Starting phenix.real_space_refine on Thu Jul 2 01:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtb_18648/07_2026/8qtb_18648.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 66 5.16 5 C 3160 2.51 5 N 850 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5050 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2524 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} 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: 1.35, per 1000 atoms: 0.27 Number of scatterers: 5050 At special positions: 0 Unit cell: (102.34, 86.86, 76.54, 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 66 16.00 O 972 8.00 N 850 7.00 C 3160 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: 0.25 Conformation dependent library (CDL) restraints added in 119.3 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 25.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 1026 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 1097 through 1102 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 4.032A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1150 removed outlier: 3.856A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A1150 " --> pdb=" O CYS A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1169 Processing helix chain 'B' and resid 1026 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 1097 through 1102 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1103 through 1110 removed outlier: 4.034A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1150 removed outlier: 3.856A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B1150 " --> pdb=" O CYS B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 4.038A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 984 removed outlier: 5.954A pdb=" N GLU A 972 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.894A 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 1179 removed outlier: 3.784A pdb=" N GLY A1205 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 918 through 920 removed outlier: 4.039A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 984 removed outlier: 5.954A pdb=" N GLU B 972 " --> pdb=" O ILE B 983 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 944 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 931 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.894A 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 1179 removed outlier: 3.784A pdb=" N GLY B1205 " --> pdb=" O GLN B1179 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 504 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: 0.50 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1678 1.34 - 1.46: 1200 1.46 - 1.58: 2232 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 5180 Sorted by residual: bond pdb=" N THR B 940 " pdb=" CA THR B 940 " ideal model delta sigma weight residual 1.460 1.471 -0.012 1.54e-02 4.22e+03 5.82e-01 bond pdb=" N THR A 940 " pdb=" CA THR A 940 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.54e-02 4.22e+03 5.54e-01 bond pdb=" CA THR B 940 " pdb=" CB THR B 940 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.70e-02 3.46e+03 4.78e-01 bond pdb=" CA THR A 940 " pdb=" CB THR A 940 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.70e-02 3.46e+03 4.09e-01 bond pdb=" C ALA B1138 " pdb=" O ALA B1138 " ideal model delta sigma weight residual 1.236 1.243 -0.006 1.15e-02 7.56e+03 2.94e-01 ... (remaining 5175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 6777 0.79 - 1.59: 209 1.59 - 2.38: 29 2.38 - 3.17: 29 3.17 - 3.96: 8 Bond angle restraints: 7052 Sorted by residual: 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 122.46 125.27 -2.81 1.41e+00 5.03e-01 3.96e+00 angle pdb=" C LYS A1016 " pdb=" N LYS A1017 " pdb=" CA LYS A1017 " ideal model delta sigma weight residual 122.56 120.51 2.05 1.50e+00 4.44e-01 1.86e+00 angle pdb=" CA THR A 940 " pdb=" CB THR A 940 " pdb=" CG2 THR A 940 " ideal model delta sigma weight residual 110.50 112.81 -2.31 1.70e+00 3.46e-01 1.84e+00 angle pdb=" CA THR B 940 " pdb=" CB THR B 940 " pdb=" CG2 THR B 940 " ideal model delta sigma weight residual 110.50 112.78 -2.28 1.70e+00 3.46e-01 1.80e+00 ... (remaining 7047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2898 17.41 - 34.83: 209 34.83 - 52.24: 34 52.24 - 69.66: 6 69.66 - 87.07: 2 Dihedral angle restraints: 3149 sinusoidal: 1251 harmonic: 1898 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 -179.93 -87.07 1 1.00e+01 1.00e-02 9.11e+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 -179.93 -87.07 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A1185 " pdb=" SG CYS A1185 " pdb=" SG CYS A1196 " pdb=" CB CYS