Starting phenix.real_space_refine on Sun Apr 27 08:13:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1z_18829/04_2025/8r1z_18829.cif" } resolution = 3.2 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 64 5.16 5 C 3152 2.51 5 N 842 2.21 5 O 968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2513 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 21, 'TRANS': 307} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 6.72, per 1000 atoms: 1.34 Number of scatterers: 5028 At special positions: 0 Unit cell: (78.7152, 107.493, 71.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 64 16.00 O 968 8.00 N 842 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 774.0 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 22.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 934 through 936 No H-bonds generated for 'chain 'A' and resid 934 through 936' Processing helix chain 'A' and resid 1025 through 1029 Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1130 through 1148 removed outlier: 3.819A pdb=" N CYS A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1142 " --> pdb=" O ALA A1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 936 No H-bonds generated for 'chain 'B' and resid 934 through 936' Processing helix chain 'B' and resid 1025 through 1029 Processing helix chain 'B' and resid 1057 through 1064 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1096 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1103 through 1108 Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1148 removed outlier: 3.819A pdb=" N CYS B1134 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 905 removed outlier: 3.505A pdb=" N ASN A1023 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A1011 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 910 through 912 removed outlier: 3.534A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 979 through 983 removed outlier: 3.522A pdb=" N SER A 976 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 972 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 964 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 963 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A1033 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1176 through 1178 removed outlier: 3.742A pdb=" N HIS A1177 " --> pdb=" O TYR A1207 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A1207 " --> pdb=" O HIS A1177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 903 through 905 removed outlier: 3.506A pdb=" N ASN B1023 " --> pdb=" O VAL B1011 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B1011 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.534A pdb=" N TYR B 911 " --> pdb=" O TYR B 919 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.522A pdb=" N SER B 976 " --> pdb=" O LYS B 979 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 972 " --> pdb=" O ILE B 983 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 964 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS B1033 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1176 through 1178 removed outlier: 3.742A pdb=" N HIS B1177 " --> pdb=" O TYR B1207 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B1207 " --> pdb=" O HIS B1177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 150 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1664 1.35 - 1.46: 1240 1.46 - 1.58: 2190 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 5162 Sorted by residual: bond pdb=" CA CYS B1161 " pdb=" C CYS B1161 " ideal model delta sigma weight residual 1.534 1.525 0.010 9.50e-03 1.11e+04 1.02e+00 bond pdb=" CA ILE A1000 " pdb=" C ILE A1000 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.12e-02 7.97e+03 7.84e-01 bond pdb=" CA CYS A1161 " pdb=" C CYS A1161 " ideal model delta sigma weight residual 1.534 1.526 0.008 9.50e-03 1.11e+04 7.84e-01 bond pdb=" CA ILE B1000 " pdb=" C ILE B1000 " ideal model delta sigma weight residual 1.530 1.521 0.010 1.12e-02 7.97e+03 7.45e-01 bond pdb=" CA LEU B 968 " pdb=" C LEU B 968 " ideal model delta sigma weight residual 1.526 1.518 0.009 1.03e-02 9.43e+03 7.41e-01 ... (remaining 5157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 6653 0.92 - 1.83: 295 1.83 - 2.75: 48 2.75 - 3.66: 28 3.66 - 4.58: 8 Bond angle restraints: 7032 Sorted by residual: angle pdb=" N ILE B1000 " pdb=" CA ILE B1000 " pdb=" C ILE B1000 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N ILE A1000 " pdb=" CA ILE A1000 " pdb=" C ILE A1000 " ideal model delta sigma weight residual 111.91 108.71 3.20 8.90e-01 1.26e+00 1.29e+01 angle pdb=" C THR B 940 " pdb=" N GLN B 941 " pdb=" CA GLN B 941 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.18e+00 angle pdb=" C THR A 940 " pdb=" N GLN A 941 " pdb=" CA GLN A 941 