Starting phenix.real_space_refine on Thu Oct 22 21:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wwv_66322/10_2026/9wwv_66322.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 P 4 5.49 5 S 26 5.16 5 C 3605 2.51 5 N 965 2.21 5 O 1109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5709 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2804 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2817 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.23 Number of scatterers: 5709 At special positions: 0 Unit cell: (58.24, 85.696, 107.328, 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) S 26 16.00 P 4 15.00 O 1109 8.00 N 965 7.00 C 3605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 326.9 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 36.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'E' and resid 1019 through 1031 removed outlier: 3.537A pdb=" N GLU E1024 " --> pdb=" O PRO E1020 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E1025 " --> pdb=" O LYS E1021 " (cutoff:3.500A) Processing helix chain 'E' and resid 1040 through 1044 removed outlier: 3.582A pdb=" N SER E1044 " --> pdb=" O GLN E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1053 Processing helix chain 'E' and resid 1060 through 1065 Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.884A pdb=" N ALA E1081 " --> pdb=" O ASP E1077 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E1083 " --> pdb=" O GLU E1079 " (cutoff:3.500A) Processing helix chain 'E' and resid 1098 through 1108 removed outlier: 4.142A pdb=" N MET E1102 " --> pdb=" O ASN E1098 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E1103 " --> pdb=" O PRO E1099 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E1104 " --> pdb=" O GLU E1100 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E1105 " --> pdb=" O LEU E1101 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG E1108 " --> pdb=" O LYS E1104 " (cutoff:3.500A) Processing helix chain 'E' and resid 1122 through 1126 removed outlier: 4.078A pdb=" N SER E1126 " --> pdb=" O ARG E1123 " (cutoff:3.500A) Processing helix chain 'E' and resid 1128 through 1144 Processing helix chain 'E' and resid 1176 through 1187 Processing helix chain 'E' and resid 1202 through 1206 Processing helix chain 'E' and resid 1225 through 1231 Processing helix chain 'E' and resid 1231 through 1242 removed outlier: 4.162A pdb=" N GLU E1240 " --> pdb=" O LYS E1236 " (cutoff:3.500A) Processing helix chain 'E' and resid 1244 through 1249 removed outlier: 3.662A pdb=" N GLU E1248 " --> pdb=" O ALA E1244 " (cutoff:3.500A) Processing helix chain 'E' and resid 1270 through 1274 Processing helix chain 'E' and resid 1315 through 1318 Processing helix chain 'E' and resid 1319 through 1324 removed outlier: 3.732A pdb=" N SER E1324 " --> pdb=" O PRO E1320 " (cutoff:3.500A) Processing helix chain 'E' and resid 1324 through 1339 removed outlier: 4.784A pdb=" N ASN E1330 " --> pdb=" O LEU E1326 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1030 Processing helix chain 'F' and resid 1048 through 1053 Processing helix chain 'F' and resid 1062 through 1066 Processing helix chain 'F' and resid 1076 through 1083 removed outlier: 3.864A pdb=" N ALA F1081 " --> pdb=" O ASP F1077 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F1082 " --> pdb=" O ASP F1078 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F1083 " --> pdb=" O GLU F1079 " (cutoff:3.500A) Processing helix chain 'F' and resid 1098 through 1107 removed outlier: 3.723A pdb=" N MET F1102 " --> pdb=" O ASN F1098 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN F1103 " --> pdb=" O PRO F1099 " (cutoff:3.500A) Processing helix chain 'F' and resid 1121 through 1125 Processing helix chain 'F' and resid 1128 through 1133 removed outlier: 3.540A pdb=" N SER F1132 " --> pdb=" O ASP F1128 " (cutoff:3.500A) Processing helix chain 'F' and resid 1134 through 1144 removed outlier: 3.961A pdb=" N GLY F1138 " --> pdb=" O ALA F1134 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR F1139 " --> pdb=" O ASN F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1175 through 1180 Processing helix chain 'F' and resid 1202 through 1207 Processing helix chain 'F' and resid 1231 through 1245 removed outlier: 4.526A pdb=" N ALA F1243 " --> pdb=" O MET F1239 " (cutoff:3.500A) Processing helix chain 'F' and resid 1270 through 1275 Processing helix chain 'F' and resid 1314 through 1319 removed outlier: 3.910A pdb=" N LEU F1319 " --> pdb=" O PRO F1316 " (cutoff:3.500A) Processing helix chain 'F' and resid 1324 through 1340 Processing