Starting phenix.real_space_refine on Sun Apr 27 08:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_18648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_18648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_18648.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_18648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtb_18648/04_2025/8qtb_18648.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.62, per 1000 atoms: 0.91 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: 1.41 Conformation dependent library (CDL) restraints added in 590.8 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: 0.60 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: 1.80 Time building geometry restraints manager: 1.39 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 2.510 nonbonded pdb=" OD1 ASP A1040 " pdb="CA CA A1501 " model vdw 2.350 2.510 nonbonded pdb=" OD1 ASP A1046 " pdb="CA CA A1501 " model vdw 2.353 2.510 ... (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: 0.03 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: 11.770 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:47.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.000 TRP A1155 HIS 0.001 0.000 HIS A1147 PHE 0.005 0.001 PHE A 944 TYR 0.004 0.000 TYR A1142 ARG 0.001 0.000 ARG B1198 Details of bonding type rmsd hydrogen bonds : bond 0.21085 ( 188) hydrogen bonds : angle 7.03719 ( 504) SS BOND : bond 0.00178 ( 29) SS BOND : angle 0.47465 ( 58) covalent geometry : bond 0.00156 ( 5180) covalent geometry : angle 0.38973 ( 7052) *********************** 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 : 0.591 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: 1.6917 time to fit residues: 85.9667 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.0070 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049554 restraints weight = 14909.387| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.78 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5209 Z= 0.166 Angle : 0.565 6.449 7110 Z= 0.301 Chirality : 0.044 0.141 760 Planarity : 0.003 0.022 934 Dihedral : 3.389 11.338 710 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.43 % Allowed : 12.86 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 658 helix: 2.33 (0.43), residues: 116 sheet: 2.67 (0.48), residues: 122 loop : -0.79 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1155 HIS 0.002 0.001 HIS A1109 PHE 0.006 0.001 PHE A1135 TYR 0.009 0.001 TYR A 911 ARG 0.002 0.000 ARG B1031 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 188) hydrogen bonds : angle 4.83315 ( 504) SS BOND : bond 0.00296 ( 29) SS BOND : angle 0.80991 ( 58) covalent geometry : bond 0.00371 ( 5180) covalent geometry : angle 0.56246 ( 7052) *********************** 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 31 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9317 (mmm) cc_final: 0.9025 (mmp) REVERT: B 1186 LEU cc_start: 0.8586 (tp) cc_final: 0.8300 (pt) REVERT: B 1222 MET cc_start: 0.9330 (mmm) cc_final: 0.9031 (mmp) outliers start: 8 outliers final: 2 residues processed: 29 average time/residue: 1.9613 time to fit residues: 59.3620 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 28 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049657 restraints weight = 14851.177| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.75 r_work: 0.2593 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5209 Z= 0.125 Angle : 0.529 7.375 7110 Z= 0.276 Chirality : 0.044 0.153 760 Planarity : 0.003 0.023 934 Dihedral : 3.384 11.749 710 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.21 % Allowed : 11.79 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 658 helix: 2.23 (0.43), residues: 116 sheet: 2.46 (0.47), residues: 122 loop : -0.87 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B1014 HIS 0.001 0.000 HIS A1147 PHE 0.006 0.001 PHE A1135 TYR 0.025 0.001 TYR A 993 ARG 0.002 0.000 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 188) hydrogen bonds : angle 4.39850 ( 504) SS BOND : bond 0.00261 ( 29) SS BOND : angle 0.68455 ( 58) covalent geometry : bond 0.00282 ( 5180) covalent geometry : angle 0.52727 ( 7052) *********************** 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 36 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9385 (mmm) cc_final: 0.9001 (mmp) REVERT: B 1222 MET cc_start: 0.9367 (mmm) cc_final: 0.9010 (mmp) outliers start: 18 outliers final: 6 residues processed: 34 average time/residue: 1.3737 time to fit residues: 49.4388 Evaluate side-chains 22 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain B residue 995 ILE 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 60 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.0030 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.9972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049782 restraints weight = 15191.172| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.76 r_work: 0.2591 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5209 Z= 0.119 Angle : 0.530 7.202 7110 Z= 0.273 Chirality : 0.043 0.152 760 Planarity : 0.003 0.024 934 Dihedral : 3.388 12.025 710 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.14 % Allowed : 13.