Starting phenix.real_space_refine on Thu Jul 2 01:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1u_18828/07_2026/8r1u_18828.map" } resolution = 3.19 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= 0.013 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 3154 2.51 5 N 846 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2515 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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 1.38, per 1000 atoms: 0.27 Number of scatterers: 5032 At special positions: 0 Unit cell: (92.2019, 101.681, 74.1062, 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 966 8.00 N 846 7.00 C 3154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, 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 A1174 " - pdb=" SG CYS B1174 " 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: 0.37 Conformation dependent library (CDL) restraints added in 143.4 milliseconds 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 6 sheets defined 22.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1058 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 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' 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 removed outlier: 3.883A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1150 removed outlier: 3.991A pdb=" N ALA A1138 " --> pdb=" O CYS A1134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A1150 " --> pdb=" O CYS A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1058 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 1097 through 1099 No H-bonds generated for 'chain 'B' and resid 1097 through 1099' 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 removed outlier: 3.882A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1150 removed outlier: 3.991A pdb=" N ALA B1138 " --> pdb=" O CYS B1134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B1150 " --> pdb=" O CYS B1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 3.511A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1011 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A1014 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 982 removed outlier: 5.842A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AA4, first strand: chain 'B' and resid 918 through 920 removed outlier: 3.512A pdb=" N TYR B 911 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B1011 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP B1014 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 982 removed outlier: 5.841A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 944 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN B 931 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1176 through 1178 152 hydrogen bonds defined for protein. 414 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: 0.48 Time building geometry restraints manager: 0.53 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: 1666 1.35 - 1.46: 1239 1.46 - 1.58: 2193 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 5166 Sorted by residual: bond pdb=" CA CYS A1161 " pdb=" CB CYS A1161 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.62e+00 bond pdb=" CA CYS B1161 " pdb=" CB CYS B1161 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.40e+00 bond pdb=" CA CYS B1161 " pdb=" C CYS B1161 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.79e-01 bond pdb=" CA CYS A1161 " pdb=" C CYS A1161 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.13e-01 bond pdb=" N GLY B 954 " pdb=" CA GLY B 954 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.32e-02 5.74e+03 7.13e-01 ... (remaining 5161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 6816 1.06 - 2.12: 156 2.12 - 3.18: 54 3.18 - 4.24: 6 4.24 - 5.30: 4 Bond angle restraints: 7036 Sorted by residual: angle pdb=" C ASP B1015 " pdb=" N LYS B1016 " pdb=" CA LYS B1016 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C ASP A1015 " pdb=" N LYS A1016 " pdb=" CA LYS A1016 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 angle pdb=" C SER A 939 " pdb=" N THR A 940 " pdb=" CA THR A 940 " ideal model delta sigma weight residual 122.46 125.30 -2.84 1.41e+00 5.03e-01 4.06e+00 angle pdb=" C SER B 939 " pdb=" N THR B 940 " pdb=" CA THR B 940 " ideal model delta sigma weight residual 122.46 125.26 -2.80 1.41e+00 5.03e-01 3.93e+00 angle pdb=" N PRO A1215 " pdb=" CA PRO A1215 " pdb=" C PRO A1215 " ideal model delta sigma weight residual 114.92 112.81 2.11 1.19e+00 7.06e-01 3.16e+00 ... (remaining 7031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 2738 16.23 - 32.47: 285 32.47 - 48.70: 76 48.70 - 64.93: 18 64.93 - 81.17: 12 Dihedral angle restraints: 3129 sinusoidal: 1243 harmonic: 1886 Sorted by residual: dihedral pdb=" CB CYS A1106 " pdb=" SG CYS A1106 " pdb=" SG CYS A1146 " pdb=" CB CYS A1146 " ideal model delta sinusoidal sigma weight residual -86.00 -166.05 80.05 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B1106 " pdb=" SG CYS B1106 " pdb=" SG CYS B1146 " pdb=" CB CYS B1146 " ideal model