helix chain 'F' and resid 1352 through 1359 Processing sheet with id=AA1, first strand: chain 'E' and resid 1003 through 1004 removed outlier: 4.082A pdb=" N GLY E1004 " --> pdb=" O ILE E1068 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 1300 through 1301 removed outlier: 4.064A pdb=" N PHE E1301 " --> pdb=" O VAL E1309 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1063 1.31 - 1.44: 1374 1.44 - 1.56: 3314 1.56 - 1.68: 8 1.68 - 1.81: 48 Bond restraints: 5807 Sorted by residual: bond pdb=" CA ALA E1176 " pdb=" C ALA E1176 " ideal model delta sigma weight residual 1.517 1.469 0.049 6.30e-03 2.52e+04 5.96e+01 bond pdb=" CA SER E1323 " pdb=" C SER E1323 " ideal model delta sigma weight residual 1.526 1.466 0.060 9.20e-03 1.18e+04 4.26e+01 bond pdb=" CA ALA F1176 " pdb=" C ALA F1176 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.07e-02 8.73e+03 2.84e+01 bond pdb=" CA THR F1303 " pdb=" C THR F1303 " ideal model delta sigma weight residual 1.525 1.472 0.053 1.11e-02 8.12e+03 2.29e+01 bond pdb=" CA SER F1323 " pdb=" C SER F1323 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.27e+01 ... (remaining 5802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 7142 2.66 - 5.33: 616 5.33 - 7.99: 101 7.99 - 10.66: 34 10.66 - 13.32: 7 Bond angle restraints: 7900 Sorted by residual: angle pdb=" N ILE F1181 " pdb=" CA ILE F1181 " pdb=" C ILE F1181 " ideal model delta sigma weight residual 111.58 100.09 11.49 1.06e+00 8.90e-01 1.17e+02 angle pdb=" N ILE F1142 " pdb=" CA ILE F1142 " pdb=" C ILE F1142 " ideal model delta sigma weight residual 113.10 103.96 9.14 9.70e-01 1.06e+00 8.88e+01 angle pdb=" N TYR E1327 " pdb=" CA TYR E1327 " pdb=" C TYR E1327 " ideal model delta sigma weight residual 114.62 104.22 10.40 1.14e+00 7.69e-01 8.32e+01 angle pdb=" N ASN F1135 " pdb=" CA ASN F1135 " pdb=" C ASN F1135 " ideal model delta sigma weight residual 113.50 102.91 10.59 1.23e+00 6.61e-01 7.42e+01 angle pdb=" N ALA E1244 " pdb=" CA ALA E1244 " pdb=" C ALA E1244 " ideal model delta sigma weight residual 113.55 103.63 9.92 1.26e+00 6.30e-01 6.19e+01 ... (remaining 7895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2731 17.84 - 35.68: 412 35.68 - 53.51: 298 53.51 - 71.35: 115 71.35 - 89.19: 30 Dihedral angle restraints: 3586 sinusoidal: 1453 harmonic: 2133 Sorted by residual: dihedral pdb=" C PRO F1316 " pdb=" N PRO F1316 " pdb=" CA PRO F1316 " pdb=" CB PRO F1316 " ideal model delta harmonic sigma weight residual -120.70 -112.43 -8.27 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" CA ASN F1288 " pdb=" CB ASN F1288 " pdb=" CG ASN F1288 " pdb=" OD1 ASN F1288 " ideal model delta sinusoidal sigma weight residual -90.00 -161.30 71.30 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN F1185 " pdb=" CB ASN F1185 " pdb=" CG ASN F1185 " pdb=" OD1 ASN F1185 " ideal model delta sinusoidal sigma weight residual -90.00 -160.40 70.40 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 3583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 578 0.047 - 0.093: 238 0.093 - 0.140: 82 0.140 - 0.187: 29 0.187 - 0.234: 7 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA THR E1011 " pdb=" N THR E1011 " pdb=" C THR E1011 " pdb=" CB THR E1011 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE F1181 " pdb=" N ILE F1181 " pdb=" C ILE F1181 " pdb=" CB ILE F1181 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C3D NAD E1401 " pdb=" C2D NAD E1401 " pdb=" C4D NAD E1401 " pdb=" O3D NAD E1401 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 931 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F1319 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO F1320 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F1320 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F1320 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E1094 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO E1095 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E1095 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E1095 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E1118 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO E1119 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO E1119 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E1119 " 0.029 5.00e-02 4.00e+02 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 2 1.99 - 2.72: 1464 2.72 - 3.45: 9204 3.45 - 4.17: 15020 4.17 - 4.90: 25299 Nonbonded interactions: 50989 Sorted by model distance: nonbonded pdb=" CE MET F1001 " pdb=" CD1 ILE F1068 " model vdw 1.263 3.880 nonbonded pdb=" CG MET F1001 " pdb=" CE1 PHE F1031 " model vdw 1.791 3.740 nonbonded pdb=" CB MET F1001 " pdb=" CD1 PHE F1031 " model vdw 2.047 3.740 nonbonded pdb=" CG MET F1001 " pdb=" CD1 PHE F1031 " model vdw 2.237 3.740 nonbonded pdb=" CE MET F1001 " pdb=" CG1 ILE F1068 " model vdw 2.238 3.860 ... (remaining 50984 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1001 through 1374 or resid 1401)) selection = (chain 'F' and resid 1001 through 1401) } 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: 1.550 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.015 0.072 5807 Z= 1.086 Angle : 1.707 13.322 7900 Z= 1.083 Chirality : 0.062 0.234 934 Planarity : 0.006 0.074 1019 Dihedral : 26.257 89.188 2212 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 56.88 Ramachandran Plot: Outliers : 17.67 % Allowed : 32.13 % Favored : 50.20 % Rotamer: Outliers : 45.38 % Allowed : 16.13 % Favored : 38.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.28 (0.16), residues: 747 helix: -5.02 (0.13), residues: 240 sheet: -6.23 (0.36), residues: 41 loop : -6.11 (0.17), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1108 TYR 0.017 0.002 TYR E1226 PHE 0.025 0.002 PHE F1234 TRP 0.017 0.002 TRP F1368 HIS 0.003 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.01488 / 1.09 ( 5807) covalent geometry : angle 1.70748 / 1.08 ( 7900) hydrogen bonds : bond 0.25984 / 17.97 ( 129) hydrogen bonds : angle 12.50516 / 8.28 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 196 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1010 LEU cc_start: 0.7746 (mp) cc_final: 0.7490 (mm) REVERT: E 1015 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7394 (mtm110) REVERT: E 1016 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8503 (p) REVERT: E 1144 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: E 1148 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: E 1201 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8502 (ttmt) REVERT: F 1140 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (tpt170) REVERT: F 1144 GLU cc_start: 0.7158 (tt0) cc_final: 0.6931 (mt-10) REVERT: F 1167 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8619 (ttmt) REVERT: F 1230 MET cc_start: 0.6937 (ttm) cc_final: 0.6520 (ttt) REVERT: F 1235 ILE cc_start: 0.8688 (mm) cc_final: 0.8389 (mm) REVERT: F 1245 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7833 (mm-40) REVERT: F 1307 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8780 (t) REVERT: F 1373 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6232 (mp) outliers start: 270 outliers final: 73 residues processed: 370 average time/residue: 0.0815 time to fit residues: 38.0411 Evaluate side-chains 220 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 137 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1003 ILE Chi-restraints excluded: chain E residue 1015 ARG Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1019 THR Chi-restraints excluded: chain E residue 1029 LEU Chi-restraints excluded: chain E residue 1037 SER Chi-restraints excluded: chain E residue 1044 SER Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1057 ILE Chi-restraints excluded: chain E residue 1061 ASN Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1093 ILE Chi-restraints excluded: chain E residue 1105 LEU Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain E residue 1121 ILE Chi-restraints excluded: chain E residue 1127 LEU Chi-restraints excluded: chain E residue 1131 SER Chi-restraints excluded: chain E residue 1144 GLU Chi-restraints excluded: chain E residue 1148 GLU Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1169 MET Chi-restraints excluded: chain E residue 1181 ILE Chi-restraints excluded: chain E residue 1186 SER Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1201 LYS Chi-restraints excluded: chain E residue 1205 GLN Chi-restraints excluded: chain E residue 1213 GLU Chi-restraints excluded: chain E residue 1240 GLU Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1267 ILE Chi-restraints excluded: chain E residue 1271 MET Chi-restraints excluded: chain E residue 1280 VAL Chi-restraints excluded: chain E residue 1302 THR Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1313 THR Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1329 THR Chi-restraints excluded: chain E residue 1346 ILE Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain E residue 1373 ILE Chi-restraints excluded: chain F residue 1003 ILE Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1051 VAL Chi-restraints excluded: chain F residue 1068 ILE Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1071 