BOND : angle 0.62626 ( 56) hydrogen bonds : bond 0.03113 ( 150) hydrogen bonds : angle 4.25412 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.77 seconds wall clock time: 19 minutes 2.52 seconds (1142.52 seconds total)