delta sinusoidal sigma weight residual -86.00 -166.03 80.03 1 1.00e+01 1.00e-02 7.94e+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 -86.00 -159.20 73.20 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 3126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 413 0.024 - 0.049: 194 0.049 - 0.073: 54 0.073 - 0.097: 49 0.097 - 0.121: 44 Chirality restraints: 754 Sorted by residual: chirality pdb=" CG LEU B1203 " pdb=" CB LEU B1203 " pdb=" CD1 LEU B1203 " pdb=" CD2 LEU B1203 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CG LEU A1203 " pdb=" CB LEU A1203 " pdb=" CD1 LEU A1203 " pdb=" CD2 LEU A1203 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA LYS A1016 " pdb=" N LYS A1016 " pdb=" C LYS A1016 " pdb=" CB LYS A1016 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 751 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1157 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A1158 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1157 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO B1158 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B1158 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B1158 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1025 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B1026 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B1026 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B1026 " 0.014 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 836 2.76 - 3.30: 4701 3.30 - 3.83: 8342 3.83 - 4.37: 9045 4.37 - 4.90: 15462 Nonbonded interactions: 38386 Sorted by model distance: nonbonded pdb=" OG SER A1025 " pdb=" OE1 GLU A1027 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B1025 " pdb=" OE1 GLU B1027 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASN B1045 " pdb="CA CA B1401 " model vdw 2.277 3.250 nonbonded pdb=" OD1 ASN A1045 " pdb="CA CA A1401 " model vdw 2.277 3.250 nonbonded pdb=" OD2 ASP B1079 " pdb=" OG1 THR B1082 " model vdw 2.287 3.040 ... (remaining 38381 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: 1.700 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: 0.000 Process input model: 5.350 Find NCS groups from input model: 0.030 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.002 0.019 5195 Z= 0.107 Angle : 0.458 5.301 7094 Z= 0.242 Chirality : 0.042 0.121 754 Planarity : 0.003 0.029 930 Dihedral : 14.256 81.168 1838 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 18.71 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.33), residues: 654 helix: 0.59 (0.48), residues: 128 sheet: 1.80 (0.77), residues: 52 loop : -1.20 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1198 TYR 0.004 0.001 TYR B1116 PHE 0.005 0.001 PHE B1135 TRP 0.003 0.001 TRP B1201 HIS 0.001 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 5166) covalent geometry : angle 0.45755 / 0.24 ( 7036) SS BOND : bond 0.00176 / 0.12 ( 29) SS BOND : angle 0.49112 / 0.34 ( 58) hydrogen bonds : bond 0.18048 / 12.77 ( 152) hydrogen bonds : angle 7.39812 / 5.07 ( 414) *********************** 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 28 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8302 (t0) cc_final: 0.7984 (t70) REVERT: B 1122 ASP cc_start: 0.8299 (t0) cc_final: 0.7982 (t0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1261 time to fit residues: 4.2694 Evaluate side-chains 15 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.077107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056774 restraints weight = 19253.494| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 5.74 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5195 Z= 0.168 Angle : 0.523 5.482 7094 Z= 0.280 Chirality : 0.045 0.131 754 Planarity : 0.003 0.031 930 Dihedral : 3.152 10.633 706 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.08 % Allowed : 17.63 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.32), residues: 654 helix: 0.33 (0.47), residues: 128 sheet: 1.90 (0.73), residues: 52 loop : -1.28 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1198 TYR 0.010 0.001 TYR A 911 PHE 0.008 0.001 PHE A1047 TRP 0.004 0.001 TRP B1201 HIS 0.005 0.001 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 5166) covalent geometry : angle 0.52237 / 0.28 ( 7036) SS BOND : bond 0.00211 / 0.14 ( 29) SS BOND : angle 0.58668 / 0.41 ( 58) hydrogen bonds : bond 0.04571 / 3.20 ( 152) hydrogen bonds : angle 5.84834 / 4.07 ( 414) *********************** 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 22 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: A 1122 ASP cc_start: 0.8336 (t0) cc_final: 0.7976 (t0) REVERT: B 1046 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: B 1122 ASP cc_start: 0.8342 (t0) cc_final: 0.7985 (t0) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.1211 time to fit residues: 3.0900 Evaluate side-chains 20 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 HIS B1107 HIS ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.078547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058381 