LYS Chi-restraints excluded: chain F residue 1089 LEU Chi-restraints excluded: chain F residue 1105 LEU Chi-restraints excluded: chain F residue 1108 ARG Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1122 SER Chi-restraints excluded: chain F residue 1126 SER Chi-restraints excluded: chain F residue 1131 SER Chi-restraints excluded: chain F residue 1140 ARG Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1158 THR Chi-restraints excluded: chain F residue 1167 LYS Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1219 GLU Chi-restraints excluded: chain F residue 1224 ASP Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1245 GLN Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1269 ARG Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1295 THR Chi-restraints excluded: chain F residue 1305 ASN Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1324 SER Chi-restraints excluded: chain F residue 1346 ILE Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1349 ASP Chi-restraints excluded: chain F residue 1350 PHE Chi-restraints excluded: chain F residue 1367 THR Chi-restraints excluded: chain F residue 1373 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1061 ASN ** E1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN E1291 ASN ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1333 ASN F1000 HIS F1288 ASN F1333 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122411 restraints weight = 6536.149| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.89 r_work: 0.3326 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5807 Z= 0.203 Angle : 0.937 8.526 7900 Z= 0.485 Chirality : 0.050 0.197 934 Planarity : 0.006 0.059 1019 Dihedral : 16.914 93.692 1067 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 1.47 % Allowed : 21.29 % Favored : 77.24 % Rotamer: Outliers : 14.45 % Allowed : 24.54 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.21 (0.23), residues: 747 helix: -3.43 (0.22), residues: 267 sheet: -5.78 (0.31), residues: 58 loop : -4.55 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F1015 TYR 0.012 0.002 TYR E1226 PHE 0.018 0.002 PHE E1194 TRP 0.007 0.002 TRP F1094 HIS 0.003 0.001 HIS F1000 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 ( 5807) covalent geometry : angle 0.93676 / 0.49 ( 7900) hydrogen bonds : bond 0.05383 / 3.54 ( 129) hydrogen bonds : angle 6.98107 / 4.69 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 158 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1003 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8096 (pt) REVERT: E 1015 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8405 (ptt90) REVERT: E 1045 PHE cc_start: 0.8275 (m-80) cc_final: 0.7959 (m-80) REVERT: E 1064 TRP cc_start: 0.8283 (m100) cc_final: 0.8033 (m100) REVERT: E 1111 THR cc_start: 0.8312 (m) cc_final: 0.7995 (p) REVERT: E 1113 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7142 (mtt) REVERT: E 1115 MET cc_start: 0.8889 (mmm) cc_final: 0.8307 (mmt) REVERT: E 1186 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7754 (p) REVERT: E 1195 ASP cc_start: 0.8141 (t70) cc_final: 0.7790 (t70) REVERT: E 1199 GLU cc_start: 0.8281 (tp30) cc_final: 0.8058 (tp30) REVERT: E 1201 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8207 (ttmt) REVERT: E 1203 GLN cc_start: 0.7854 (mp10) cc_final: 0.7582 (mp10) REVERT: E 1234 PHE cc_start: 0.7466 (t80) cc_final: 0.7081 (t80) REVERT: E 1275 MET cc_start: 0.8924 (mtm) cc_final: 0.8579 (mtp) REVERT: E 1330 ASN cc_start: 0.8118 (m110) cc_final: 0.7760 (m110) REVERT: F 1002 ARG cc_start: 0.7224 (mtp85) cc_final: 0.7010 (mtp180) REVERT: F 1009 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7989 (ttt180) REVERT: F 1068 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (mt) REVERT: F 1079 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6688 (mt-10) REVERT: F 1083 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (mp) REVERT: F 1153 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8652 (t80) REVERT: F 1210 GLU cc_start: 0.7663 (tt0) cc_final: 0.7297 (tm-30) REVERT: F 1230 MET cc_start: 0.5813 (ttm) cc_final: 0.5404 (ttt) REVERT: F 1235 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8064 (mm) outliers start: 86 outliers final: 35 residues processed: 214 average time/residue: 0.0629 time to fit residues: 18.1322 Evaluate side-chains 162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1003 ILE Chi-restraints excluded: chain E residue 1015 ARG Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1029 LEU Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1105 