A1196 " ideal model delta sinusoidal sigma weight residual 93.00 39.71 53.29 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 3146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 432 0.024 - 0.047: 187 0.047 - 0.071: 58 0.071 - 0.095: 33 0.095 - 0.118: 50 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA VAL B 905 " pdb=" N VAL B 905 " pdb=" C VAL B 905 " pdb=" CB VAL B 905 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL A 905 " pdb=" N VAL A 905 " pdb=" C VAL A 905 " pdb=" CB VAL A 905 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-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 3.38e-01 ... (remaining 757 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1018 " -0.005 2.00e-02 2.50e+03 9.70e-03 9.41e-01 pdb=" C THR A1018 " 0.017 2.00e-02 2.50e+03 pdb=" O THR A1018 " -0.006 2.00e-02 2.50e+03 pdb=" N SER A1019 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B1025 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.21e-01 pdb=" N PRO B1026 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO B1026 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B1026 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1025 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.02e-01 pdb=" N PRO A1026 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " 0.013 5.00e-02 4.00e+02 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1805 2.85 - 3.36: 4388 3.36 - 3.88: 8161 3.88 - 4.39: 8984 4.39 - 4.90: 15436 Nonbonded interactions: 38774 Sorted by model distance: nonbonded pdb=" OD2 ASP A1079 " pdb=" OG1 THR A1082 " model vdw 2.338 3.040 nonbonded pdb=" OD2 ASP B1079 " pdb=" OG1 THR B1082 " model vdw 2.338 3.040 nonbonded pdb=" OD1 ASP B1040 " pdb="CA CA B1501 " model vdw 2.350 3.250 nonbonded pdb=" OD1 ASP A1040 " pdb="CA CA A1501 " model vdw 2.350 3.250 nonbonded pdb=" OD1 ASP A1046 " pdb="CA CA A1501 " model vdw 2.353 3.250 ... (remaining 38769 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: 1.660 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 0.016 5209 Z= 0.077 Angle : 0.390 3.963 7110 Z= 0.204 Chirality : 0.041 0.118 760 Planarity : 0.003 0.024 934 Dihedral : 11.054 55.271 1850 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.32), residues: 658 helix: 2.40 (0.43), residues: 114 sheet: 2.78 (0.48), residues: 104 loop : -0.71 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1198 TYR 0.004 0.000 TYR A1142 PHE 0.005 0.001 PHE A 944 TRP 0.003 0.000 TRP A1155 HIS 0.001 0.000 HIS A1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00156 / 0.08 ( 5180) covalent geometry : angle 0.38973 / 0.20 ( 7052) SS BOND : bond 0.00178 / 0.13 ( 29) SS BOND : angle 0.47465 / 0.33 ( 58) hydrogen bonds : bond 0.21085 / 14.44 ( 188) hydrogen bonds : angle 7.03719 / 4.93 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 LYS cc_start: 0.9250 (ptpt) cc_final: 0.8908 (mtmm) REVERT: A 998 MET cc_start: 0.9340 (mtp) cc_final: 0.9005 (mtt) REVERT: A 1222 MET cc_start: 0.9257 (mmm) cc_final: 0.8975 (mmp) REVERT: B 979 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8883 (mtmm) REVERT: B 998 MET cc_start: 0.9341 (mtp) cc_final: 0.9016 (mtt) REVERT: B 1186 LEU cc_start: 0.8520 (tp) cc_final: 0.8259 (pt) REVERT: B 1222 MET cc_start: 0.9272 (mmm) cc_final: 0.8994 (mmp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.5795 time to fit residues: 29.3534 Evaluate side-chains 23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.067572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.046893 restraints weight = 15398.302| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 4.79 r_work: 0.2514 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5209 Z= 0.276 Angle : 0.629 6.094 7110 Z= 0.340 Chirality : 0.046 0.146 760 Planarity : 0.004 0.021 934 Dihedral : 3.837 11.795 710 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.07 % Allowed : 13.75 % Favored : 85.18 % 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 (0.32), residues: 658 helix: 2.17 (0.44), residues: 116 sheet: 2.57 (0.47), residues: 122 loop : -0.82 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1031 TYR 0.012 0.001 TYR A 911 PHE 0.009 0.001 PHE A1135 TRP 0.009 0.001 TRP B1155 HIS 0.003 0.001 HIS A1109 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.28 ( 5180) covalent geometry : angle 0.62489 / 0.34 ( 7052) SS BOND : bond 0.00414 / 0.28 ( 29) SS BOND : angle 0.97916 / 0.67 ( 58) hydrogen bonds : bond 0.06027 / 4.18 ( 188) hydrogen bonds : angle 4.98924 / 3.49 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9344 (mmm) cc_final: 0.8978 (mmp) REVERT: B 1222 MET cc_start: 0.9351 (mmm) cc_final: 