restraints weight = 18976.548| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 5.67 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5195 Z= 0.097 Angle : 0.451 4.745 7094 Z= 0.239 Chirality : 0.043 0.127 754 Planarity : 0.003 0.033 930 Dihedral : 3.027 10.180 706 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.44 % Allowed : 18.53 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.33), residues: 654 helix: 1.06 (0.49), residues: 116 sheet: 0.99 (0.62), residues: 82 loop : -1.20 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1198 TYR 0.006 0.001 TYR A 906 PHE 0.006 0.001 PHE B1135 TRP 0.002 0.000 TRP A1065 HIS 0.004 0.001 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 5166) covalent geometry : angle 0.45042 / 0.24 ( 7036) SS BOND : bond 0.00170 / 0.12 ( 29) SS BOND : angle 0.47443 / 0.32 ( 58) hydrogen bonds : bond 0.03651 / 2.57 ( 152) hydrogen bonds : angle 5.22225 / 3.64 ( 414) *********************** 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 27 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: A 1106 CYS cc_start: 0.7398 (m) cc_final: 0.7029 (t) REVERT: A 1122 ASP cc_start: 0.8298 (t0) cc_final: 0.7959 (t0) REVERT: B 1046 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: B 1122 ASP cc_start: 0.8321 (t0) cc_final: 0.7979 (t0) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.1188 time to fit residues: 3.7135 Evaluate side-chains 24 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 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 = 0.3781 r_free = 0.3781 target = 0.078214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.057917 restraints weight = 18669.819| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 5.66 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5195 Z= 0.116 Angle : 0.455 4.029 7094 Z= 0.242 Chirality : 0.044 0.126 754 Planarity : 0.003 0.033 930 Dihedral : 3.134 9.983 706 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 18.53 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.33), residues: 654 helix: 0.85 (0.48), residues: 116 sheet: 1.16 (0.62), residues: 82 loop : -1.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1198 TYR 0.008 0.001 TYR B1142 PHE 0.006 0.001 PHE B1135 TRP 0.003 0.001 TRP B1014 HIS 0.004 0.001 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 5166) covalent geometry : angle 0.45210 / 0.24 ( 7036) SS BOND : bond 0.00238 / 0.18 ( 29) SS BOND : angle 0.74883 / 0.49 ( 58) hydrogen bonds : bond 0.03694 / 2.58 ( 152) hydrogen bonds : angle 5.08910 / 3.55 ( 414) *********************** 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 28 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: A 1106 CYS cc_start: 0.7447 (m) cc_final: 0.6694 (t) REVERT: A 1122 ASP cc_start: 0.8319 (t0) cc_final: 0.7975 (t0) REVERT: B 1046 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: B 1122 ASP cc_start: 0.8337 (t0) cc_final: 0.7993 (t0) outliers start: 9 outliers final: 4 residues processed: 27 average time/residue: 0.1095 time to fit residues: 3.5851 Evaluate side-chains 26 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.077546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056954 restraints weight = 19541.032| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 5.82 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5195 Z= 0.143 Angle : 0.470 3.715 7094 Z= 0.251 Chirality : 0.044 0.124 754 Planarity : 0.003 0.034 930 Dihedral : 3.258 10.834 706 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.26 % Allowed : 20.50 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.33), residues: 654 helix: 0.89 (0.48), residues: 116 sheet: 1.30 (0.63), residues: 82 loop : -1.19 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1031 TYR 0.008 0.001 TYR B1116 PHE 0.006 0.001 PHE B1135 TRP 0.005 0.001 TRP B1014 HIS 0.004 0.001 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5166) covalent geometry : angle 0.46799 / 0.25 ( 7036) SS BOND : bond 0.00209 / 0.15 ( 29) SS BOND : angle 0.65995 / 0.43 ( 58) hydrogen bonds : bond 0.03873 / 2.72 ( 152) hydrogen bonds : angle 5.04981 / 3.53 ( 414) *********************** 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 27 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: A 1106 CYS cc_start: 0.7419 (m) cc_final: 0.6658 (t) REVERT: A 1122 ASP cc_start: 0.8338 (t0) cc_final: 0.7992 (t0) REVERT: B 1046 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: B 1122 ASP cc_start: 0.8345 (t0) cc_final: 0.7997 (t0) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.1689 time to fit residues: 5.1040 Evaluate side-chains 22 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 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 = 0.3739 r_free = 0.3739 target = 0.076557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056204 restraints weight = 19350.399| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 5.76 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5195 Z= 0.183 Angle : 0.528 7.471 7094 Z= 0.280 Chirality : 0.045 0.197 754 Planarity : 0.003 0.034 930 Dihedral : 3.432 11.904 706 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.80 % Allowed : 21.58 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.33), residues: 654 helix: 0.48 (0.46), residues: 128 sheet: 1.44 (0.63), residues: 80 loop : -1.33 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1187 TYR 0.010 0.001 TYR B1116 PHE 0.008 0.001 PHE B1217 TRP 0.006 0.001 TRP B1014 HIS 0.005 0.001 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 5166) covalent geometry : angle 0.52698 / 0.28 ( 7036) SS BOND : bond 0.00243 / 0.18 ( 29) SS BOND : angle 0.66965 / 0.44 ( 58) hydrogen bonds : bond 0.04164 / 2.93 ( 152) hydrogen bonds : angle 5.10559 / 3.57 ( 414) *********************** 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 27 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: A 1122 ASP cc_start: 0.8375 (t0) cc_final: 0.8029 (t0) REVERT: B 1046 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: B 1122 ASP cc_start: 0.8356 (t0) cc_final: 0.8010 (t0) outliers start: 10 outliers final: 8 residues processed: 27 average time/residue: 0.0956 time to fit residues: 3.4105 Evaluate side-chains 25 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 15 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 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 = 0.3759 r_free = 0.3759 target = 0.077646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057306 restraints weight = 19060.965| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 5.77 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5195 Z= 0.113 Angle : 0.482 5.905 7094 Z= 0.255 Chirality : 0.044 0.157 754 Planarity : 0.003 0.036 930 Dihedral : 3.290 10.696 706 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 21.40 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.33), residues: 654 helix: 0.48 (0.47), residues: 130 sheet: 1.42 (0.63), residues: 80 loop : -1.31 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1187 TYR 0.010 0.001 TYR B1142 PHE 0.006 0.001 PHE B1135 TRP 0.002 0.000 TRP A1090 HIS 0.004 0.001 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 5166) covalent geometry : angle 0.48026 / 0.25 ( 7036) SS BOND : bond 0.00219 / 0.17 ( 29) SS BOND : angle 0.68581 / 0.44 ( 58) hydrogen bonds : bond 0.03515 / 2.49 ( 152) hydrogen bonds : angle 4.86325 / 3.40 ( 414) *********************** 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 27 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: A 1099 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7389 (m-70) REVERT: A 1106 CYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6484 (t) REVERT: A 1122 ASP cc_start: 0.8312 (t0) cc_final: 0.7970 (t0) REVERT: B 1046 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: B 1122 ASP cc_start: 0.8326 (t0) cc_final: 0.7982 (t0) outliers start: 11 outliers final: 6 residues processed: 26 average time/residue: 0.0996 time to fit residues: 3.3727 Evaluate side-chains 26 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 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 = 0.3744 r_free = 0.3744 target = 0.076850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056548 restraints weight = 19227.348| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.71 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5195 Z= 0.149 Angle : 0.498 5.066 7094 Z= 0.264 Chirality : 0.044 0.139 754 Planarity : 0.003 0.034 930 Dihedral : 3.399 11.572 706 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.34 % Allowed : 20.86 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.33), residues: 654 helix: 0.54 (0.46), residues: 128 sheet: 1.45 (0.63), residues: 80 loop : -1.34 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1187 TYR 0.008 0.001 TYR A 911 PHE 0.006 0.001 PHE B1135 TRP 0.004 0.001 TRP A1201 HIS 0.004 0.001 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 5166) covalent geometry : angle 0.49515 / 0.26 ( 7036) SS BOND : bond 0.00235 / 0.17 ( 29) SS BOND : angle 0.74417 / 0.48 ( 58) hydrogen bonds : bond 0.03877 / 2.73 ( 152) hydrogen bonds : angle 4.93938 / 3.45 ( 414) *********************** 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 28 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 15 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: A 1099 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7417 (m-70) REVERT: A 1122 ASP cc_start: 0.8353 (t0) cc_final: 0.8008 (t0) REVERT: B 1046 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: B 1099 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7434 (m-70) REVERT: B 1122 ASP cc_start: 0.8344 (t0) cc_final: 0.7994 (t0) outliers start: 13 outliers final: 9 residues processed: 28 average time/residue: 0.0956 time to fit residues: 3.5250 Evaluate side-chains 27 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1099 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 58 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 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 = 0.3766 r_free = 0.3766 target = 0.077995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.057766 restraints weight = 18884.078| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 5.68 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5195 Z= 0.098 Angle : 0.493 8.277 7094 Z= 0.258 Chirality : 0.044 0.138 754 Planarity : 0.003 0.036 930 Dihedral : 3.268 10.823 706 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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 are not related in a simple way. whole: -0.78 (0.32), residues: 654 helix: 0.52 (0.47), residues: 130 sheet: 1.36 (0.62), residues: 80 loop : -1.29 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1187 TYR 0.008 0.001 TYR B1142 PHE 0.006 0.001 PHE B1217 TRP 0.002 0.000 TRP A1155 HIS 0.003 0.000 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 5166) covalent geometry : angle 0.49197 / 0.26 ( 7036) SS BOND : bond 0.00201 / 0.15 ( 29) SS BOND : angle 0.63239 / 0.40 ( 58) hydrogen bonds : bond 0.03347 / 2.36 ( 152) hydrogen bonds : angle 4.76078 / 3.33 ( 414) *********************** 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 32 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: A 1099 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7432 (m-70) REVERT: A 1106 CYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6511 (t) REVERT: A 1122 ASP cc_start: 0.8331 (t0) cc_final: 0.7989 (t0) REVERT: B 1046 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: B 1099 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7432 (m-70) REVERT: B 1122 ASP cc_start: 0.8339 (t0) cc_final: 0.7993 (t0) outliers start: 13 outliers final: 8 residues processed: 30 average time/residue: 0.0680 time to fit residues: 2.7551 Evaluate side-chains 31 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1099 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1109 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.079091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058718 restraints weight = 18927.711| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.76 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5195 Z= 0.090 Angle : 0.474 6.322 7094 Z= 0.247 Chirality : 0.044 0.127 754 Planarity : 0.003 0.037 930 Dihedral : 3.130 10.677 706 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.98 % Allowed : 19.78 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.32), residues: 654 helix: 0.53 (0.46), residues: 130 sheet: 1.21 (0.61), residues: 82 loop : -1.22 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1187 TYR 0.009 0.001 TYR A 906 PHE 0.005 0.001 PHE B1135 TRP 0.005 0.001 TRP A1155 HIS 0.002 0.000 HIS A1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 5166) covalent geometry : angle 0.47313 / 0.25 ( 7036) SS BOND : bond 0.00193 / 0.15 ( 29) SS BOND : angle 0.54876 / 0.35 ( 58) hydrogen bonds : bond 0.02930 / 2.05 ( 152) hydrogen bonds : angle 4.57079 / 3.19 ( 414) ********************** 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 34 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1046 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: A 1106 CYS cc_start: 0.7215 (m) cc_final: 0.6445 (t) REVERT: A 1122 ASP cc_start: 0.8338 (t0) cc_final: 0.8021 (t0) REVERT: B 1046 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: B 1099 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7484 (m-70) REVERT: B 1122 ASP cc_start: 0.8331 (t0) cc_final: 0.7993 (t0) outliers start: 11 outliers final: 6 residues processed: 32 average time/residue: 0.0816 time to fit residues: 3.4966 Evaluate side-chains 28 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1099 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 61 optimal weight: 8.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1109 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.077459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057050 restraints weight = 19285.602| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 5.75 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5195 Z= 0.147 Angle : 0.499 6.147 7094 Z= 0.265 Chirality : 0.044 0.140 754 Planarity : 0.003 0.034 930 Dihedral : 3.328 10.672 706 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.16 % Allowed : 19.96 % 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 are not related in a simple way. whole: -0.72 (0.33), residues: 654 helix: 0.58 (0.46), residues: 128 sheet: 1.43 (0.63), residues: 80 loop : -1.25 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1187 TYR 0.008 0.001 TYR B1142 PHE 0.007 0.001 PHE B1217 TRP 0.005 0.001 TRP B1014 HIS 0.008 0.001 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 5166) covalent geometry : angle 0.49682 / 0.26 ( 7036) SS BOND : bond 0.00196 / 0.14 ( 29) SS BOND : angle 0.71796 / 0.47 ( 58) hydrogen bonds : bond 0.03722 / 2.62 ( 152) hydrogen bonds : angle 4.84819 / 3.35 ( 414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.78 seconds wall clock time: 18 minutes 41.44 seconds (1121.44 seconds total)