LEU Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain E residue 1121 ILE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1142 ILE Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 SER Chi-restraints excluded: chain E residue 1201 LYS Chi-restraints excluded: chain E residue 1215 ASP Chi-restraints excluded: chain E residue 1240 GLU Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1022 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1051 VAL Chi-restraints excluded: chain F residue 1068 ILE Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1083 LEU Chi-restraints excluded: chain F residue 1105 LEU Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1153 PHE Chi-restraints excluded: chain F residue 1158 THR Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1235 ILE Chi-restraints excluded: chain F residue 1279 SER Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1305 ASN Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [40, 34, 9, 44, 2, 57, 22, 45, 37, 33, 62] chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1052 GLN E1061 ASN E1109 ASN E1135 ASN ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112327 restraints weight = 6662.019| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.05 r_work: 0.3112 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5807 Z= 0.209 Angle : 0.842 9.206 7900 Z= 0.426 Chirality : 0.049 0.222 934 Planarity : 0.005 0.048 1019 Dihedral : 13.116 89.472 957 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.94 % Allowed : 20.88 % Favored : 78.18 % Rotamer: Outliers : 9.92 % Allowed : 26.89 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.26), residues: 747 helix: -2.19 (0.28), residues: 269 sheet: -5.81 (0.31), residues: 69 loop : -3.79 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E1108 TYR 0.015 0.002 TYR E1226 PHE 0.011 0.002 PHE E1194 TRP 0.011 0.002 TRP E1094 HIS 0.004 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 5807) covalent geometry : angle 0.84219 / 0.43 ( 7900) hydrogen bonds : bond 0.04678 / 2.92 ( 129) hydrogen bonds : angle 6.05345 / 4.18 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1016 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8389 (p) REVERT: E 1045 PHE cc_start: 0.8178 (m-80) cc_final: 0.7875 (m-80) REVERT: E 1056 GLU cc_start: 0.7698 (tt0) cc_final: 0.6498 (mp0) REVERT: E 1102 MET cc_start: 0.9065 (mmm) cc_final: 0.8821 (mmt) REVERT: E 1113 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6654 (mtm) REVERT: E 1186 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7602 (p) REVERT: E 1195 ASP cc_start: 0.8293 (t70) cc_final: 0.8039 (t0) REVERT: E 1201 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8165 (ttmt) REVERT: E 1203 GLN cc_start: 0.7737 (mp10) cc_final: 0.7503 (mp10) REVERT: E 1234 PHE cc_start: 0.7702 (t80) cc_final: 0.7458 (t80) REVERT: E 1240 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: E 1359 THR cc_start: 0.7761 (t) cc_final: 0.7282 (t) REVERT: F 1009 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7794 (ttt180) REVERT: F 1028 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7704 (mttt) REVERT: F 1068 ILE cc_start: 0.8508 (pt) cc_final: 0.7982 (mt) REVERT: F 1079 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6900 (mt-10) REVERT: F 1083 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8212 (mp) REVERT: F 1102 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7736 (mtm) REVERT: F 1113 MET cc_start: 0.8021 (mmp) cc_final: 0.7805 (mmm) REVERT: F 1213 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8121 (mm-30) outliers start: 59 outliers final: 30 residues processed: 169 average time/residue: 0.0635 time to fit residues: 14.5792 Evaluate side-chains 149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1105 LEU Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 SER Chi-restraints excluded: chain E residue 1201 LYS Chi-restraints excluded: chain E residue 1240 GLU Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain E residue 1360 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1083 LEU Chi-restraints excluded: chain F residue 1102 MET Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1158 THR Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1206 SER Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1231 SER Chi-restraints excluded: chain F residue 1279 SER Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1366 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [2, 36, 54, 24, 10, 30, 64, 28, 53, 67, 33] chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1322 