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.11e+00 angle pdb=" C CYS A1161 " pdb=" CA CYS A1161 " pdb=" CB CYS A1161 " ideal model delta sigma weight residual 111.20 109.63 1.57 7.10e-01 1.98e+00 4.88e+00 ... (remaining 7027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 2737 15.36 - 30.72: 271 30.72 - 46.07: 80 46.07 - 61.43: 22 61.43 - 76.79: 12 Dihedral angle restraints: 3122 sinusoidal: 1236 harmonic: 1886 Sorted by residual: dihedral pdb=" CB CYS A 953 " pdb=" SG CYS A 953 " pdb=" SG CYS A 960 " pdb=" CB CYS A 960 " ideal model delta sinusoidal sigma weight residual 93.00 167.88 -74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B 953 " pdb=" SG CYS B 953 " pdb=" SG CYS B 960 " pdb=" CB CYS B 960 " ideal model delta sinusoidal sigma weight residual 93.00 167.88 -74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 903 " pdb=" SG CYS A 903 " pdb=" SG CYS A1036 " pdb=" CB CYS A1036 " ideal model delta sinusoidal sigma weight residual -86.00 -123.83 37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 3119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 425 0.024 - 0.048: 148 0.048 - 0.072: 91 0.072 - 0.096: 58 0.096 - 0.120: 32 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA PRO A1026 " pdb=" N PRO A1026 " pdb=" C PRO A1026 " pdb=" CB PRO A1026 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA PRO B1026 " pdb=" N PRO B1026 " pdb=" C PRO B1026 " pdb=" CB PRO B1026 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ILE A 964 " pdb=" N ILE A 964 " pdb=" C ILE A 964 " pdb=" CB ILE A 964 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 751 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B1025 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B1026 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B1026 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B1026 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1025 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A1026 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B1071 " -0.012 5.00e-02 4.00e+02 1.79e-02 5.13e-01 pdb=" N PRO B1072 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO B1072 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO B1072 " -0.010 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1641 2.81 - 3.34: 4924 3.34 - 3.86: 8710 3.86 - 4.38: 9485 4.38 - 4.90: 15706 Nonbonded interactions: 40466 Sorted by model distance: nonbonded pdb=" OD1 ASN B1038 " pdb="CA CA B1401 " model vdw 2.292 2.510 nonbonded pdb=" OD1 ASN A1038 " pdb="CA CA A1401 " model vdw 2.293 2.510 nonbonded pdb=" ND2 ASN B1191 " pdb=" O ASP B1195 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN A1191 " pdb=" O ASP A1195 " model vdw 2.296 3.120 nonbonded pdb=" OD2 ASP A1079 " pdb=" OG1 THR A1082 " model vdw 2.301 3.040 ... (remaining 40461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 1.280 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:4.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5190 Z= 0.130 Angle : 0.486 4.577 7088 Z= 0.274 Chirality : 0.042 0.120 754 Planarity : 0.003 0.032 930 Dihedral : 14.163 76.791 1834 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 16.01 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.34), residues: 654 helix: 0.69 (0.44), residues: 130 sheet: 1.39 (0.56), residues: 92 loop : -0.80 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1065 HIS 0.002 0.001 HIS B1147 PHE 0.007 0.001 PHE A 944 TYR 0.006 0.001 TYR A1207 ARG 0.001 0.000 ARG A1190 Details of bonding type rmsd hydrogen bonds : bond 0.19432 ( 150) hydrogen bonds : angle 7.16373 ( 402) SS BOND : bond 0.00256 ( 28) SS BOND : angle 0.64891 ( 56) covalent geometry : bond 0.00268 ( 5162) covalent geometry : angle 0.48450 ( 7032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 927 TYR cc_start: 0.8183 (m-80) cc_final: 0.7913 (m-80) REVERT: A 1109 HIS cc_start: 0.8992 (t-90) cc_final: 0.8766 (t-90) REVERT: A 1122 ASP cc_start: 0.8656 (t0) cc_final: 0.8214 (t0) REVERT: A 1187 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.7980 (tpt-90) REVERT: A 1199 ASP cc_start: 0.8550 (p0) cc_final: 0.8109 (p0) REVERT: B 1109 HIS cc_start: 0.8973 (t-90) cc_final: 0.8761 (t-90) REVERT: B 1122 ASP cc_start: 0.8639 (t0) cc_final: 0.8198 (t0) REVERT: B 1199 ASP cc_start: 0.8583 (p0) cc_final: 0.8212 (p0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.3643 time to fit residues: 24.5850 Evaluate side-chains 34 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.075819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.058165 restraints weight = 21682.537| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 6.66 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5190 Z= 0.125 Angle : 0.539 5.449 7088 Z= 0.282 Chirality : 