0.8984 (mmp) outliers start: 6 outliers final: 2 residues processed: 22 average time/residue: 0.8226 time to fit residues: 18.7902 Evaluate side-chains 14 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 1012 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.069285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.048473 restraints weight = 15078.450| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 4.79 r_work: 0.2553 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5209 Z= 0.141 Angle : 0.539 7.526 7110 Z= 0.284 Chirality : 0.044 0.147 760 Planarity : 0.003 0.022 934 Dihedral : 3.647 12.416 710 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.50 % Allowed : 13.04 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.32), residues: 658 helix: 2.08 (0.43), residues: 116 sheet: 2.43 (0.47), residues: 122 loop : -0.87 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1031 TYR 0.007 0.001 TYR B 911 PHE 0.007 0.001 PHE A1135 TRP 0.002 0.001 TRP B1014 HIS 0.001 0.000 HIS B1109 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 5180) covalent geometry : angle 0.53705 / 0.28 ( 7052) SS BOND : bond 0.00288 / 0.21 ( 29) SS BOND : angle 0.72928 / 0.50 ( 58) hydrogen bonds : bond 0.04621 / 3.22 ( 188) hydrogen bonds : angle 4.49340 / 3.12 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9408 (mmm) cc_final: 0.9040 (mmp) REVERT: B 1222 MET cc_start: 0.9401 (mmm) cc_final: 0.9037 (mmp) outliers start: 14 outliers final: 3 residues processed: 31 average time/residue: 0.4597 time to fit residues: 14.9981 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.045416 restraints weight = 15387.003| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 4.80 r_work: 0.2483 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5209 Z= 0.286 Angle : 0.609 7.334 7110 Z= 0.325 Chirality : 0.046 0.162 760 Planarity : 0.004 0.024 934 Dihedral : 4.049 12.998 710 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.86 % Allowed : 13.21 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.32), residues: 658 helix: 2.08 (0.45), residues: 118 sheet: 2.23 (0.48), residues: 122 loop : -0.99 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1198 TYR 0.009 0.001 TYR B 911 PHE 0.009 0.001 PHE A1135 TRP 0.008 0.001 TRP A1155 HIS 0.004 0.001 HIS A1109 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 ( 5180) covalent geometry : angle 0.60568 / 0.32 ( 7052) SS BOND : bond 0.00435 / 0.29 ( 29) SS BOND : angle 0.94523 / 0.66 ( 58) hydrogen bonds : bond 0.06044 / 4.23 ( 188) hydrogen bonds : angle 4.69522 / 3.26 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 15 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1187 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7056 (mtp-110) REVERT: A 1222 MET cc_start: 0.9390 (mmm) cc_final: 0.9015 (mmp) REVERT: B 1222 MET cc_start: 0.9385 (mmm) cc_final: 0.9006 (mmp) outliers start: 16 outliers final: 5 residues processed: 31 average time/residue: 0.5441 time to fit residues: 17.7105 Evaluate side-chains 20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.0570 chunk 64 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3262 r_free = 0.3262 target = 0.069625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.048838 restraints weight = 15282.556| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 4.79 r_work: 0.2567 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5209 Z= 0.111 Angle : 0.539 8.945 7110 Z= 0.278 Chirality : 0.044 0.154 760 Planarity : 0.003 0.024 934 Dihedral : 3.665 13.561 710 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.96 % Allowed : 13.21 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.31), residues: 658 helix: 1.95 (0.43), residues: 116 sheet: 2.11 (0.46), residues: 122 loop : -0.96 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1031 TYR 0.005 0.001 TYR B1142 PHE 0.007 0.001 PHE B1135 TRP 0.003 0.000 TRP B1155 HIS 0.003 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5180) covalent geometry : angle 0.53808 / 0.28 ( 7052) SS BOND : bond 0.00237 / 0.18 ( 29) SS BOND : angle 0.68137 / 0.47 ( 58) hydrogen bonds : bond 0.03856 / 2.70 ( 188) hydrogen bonds : angle 4.18212 / 2.89 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1186 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8556 (pt) REVERT: A 1187 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6986 (mtp-110) REVERT: A 1222 MET cc_start: 0.9419 (mmm) cc_final: 0.9040 (mmp) REVERT: B 926 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8502 (mm-30) REVERT: B 1222 MET cc_start: 0.9404 (mmm) cc_final: 0.9025 (mmp) outliers start: 11 outliers final: 3 