GLN F1333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117314 restraints weight = 6605.753| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.00 r_work: 0.3145 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5807 Z= 0.152 Angle : 0.754 7.552 7900 Z= 0.380 Chirality : 0.047 0.230 934 Planarity : 0.005 0.038 1019 Dihedral : 11.953 85.945 937 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 16.33 % Favored : 83.13 % Rotamer: Outliers : 7.90 % Allowed : 31.76 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.29), residues: 747 helix: -1.36 (0.31), residues: 265 sheet: -5.61 (0.35), residues: 67 loop : -3.12 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F1362 TYR 0.017 0.002 TYR E1327 PHE 0.015 0.001 PHE E1050 TRP 0.010 0.001 TRP F1368 HIS 0.002 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 5807) covalent geometry : angle 0.75395 / 0.38 ( 7900) hydrogen bonds : bond 0.04081 / 2.61 ( 129) hydrogen bonds : angle 5.56280 / 3.94 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1016 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8183 (p) REVERT: E 1045 PHE cc_start: 0.8135 (m-80) cc_final: 0.7827 (m-80) REVERT: E 1056 GLU cc_start: 0.7357 (tt0) cc_final: 0.6298 (mp0) REVERT: E 1100 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: E 1203 GLN cc_start: 0.7652 (mp10) cc_final: 0.7413 (mp10) REVERT: E 1213 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6722 (tp30) REVERT: E 1214 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6889 (pp) REVERT: E 1217 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7476 (mtmt) REVERT: E 1240 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: E 1299 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7505 (mm-30) REVERT: E 1314 ASP cc_start: 0.7518 (t0) cc_final: 0.6748 (p0) REVERT: F 1028 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7663 (mttt) REVERT: F 1042 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7678 (tt) REVERT: F 1068 ILE cc_start: 0.8463 (pt) cc_final: 0.8092 (mt) REVERT: F 1079 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6923 (mt-10) REVERT: F 1102 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7330 (mtm) REVERT: F 1162 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7367 (tmtt) REVERT: F 1169 MET cc_start: 0.9190 (tmm) cc_final: 0.8781 (tmm) REVERT: F 1213 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8014 (mm-30) outliers start: 47 outliers final: 24 residues processed: 153 average time/residue: 0.0627 time to fit residues: 12.7141 Evaluate side-chains 140 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1029 LEU Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1100 GLU Chi-restraints excluded: chain E residue 1105 LEU Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1240 GLU Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1102 MET Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [1, 3, 26, 18, 31, 41, 29, 24, 56, 37, 60] chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1012 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112679 restraints weight = 6772.676| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.06 r_work: 0.3094 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5807 Z= 0.193 Angle : 0.780 12.981 7900 Z= 0.385 Chirality : 0.046 0.221 934 Planarity : 0.005 0.038 1019 Dihedral : 11.192 84.491 927 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.54 % Allowed : 16.87 % Favored : 82.60 % Rotamer: Outliers : 7.23 % Allowed : 31.76 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.30), residues: 747 helix: -1.17 (0.32), residues: 268 sheet: -5.66 (0.31), residues: 76 loop : -2.97 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1362 TYR 0.014 0.002 TYR E1327 PHE 0.010 0.001 PHE E1216 TRP 0.010 0.002 TRP F1368 HIS 0.003 0.002 HIS F1000 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 5807) covalent geometry : angle 0.78026 / 0.38 ( 7900) hydrogen bonds : bond 0.04319 / 2.73 ( 129) hydrogen bonds : angle 5.39981 / 3.85 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1016 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8415 (p) REVERT: E 1045 PHE cc_start: 0.8148 (m-80) cc_final: 0.7802 (m-80) REVERT: E 1152 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: E 1203 GLN cc_start: 0.7747 (mp10) cc_final: 0.7487 (mp10) REVERT: E 1213 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6356 (tp30) REVERT: E 1217 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7537 (mttt) REVERT: E 1240 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: E 1299 