0.045 0.144 754 Planarity : 0.004 0.050 930 Dihedral : 3.573 14.531 704 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.16 % Allowed : 19.06 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.34), residues: 654 helix: 0.52 (0.44), residues: 130 sheet: 1.42 (0.54), residues: 92 loop : -0.80 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1090 HIS 0.003 0.001 HIS B1107 PHE 0.018 0.002 PHE A1061 TYR 0.008 0.001 TYR B1116 ARG 0.004 0.001 ARG B1198 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 150) hydrogen bonds : angle 5.27644 ( 402) SS BOND : bond 0.00274 ( 28) SS BOND : angle 0.54140 ( 56) covalent geometry : bond 0.00279 ( 5162) covalent geometry : angle 0.53870 ( 7032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8867 (t-90) cc_final: 0.8660 (t-90) REVERT: A 1122 ASP cc_start: 0.8572 (t0) cc_final: 0.8135 (t0) REVERT: A 1187 ARG cc_start: 0.8242 (ptp-170) cc_final: 0.7959 (tpt-90) REVERT: B 1109 HIS cc_start: 0.8905 (t-90) cc_final: 0.8697 (t-90) REVERT: B 1122 ASP cc_start: 0.8631 (t0) cc_final: 0.8235 (t0) outliers start: 12 outliers final: 9 residues processed: 42 average time/residue: 0.5098 time to fit residues: 25.6528 Evaluate side-chains 45 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.075824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.058015 restraints weight = 22215.443| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 6.74 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5190 Z= 0.106 Angle : 0.515 5.588 7088 Z= 0.266 Chirality : 0.045 0.190 754 Planarity : 0.003 0.025 930 Dihedral : 3.507 13.761 704 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.98 % Allowed : 19.96 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.34), residues: 654 helix: 0.78 (0.46), residues: 126 sheet: 1.54 (0.55), residues: 92 loop : -0.92 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1014 HIS 0.003 0.001 HIS B1107 PHE 0.019 0.001 PHE A1061 TYR 0.014 0.001 TYR B 927 ARG 0.005 0.000 ARG B1187 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 150) hydrogen bonds : angle 4.91250 ( 402) SS BOND : bond 0.00244 ( 28) SS BOND : angle 0.54803 ( 56) covalent geometry : bond 0.00247 ( 5162) covalent geometry : angle 0.51465 ( 7032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8855 (t-90) cc_final: 0.8641 (t-90) REVERT: A 1122 ASP cc_start: 0.8572 (t0) cc_final: 0.8132 (t0) REVERT: A 1187 ARG cc_start: 0.8249 (ptp-170) cc_final: 0.7842 (tpp-160) REVERT: B 1109 HIS cc_start: 0.8894 (t-90) cc_final: 0.8683 (t-90) REVERT: B 1122 ASP cc_start: 0.8614 (t0) cc_final: 0.8191 (t0) REVERT: B 1198 ARG cc_start: 0.8973 (tpt170) cc_final: 0.8686 (tpm170) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.5393 time to fit residues: 28.6116 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.074785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.056829 restraints weight = 22376.888| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 6.72 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5190 Z= 0.151 Angle : 0.534 4.706 7088 Z= 0.277 Chirality : 0.045 0.171 754 Planarity : 0.003 0.029 930 Dihedral : 3.620 13.927 704 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.34 % Allowed : 20.50 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.34), residues: 654 helix: 0.55 (0.46), residues: 130 sheet: 1.37 (0.55), residues: 92 loop : -0.91 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1014 HIS 0.003 0.001 HIS B 933 PHE 0.025 0.002 PHE A1061 TYR 0.009 0.001 TYR A 911 ARG 0.006 0.000 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 150) hydrogen bonds : angle 4.77721 ( 402) SS BOND : bond 0.00271 ( 28) SS BOND : angle 0.76327 ( 56) covalent geometry : bond 0.00338 ( 5162) covalent geometry : angle 0.53209 ( 7032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8855 (t-90) cc_final: 0.8629 (t-90) REVERT: A 1122 ASP cc_start: 0.8565 (t0) cc_final: 0.8103 (t0) REVERT: B 1109 HIS cc_start: 0.8902 (t-90) cc_final: 0.8689 (t-90) REVERT: B 1122 ASP cc_start: 0.8593 (t0) cc_final: 0.8150 (t0) REVERT: B 1198 ARG cc_start: 0.8974 (tpt170) cc_final: 0.8674 (tpm170) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.5545 time to fit residues: 28.1058 Evaluate side-chains 43 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.076310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.058226 restraints weight = 21990.562| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 6.76 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5190 Z= 0.097 Angle : 0.546 7.870 7088 Z= 0.279 Chirality : 0.045 0.177 754 Planarity : 0.004 0.035 930 Dihedral : 3.519 13.477 704 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 21.58 % Favored : 76.26 % 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 (0.34), residues: 654 helix: 0.78 (0.46), residues: 126 sheet: 1.56 (0.55), residues: 92 loop : -0.93 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1065 HIS 0.001 0.000 HIS B 933 PHE 0.021 0.002 PHE A1061 TYR 0.005 0.001 TYR A1116 ARG 0.011 0.001 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 150) hydrogen bonds : angle 4.56995 ( 402) SS BOND : bond 0.00234 ( 28) SS BOND : angle 0.56135 ( 56) covalent geometry : bond 0.00228 ( 5162) covalent geometry : angle 0.54630 ( 7032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8844 (t-90) cc_final: 0.8619 (t-90) REVERT: A 1122 ASP cc_start: 0.8564 (t0) cc_final: 0.8121 (t0) REVERT: A 1198 ARG cc_start: 0.8936 (tpt170) cc_final: 0.8608 (tpm170) REVERT: B 1109 HIS cc_start: 0.8873 (t-90) cc_final: 0.8662 (t-90) REVERT: B 1122 ASP cc_start: 0.8568 (t0) cc_final: 0.8118 (t0) outliers start: 12 outliers final: 8 residues processed: 39 average time/residue: 0.3920 time to fit residues: 18.1122 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.058182 restraints weight = 21744.763| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 6.68 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5190 Z= 0.097 Angle : 0.533 7.762 7088 Z= 0.272 Chirality : 0.044 0.172 754 Planarity : 0.003 0.029 930 Dihedral : 3.435 13.370 704 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.98 % Allowed : 21.04 % Favored : 76.98 % 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: -0.26 (0.34), residues: 654 helix: 0.87 (0.45), residues: 126 sheet: 1.58 (0.55), residues: 92 loop : -0.94 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1014 HIS 0.002 0.000 HIS B 933 PHE 0.017 0.001 PHE A1061 TYR 0.015 0.001 TYR B 927 ARG 0.010 0.001 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 150) hydrogen bonds : angle 4.42816 ( 402) SS BOND : bond 0.00230 ( 28) SS BOND : angle 0.57505 ( 56) covalent geometry : bond 0.00232 ( 5162) covalent geometry : angle 0.53260 ( 7032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8855 (t-90) cc_final: 0.8626 (t-90) REVERT: A 1122 ASP cc_start: 0.8553 (t0) cc_final: 0.8109 (t0) REVERT: A 1198 ARG cc_start: 0.8899 (tpt170) cc_final: 0.8595 (tpm170) REVERT: B 1109 HIS cc_start: 0.8852 (t-90) cc_final: 0.8639 (t-90) REVERT: B 1122 ASP cc_start: 0.8552 (t0) cc_final: 0.8095 (t0) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.3101 time to fit residues: 14.8026 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 9 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.075126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.057355 restraints weight = 21773.079| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 6.63 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5190 Z= 0.122 Angle : 0.533 7.688 7088 Z= 0.273 Chirality : 0.044 0.163 754 Planarity : 0.003 0.035 930 Dihedral : 3.459 13.487 704 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.70 % Allowed : 20.32 % Favored : 76.98 % 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: -0.33 (0.34), residues: 654 helix: 0.67 (0.45), residues: 130 sheet: 1.52 (0.54), residues: 92 loop : -0.94 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1014 HIS 0.002 0.001 HIS B 933 PHE 0.014 0.001 PHE B1061 TYR 0.016 0.001 TYR B 927 ARG 0.014 0.001 ARG A1052 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 150) hydrogen bonds : angle 4.39492 ( 402) SS BOND : bond 0.00245 ( 28) SS BOND : angle 0.60314 ( 56) covalent geometry : bond 0.00281 ( 5162) covalent geometry : angle 0.53205 ( 7032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8845 (t-90) cc_final: 0.8599 (t-90) REVERT: A 1122 ASP cc_start: 0.8537 (t0) cc_final: 0.8071 (t0) REVERT: B 1109 HIS cc_start: 0.8849 (t-90) cc_final: 0.8623 (t-90) REVERT: B 1122 ASP cc_start: 0.8565 (t0) cc_final: 0.8109 (t0) outliers start: 15 outliers final: 12 residues processed: 36 average time/residue: 0.1928 time to fit residues: 9.3527 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1097 ILE Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.076083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058264 restraints weight = 21938.277| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 6.71 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5190 Z= 0.088 Angle : 0.510 5.981 7088 Z= 0.259 Chirality : 0.044 0.170 754 Planarity : 0.003 0.031 930 Dihedral : 3.371 13.325 704 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.44 % Allowed : 21.22 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.34), residues: 654 helix: 0.92 (0.45), residues: 126 sheet: 1.62 (0.55), residues: 92 loop : -1.00 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1065 HIS 0.001 0.000 HIS B 933 PHE 0.015 0.001 PHE A1061 TYR 0.017 0.001 TYR B 927 ARG 0.006 0.001 ARG A1052 