residues processed: 27 average time/residue: 0.6104 time to fit residues: 17.1943 Evaluate side-chains 22 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3219 r_free = 0.3219 target = 0.067765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.047052 restraints weight = 15163.859| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 4.82 r_work: 0.2522 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5209 Z= 0.175 Angle : 0.553 8.263 7110 Z= 0.289 Chirality : 0.044 0.156 760 Planarity : 0.003 0.024 934 Dihedral : 3.745 13.228 710 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.14 % Allowed : 13.39 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.32), residues: 658 helix: 1.96 (0.44), residues: 116 sheet: 2.05 (0.46), residues: 122 loop : -1.02 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1198 TYR 0.008 0.001 TYR B1142 PHE 0.007 0.001 PHE B1135 TRP 0.003 0.001 TRP B1014 HIS 0.002 0.001 HIS A1109 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 5180) covalent geometry : angle 0.55057 / 0.29 ( 7052) SS BOND : bond 0.00314 / 0.22 ( 29) SS BOND : angle 0.76094 / 0.53 ( 58) hydrogen bonds : bond 0.04852 / 3.39 ( 188) hydrogen bonds : angle 4.28314 / 2.96 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1187 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.7008 (mtp-110) REVERT: A 1222 MET cc_start: 0.9399 (mmm) cc_final: 0.9030 (mmp) REVERT: B 1222 MET cc_start: 0.9388 (mmm) cc_final: 0.9016 (mmp) outliers start: 12 outliers final: 3 residues processed: 26 average time/residue: 0.6219 time to fit residues: 16.8424 Evaluate side-chains 20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3269 r_free = 0.3269 target = 0.070201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.049371 restraints weight = 15162.081| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.80 r_work: 0.2578 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5209 Z= 0.109 Angle : 0.553 10.189 7110 Z= 0.282 Chirality : 0.044 0.168 760 Planarity : 0.003 0.025 934 Dihedral : 3.558 13.047 710 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.61 % Allowed : 14.46 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.31), residues: 658 helix: 1.93 (0.43), residues: 116 sheet: 1.90 (0.45), residues: 122 loop : -0.99 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1193 TYR 0.005 0.001 TYR B1142 PHE 0.006 0.001 PHE B1135 TRP 0.004 0.000 TRP B1155 HIS 0.002 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5180) covalent geometry : angle 0.55231 / 0.28 ( 7052) SS BOND : bond 0.00252 / 0.20 ( 29) SS BOND : angle 0.68189 / 0.47 ( 58) hydrogen bonds : bond 0.03693 / 2.60 ( 188) hydrogen bonds : angle 3.96997 / 2.74 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9419 (mmm) cc_final: 0.9060 (mmp) REVERT: B 1222 MET cc_start: 0.9418 (mmm) cc_final: 0.9056 (mmp) outliers start: 9 outliers final: 5 residues processed: 24 average time/residue: 0.8928 time to fit residues: 22.1246 Evaluate side-chains 19 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1050 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1050 ARG Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3242 r_free = 0.3242 target = 0.068935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.048020 restraints weight = 15156.438| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.81 r_work: 0.2547 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5209 Z= 0.135 Angle : 0.581 9.724 7110 Z= 0.296 Chirality : 0.044 0.155 760 Planarity : 0.003 0.024 934 Dihedral : 3.594 13.956 710 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.61 % Allowed : 15.71 % Favored : 82.68 % 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: 0.22 (0.31), residues: 658 helix: 1.87 (0.43), residues: 116 sheet: 1.91 (0.45), residues: 122 loop : -0.98 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.007 0.001 TYR B1142 PHE 0.006 0.001 PHE B1135 TRP 0.003 0.000 TRP A1014 HIS 0.002 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 5180) covalent geometry : angle 0.57992 / 0.30 ( 7052) SS BOND : bond 0.00279 / 0.21 ( 29) SS BOND : angle 0.73907 / 0.51 ( 58) hydrogen bonds : bond 0.04248 / 2.98 ( 188) hydrogen bonds : angle 3.99796 / 2.75 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9368 (mmm) cc_final: 0.8994 (mmp) REVERT: B 1222 MET cc_start: 0.9353 (mmm) cc_final: 0.8978 (mmp) outliers start: 9 outliers final: 5 residues processed: 23 average time/residue: 0.7449 time to fit residues: 17.8422 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1050 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1050 