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.32), residues: 658 helix: 2.25 (0.43), residues: 116 sheet: 2.38 (0.46), residues: 122 loop : -0.88 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B1014 HIS 0.001 0.000 HIS A1109 PHE 0.005 0.001 PHE A1135 TYR 0.017 0.001 TYR B 993 ARG 0.002 0.000 ARG B1031 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 188) hydrogen bonds : angle 4.20663 ( 504) SS BOND : bond 0.00249 ( 29) SS BOND : angle 0.67709 ( 58) covalent geometry : bond 0.00267 ( 5180) covalent geometry : angle 0.52862 ( 7052) *********************** 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 29 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1186 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8233 (mm) REVERT: A 1187 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6866 (mtp-110) REVERT: A 1222 MET cc_start: 0.9384 (mmm) cc_final: 0.9011 (mmp) REVERT: B 1222 MET cc_start: 0.9372 (mmm) cc_final: 0.9006 (mmp) outliers start: 12 outliers final: 4 residues processed: 27 average time/residue: 2.1763 time to fit residues: 62.0479 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 : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.049277 restraints weight = 14977.191| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.76 r_work: 0.2580 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5209 Z= 0.125 Angle : 0.522 7.167 7110 Z= 0.271 Chirality : 0.044 0.154 760 Planarity : 0.003 0.023 934 Dihedral : 3.432 11.780 710 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.32), residues: 658 helix: 2.19 (0.43), residues: 116 sheet: 2.21 (0.46), residues: 122 loop : -0.90 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A1014 HIS 0.001 0.000 HIS A1109 PHE 0.006 0.001 PHE A1135 TYR 0.015 0.001 TYR B 993 ARG 0.001 0.000 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 188) hydrogen bonds : angle 4.11133 ( 504) SS BOND : bond 0.00260 ( 29) SS BOND : angle 0.66937 ( 58) covalent geometry : bond 0.00281 ( 5180) covalent geometry : angle 0.52043 ( 7052) *********************** 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: 12 poor density : 15 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9393 (mmm) cc_final: 0.9019 (mmp) REVERT: B 1222 MET cc_start: 0.9374 (mmm) cc_final: 0.9004 (mmp) outliers start: 12 outliers final: 6 residues processed: 25 average time/residue: 2.8369 time to fit residues: 74.3900 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 : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1151 LEU 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: 5.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.048675 restraints weight = 15133.900| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 4.74 r_work: 0.2565 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5209 Z= 0.133 Angle : 0.546 8.504 7110 Z= 0.279 Chirality : 0.044 0.154 760 Planarity : 0.004 0.056 934 Dihedral : 3.522 11.524 710 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.14 % Allowed : 13.75 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 658 helix: 2.09 (0.43), residues: 116 sheet: 2.07 (0.46), residues: 122 loop : -0.90 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1014 HIS 0.002 0.000 HIS A1109 PHE 0.006 0.001 PHE A1135 TYR 0.013 0.001 TYR A 993 ARG 0.008 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 188) hydrogen bonds : angle 4.08696 ( 504) SS BOND : bond 0.00269 ( 29) SS BOND : angle 0.69610 ( 58) covalent geometry : bond 0.00300 ( 5180) covalent geometry : angle 0.54494 ( 7052) *********************** 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 : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9376 (mmm) cc_final: 0.8998 (mmp) REVERT: B 1222 MET cc_start: 0.9356 (mmm) cc_final: 0.8987 (mmp) outliers start: 12 outliers final: 6 residues processed: 25 average time/residue: 1.4535 time to fit residues: 38.2251 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1107 HIS B1107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.048016 restraints weight = 15157.955| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 4.79 r_work: 0.2541 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5209 Z= 0.159 Angle : 0.564 9.194 7110 Z= 0.289 Chirality : 0.044 0.155 760 Planarity : 0.004 0.039 934 Dihedral : 3.610 11.002 710 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.32 % Allowed : 14.46 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 658 helix: 2.04 (0.44), residues: 116 sheet: 2.03 (0.46), residues: 122 loop : -0.93 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1155 HIS 0.002 0.000 HIS A1109 PHE 0.007 0.001 PHE B1135 TYR 0.011 0.001 TYR A 993 ARG 0.006 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 188) hydrogen bonds : angle 4.16898 ( 504) SS BOND : bond 0.00293 ( 29) SS BOND : angle 0.72909 ( 58) covalent geometry : bond 0.00356 ( 5180) covalent geometry : angle 0.56264 ( 7052) *********************** 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 27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9372 (mmm) cc_final: 0.9001 (mmp) REVERT: B 1222 MET cc_start: 0.9375 (mmm) cc_final: 0.8994 (mmp) outliers start: 13 outliers final: 6 residues processed: 27 average time/residue: 2.1466 time to fit residues: 60.4907 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER 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 65 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3244 r_free = 0.3244 target = 0.068787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.048077 restraints weight = 15235.855| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.78 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: 0.8727 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5209 