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 150) hydrogen bonds : angle 4.26331 ( 402) SS BOND : bond 0.00224 ( 28) SS BOND : angle 0.51867 ( 56) covalent geometry : bond 0.00212 ( 5162) covalent geometry : angle 0.50963 ( 7032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8865 (t-90) cc_final: 0.8625 (t-90) REVERT: A 1122 ASP cc_start: 0.8545 (t0) cc_final: 0.8084 (t0) REVERT: B 1109 HIS cc_start: 0.8844 (t-90) cc_final: 0.8609 (t-90) REVERT: B 1122 ASP cc_start: 0.8538 (t0) cc_final: 0.8081 (t0) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.2712 time to fit residues: 11.2090 Evaluate side-chains 33 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.058223 restraints weight = 22114.722| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 6.71 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5190 Z= 0.100 Angle : 0.534 9.367 7088 Z= 0.271 Chirality : 0.044 0.164 754 Planarity : 0.003 0.030 930 Dihedral : 3.357 13.271 704 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.98 % Allowed : 20.50 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.34), residues: 654 helix: 1.01 (0.45), residues: 126 sheet: 1.61 (0.54), residues: 92 loop : -0.99 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1014 HIS 0.002 0.000 HIS A 933 PHE 0.013 0.001 PHE A1061 TYR 0.016 0.001 TYR B 927 ARG 0.010 0.001 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 150) hydrogen bonds : angle 4.19317 ( 402) SS BOND : bond 0.00226 ( 28) SS BOND : angle 0.54808 ( 56) covalent geometry : bond 0.00243 ( 5162) covalent geometry : angle 0.53421 ( 7032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8873 (t-90) cc_final: 0.8630 (t-90) REVERT: A 1122 ASP cc_start: 0.8535 (t0) cc_final: 0.8070 (t0) REVERT: B 1109 HIS cc_start: 0.8848 (t-90) cc_final: 0.8615 (t-90) REVERT: B 1122 ASP cc_start: 0.8539 (t0) cc_final: 0.8081 (t0) outliers start: 11 outliers final: 11 residues processed: 36 average time/residue: 0.3341 time to fit residues: 16.0975 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.076516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.058710 restraints weight = 21861.117| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 6.72 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 5190 Z= 0.094 Angle : 0.531 9.517 7088 Z= 0.269 Chirality : 0.044 0.165 754 Planarity : 0.003 0.030 930 Dihedral : 3.279 13.120 704 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.98 % Allowed : 20.50 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.34), residues: 654 helix: 1.07 (0.45), residues: 126 sheet: 1.67 (0.55), residues: 92 loop : -0.98 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1201 HIS 0.001 0.000 HIS B 933 PHE 0.014 0.001 PHE B1061 TYR 0.018 0.001 TYR B 927 ARG 0.009 0.001 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 150) hydrogen bonds : angle 4.04561 ( 402) SS BOND : bond 0.00219 ( 28) SS BOND : angle 0.51365 ( 56) covalent geometry : bond 0.00233 ( 5162) covalent geometry : angle 0.53139 ( 7032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 HIS cc_start: 0.8859 (t-90) cc_final: 0.8617 (t-90) REVERT: A 1122 ASP cc_start: 0.8511 (t0) cc_final: 0.8047 (t0) REVERT: B 1109 HIS cc_start: 0.8843 (t-90) cc_final: 0.8612 (t-90) REVERT: B 1122 ASP cc_start: 0.8521 (t0) cc_final: 0.8073 (t0) outliers start: 11 outliers final: 11 residues processed: 37 average time/residue: 0.2596 time to fit residues: 12.7851 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1165 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.0010 chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 47 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.075707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.057986 restraints weight = 22476.250| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 6.75 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5190 Z= 0.101 Angle : 0.528 9.643 7088 Z= 0.269 Chirality : 0.044 0.161 754 Planarity : 0.003 0.029 930 Dihedral : 3.307 13.164 704 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.44 % Allowed : 21.04 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.34), residues: 654 helix: 0.98 (0.46), residues: 126 sheet: 1.64 (0.54), residues: 92 loop : -0.98 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1155 HIS 0.003 0.000 HIS A1107 PHE 0.012 0.001 PHE B1061 TYR 0.016 0.001 TYR B 927 ARG 0.006 0.000 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 150) hydrogen bonds : angle 4.05803 ( 402) SS BOND : bond 0.00214 ( 28) SS BOND : angle 0.56064 ( 56) covalent geometry : bond 0.00244 ( 5162) covalent geometry : angle 0.52810 ( 7032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.31 seconds wall clock time: 56 minutes 0.15 seconds (3360.15 seconds total)