ARG Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.070328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.049366 restraints weight = 15138.823| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.83 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5209 Z= 0.112 Angle : 0.580 10.829 7110 Z= 0.292 Chirality : 0.044 0.166 760 Planarity : 0.003 0.024 934 Dihedral : 3.512 13.720 710 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.25 % Allowed : 15.71 % Favored : 83.04 % 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: 0.21 (0.31), residues: 658 helix: 1.83 (0.43), residues: 116 sheet: 1.79 (0.45), residues: 126 loop : -0.96 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1193 TYR 0.005 0.001 TYR A1142 PHE 0.005 0.001 PHE B1135 TRP 0.004 0.000 TRP B1155 HIS 0.002 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5180) covalent geometry : angle 0.57838 / 0.29 ( 7052) SS BOND : bond 0.00262 / 0.20 ( 29) SS BOND : angle 0.70367 / 0.48 ( 58) hydrogen bonds : bond 0.03625 / 2.55 ( 188) hydrogen bonds : angle 3.84595 / 2.64 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9321 (mmm) cc_final: 0.9016 (mmp) REVERT: B 1045 ASN cc_start: 0.9513 (OUTLIER) cc_final: 0.9294 (p0) REVERT: B 1222 MET cc_start: 0.9339 (mmm) cc_final: 0.9029 (mmp) outliers start: 7 outliers final: 4 residues processed: 20 average time/residue: 0.8797 time to fit residues: 18.3068 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1050 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1045 ASN Chi-restraints excluded: chain B residue 1050 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 50 optimal weight: 6.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3229 r_free = 0.3229 target = 0.068333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.047368 restraints weight = 15167.458| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.80 r_work: 0.2530 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5209 Z= 0.158 Angle : 0.594 10.770 7110 Z= 0.305 Chirality : 0.044 0.171 760 Planarity : 0.003 0.025 934 Dihedral : 3.669 13.708 710 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.89 % Allowed : 16.07 % Favored : 83.04 % 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: 0.23 (0.32), residues: 658 helix: 1.88 (0.44), residues: 116 sheet: 1.95 (0.45), residues: 122 loop : -0.98 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1193 TYR 0.008 0.001 TYR B1142 PHE 0.007 0.001 PHE B1135 TRP 0.004 0.001 TRP B1155 HIS 0.002 0.001 HIS A1109 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 5180) covalent geometry : angle 0.59269 / 0.30 ( 7052) SS BOND : bond 0.00308 / 0.23 ( 29) SS BOND : angle 0.76941 / 0.54 ( 58) hydrogen bonds : bond 0.04549 / 3.19 ( 188) hydrogen bonds : angle 4.09352 / 2.83 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9343 (mmm) cc_final: 0.8965 (mmp) REVERT: B 1045 ASN cc_start: 0.9478 (OUTLIER) cc_final: 0.9256 (p0) REVERT: B 1148 GLU cc_start: 0.9391 (tm-30) cc_final: 0.9127 (pp20) REVERT: B 1222 MET cc_start: 0.9344 (mmm) cc_final: 0.8962 (mmp) outliers start: 5 outliers final: 4 residues processed: 20 average time/residue: 0.9463 time to fit residues: 19.6264 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1050 ARG Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1045 ASN Chi-restraints excluded: chain B residue 1050 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1107 HIS ** 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 = 0.3275 r_free = 0.3275 target = 0.070688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049769 restraints weight = 15180.183| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.84 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5209 Z= 0.110 Angle : 0.586 10.982 7110 Z= 0.296 Chirality : 0.044 0.167 760 Planarity : 0.003 0.024 934 Dihedral : 3.494 12.863 710 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.71 % Allowed : 16.43 % Favored : 82.86 % 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: 0.24 (0.31), residues: 658 helix: 1.97 (0.43), residues: 116 sheet: 1.95 (0.45), residues: 122 loop : -0.99 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1193 TYR 0.004 0.000 TYR B1142 PHE 0.004 0.001 PHE B1135 TRP 0.005 0.001 TRP A1155 HIS 0.002 0.000 HIS B1107 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5180) covalent geometry : angle 0.58510 / 0.30 ( 7052) SS BOND : bond 0.00239 / 0.18 ( 29) SS BOND : angle 0.66018 / 0.43 ( 58) hydrogen bonds : bond 0.03368 / 2.36 ( 188) hydrogen bonds : angle 3.87181 / 2.67 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.65 seconds wall clock time: 23 minutes 25.25 seconds (1405.25 seconds total)