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7538 (mm-30) REVERT: E 1314 ASP cc_start: 0.7514 (t0) cc_final: 0.6766 (p0) REVERT: F 1028 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7675 (mttt) REVERT: F 1042 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7685 (tt) REVERT: F 1068 ILE cc_start: 0.8523 (pt) cc_final: 0.8162 (mt) REVERT: F 1102 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7453 (mtm) REVERT: F 1213 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7965 (mm-30) REVERT: F 1287 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5608 (pt0) outliers start: 43 outliers final: 27 residues processed: 143 average time/residue: 0.0661 time to fit residues: 12.6535 Evaluate side-chains 137 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1152 PHE Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain E residue 1215 ASP Chi-restraints excluded: chain E residue 1240 GLU Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1102 MET Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1158 THR Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1287 GLN Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [56, 59, 25, 49, 29, 22, 5, 43, 14, 20, 35] chunk 56 optimal weight: 0.0470 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118945 restraints weight = 6620.359| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.02 r_work: 0.3289 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5807 Z= 0.134 Angle : 0.723 12.689 7900 Z= 0.354 Chirality : 0.045 0.230 934 Planarity : 0.005 0.074 1019 Dihedral : 10.399 80.148 925 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.79 % Favored : 85.81 % Rotamer: Outliers : 7.06 % Allowed : 32.61 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.30), residues: 747 helix: -1.01 (0.32), residues: 273 sheet: -5.41 (0.35), residues: 64 loop : -2.86 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1009 TYR 0.013 0.001 TYR E1327 PHE 0.009 0.001 PHE E1050 TRP 0.013 0.001 TRP F1368 HIS 0.001 0.000 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5807) covalent geometry : angle 0.72305 / 0.35 ( 7900) hydrogen bonds : bond 0.03778 / 2.36 ( 129) hydrogen bonds : angle 5.09676 / 3.72 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1013 GLU cc_start: 0.6252 (pm20) cc_final: 0.5976 (pm20) REVERT: E 1016 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8276 (p) REVERT: E 1045 PHE cc_start: 0.8122 (m-80) cc_final: 0.7839 (m-80) REVERT: E 1056 GLU cc_start: 0.7361 (tt0) cc_final: 0.6490 (mp0) REVERT: E 1128 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7847 (t0) REVERT: E 1203 GLN cc_start: 0.7684 (mp10) cc_final: 0.7473 (mp10) REVERT: E 1213 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6441 (tp30) REVERT: E 1214 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6721 (pp) REVERT: E 1217 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7584 (mttt) REVERT: E 1234 PHE cc_start: 0.7880 (t80) cc_final: 0.7602 (t80) REVERT: E 1240 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7466 (tt0) REVERT: E 1299 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7508 (mm-30) REVERT: E 1314 ASP cc_start: 0.7498 (t0) cc_final: 0.7077 (t70) REVERT: F 1009 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7851 (mtp-110) REVERT: F 1028 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7705 (mttt) REVERT: F 1042 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7672 (tt) REVERT: F 1068 ILE cc_start: 0.8525 (pt) cc_final: 0.8173 (mt) REVERT: F 1162 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7347 (tmtt) REVERT: F 1169 MET cc_start: 0.9179 (tmm) cc_final: 0.8876 (tmm) REVERT: F 1213 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7820 (mm-30) REVERT: F 1287 GLN cc_start: 0.5821 (OUTLIER) cc_final: 0.5516 (pt0) outliers start: 42 outliers final: 24 residues processed: 147 average time/residue: 0.0678 time to fit residues: 13.3824 Evaluate side-chains 137 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1187 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1287 GLN Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1353 VAL Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [6, 46, 41, 7, 27, 58, 30, 72, 42, 34, 56] chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 72 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120070 restraints weight = 6646.914| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.09 r_work: 0.3268 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5807 Z= 0.130 Angle : 0.725 12.901 7900 Z= 0.353 Chirality : 0.044 0.239 934 Planarity : 0.005 