Z= 0.146 Angle : 0.587 9.813 7110 Z= 0.297 Chirality : 0.044 0.154 760 Planarity : 0.003 0.030 934 Dihedral : 3.634 13.028 710 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.61 % Allowed : 15.18 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 658 helix: 1.94 (0.43), residues: 116 sheet: 1.97 (0.46), residues: 122 loop : -0.95 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1155 HIS 0.002 0.001 HIS A1107 PHE 0.006 0.001 PHE B1135 TYR 0.011 0.001 TYR B 993 ARG 0.006 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 188) hydrogen bonds : angle 4.06780 ( 504) SS BOND : bond 0.00281 ( 29) SS BOND : angle 0.71375 ( 58) covalent geometry : bond 0.00329 ( 5180) covalent geometry : angle 0.58563 ( 7052) *********************** 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 : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9386 (mmm) cc_final: 0.9011 (mmp) REVERT: B 1222 MET cc_start: 0.9373 (mmm) cc_final: 0.8995 (mmp) outliers start: 9 outliers final: 6 residues processed: 23 average time/residue: 2.3708 time to fit residues: 56.8965 Evaluate side-chains 21 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER 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 18 optimal weight: 0.0980 chunk 21 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 54 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3305 r_free = 0.3305 target = 0.071811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.051143 restraints weight = 14855.686| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.75 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5209 Z= 0.104 Angle : 0.600 11.492 7110 Z= 0.292 Chirality : 0.044 0.164 760 Planarity : 0.003 0.027 934 Dihedral : 3.378 12.334 710 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.25 % Allowed : 15.54 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.32), residues: 658 helix: 1.91 (0.43), residues: 116 sheet: 1.96 (0.45), residues: 122 loop : -0.92 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1155 HIS 0.003 0.000 HIS A1107 PHE 0.004 0.001 PHE B 944 TYR 0.010 0.001 TYR B 993 ARG 0.006 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 188) hydrogen bonds : angle 3.74732 ( 504) SS BOND : bond 0.00233 ( 29) SS BOND : angle 0.61260 ( 58) covalent geometry : bond 0.00239 ( 5180) covalent geometry : angle 0.59949 ( 7052) *********************** 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 23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9340 (mmm) cc_final: 0.9031 (mmp) REVERT: B 1028 PHE cc_start: 0.8992 (m-80) cc_final: 0.8181 (m-80) REVERT: B 1222 MET cc_start: 0.9355 (mmm) cc_final: 0.9040 (mmp) outliers start: 7 outliers final: 4 residues processed: 23 average time/residue: 1.6728 time to fit residues: 40.2093 Evaluate side-chains 17 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3286 r_free = 0.3286 target = 0.071221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.050411 restraints weight = 15144.850| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.85 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5209 Z= 0.115 Angle : 0.622 11.122 7110 Z= 0.305 Chirality : 0.045 0.168 760 Planarity : 0.004 0.036 934 Dihedral : 3.406 12.025 710 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.71 % Allowed : 16.07 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.32), residues: 658 helix: 1.99 (0.43), residues: 116 sheet: 1.91 (0.45), residues: 126 loop : -0.87 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B1155 HIS 0.002 0.000 HIS B1107 PHE 0.004 0.001 PHE A1135 TYR 0.010 0.001 TYR A 993 ARG 0.006 0.001 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 188) hydrogen bonds : angle 3.74444 ( 504) SS BOND : bond 0.00246 ( 29) SS BOND : angle 0.64771 ( 58) covalent geometry : bond 0.00264 ( 5180) covalent geometry : angle 0.62144 ( 7052) ********************** 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 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1222 MET cc_start: 0.9322 (mmm) cc_final: 0.9016 (mmp) REVERT: B 1028 PHE cc_start: 0.9024 (m-80) cc_final: 0.8269 (m-80) REVERT: B 1222 MET cc_start: 0.9356 (mmm) cc_final: 0.9042 (mmp) outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 1.3602 time to fit residues: 25.9830 Evaluate side-chains 18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.068874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.048003 restraints weight = 15264.109| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 4.80 r_work: 0.2542 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2882 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= 0.156 Angle : 0.632 11.118 7110 Z= 0.317 Chirality : 0.045 0.179 760 Planarity : 0.003 0.026 934 Dihedral : 3.647 13.007 710 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.71 % Allowed : 16.07 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 658 helix: 2.05 (0.44), residues: 116 sheet: 2.89 (0.47), residues: 92 loop : -0.83 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1155 HIS 0.002 0.001 HIS A1109 PHE 0.006 0.001 PHE A1135 TYR 0.010 0.001 TYR B 993 ARG 0.006 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 188) hydrogen bonds : angle 4.07027 ( 504) SS BOND : bond 0.00282 ( 29) SS BOND : angle 0.71498 ( 58) covalent geometry : bond 0.00353 ( 5180) covalent geometry : angle 0.63139 ( 7052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.28 seconds wall clock time: 65 minutes 22.32 seconds (3922.32 seconds total)