0.056 1019 Dihedral : 10.992 89.651 919 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.12 % Favored : 86.48 % Rotamer: Outliers : 6.22 % Allowed : 33.78 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.30), residues: 747 helix: -0.92 (0.32), residues: 272 sheet: -5.25 (0.37), residues: 69 loop : -2.68 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1009 TYR 0.013 0.001 TYR E1327 PHE 0.007 0.001 PHE E1031 TRP 0.019 0.001 TRP F1368 HIS 0.001 0.000 HIS F1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5807) covalent geometry : angle 0.72534 / 0.35 ( 7900) hydrogen bonds : bond 0.03687 / 2.27 ( 129) hydrogen bonds : angle 5.09637 / 3.73 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1016 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8282 (p) REVERT: E 1045 PHE cc_start: 0.8138 (m-80) cc_final: 0.7813 (m-80) REVERT: E 1056 GLU cc_start: 0.7271 (tt0) cc_final: 0.6399 (mp0) REVERT: E 1092 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7758 (t80) REVERT: E 1203 GLN cc_start: 0.7673 (mp10) cc_final: 0.7468 (mp10) REVERT: E 1213 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6640 (tp30) REVERT: E 1214 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6636 (pp) REVERT: E 1234 PHE cc_start: 0.7880 (t80) cc_final: 0.7557 (t80) REVERT: E 1240 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7511 (tt0) REVERT: E 1261 LYS cc_start: 0.7197 (mmmt) cc_final: 0.6779 (mptt) REVERT: E 1299 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7682 (tt0) REVERT: E 1314 ASP cc_start: 0.7482 (t0) cc_final: 0.7109 (t70) REVERT: F 1009 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7995 (mtp-110) REVERT: F 1028 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7692 (mttt) REVERT: F 1042 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7702 (tt) REVERT: F 1068 ILE cc_start: 0.8508 (pt) cc_final: 0.8132 (mt) REVERT: F 1079 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7150 (mm-30) REVERT: F 1102 MET cc_start: 0.8543 (mpp) cc_final: 0.7966 (tpp) REVERT: F 1162 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7078 (tptt) REVERT: F 1213 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7738 (mm-30) REVERT: F 1287 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.5501 (pt0) outliers start: 37 outliers final: 23 residues processed: 142 average time/residue: 0.0681 time to fit residues: 12.7593 Evaluate side-chains 139 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1016 VAL Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1057 ILE Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1187 LEU Chi-restraints excluded: chain E residue 1214 LEU Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1287 GLN Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [37, 56, 16, 53, 17, 43, 18, 13, 60, 6, 55] chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110407 restraints weight = 6995.805| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.10 r_work: 0.3199 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5807 Z= 0.174 Angle : 0.777 11.573 7900 Z= 0.382 Chirality : 0.045 0.213 934 Planarity : 0.005 0.046 1019 Dihedral : 10.987 89.659 919 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.13 % Favored : 84.47 % Rotamer: Outliers : 5.38 % Allowed : 34.96 % Favored : 59.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.30), residues: 747 helix: -0.99 (0.31), residues: 273 sheet: -5.23 (0.39), residues: 72 loop : -2.63 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1009 TYR 0.010 0.002 TYR E1327 PHE 0.009 0.001 PHE E1031 TRP 0.023 0.002 TRP F1368 HIS 0.002 0.001 HIS F1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 5807) covalent geometry : angle 0.77720 / 0.38 ( 7900) hydrogen bonds : bond 0.03954 / 2.44 ( 129) hydrogen bonds : angle 5.12209 / 3.75 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1045 PHE cc_start: 0.8236 (m-80) cc_final: 0.7936 (m-80) REVERT: E 1056 GLU cc_start: 0.7337 (tt0) cc_final: 0.6535 (mp0) REVERT: E 1234 PHE cc_start: 0.8092 (t80) cc_final: 0.7783 (t80) REVERT: E 1240 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7584 (tt0) REVERT: E 1261 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6944 (mptt) REVERT: E 1299 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7805 (tt0) REVERT: E 1314 ASP cc_start: 0.7505 (t0) cc_final: 0.7233 (t70) REVERT: F 1028 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7737 (mttt) REVERT: F 1042 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7844 (tt) REVERT: F 1068 ILE cc_start: 0.8594 (pt) cc_final: 0.8180 (mt) REVERT: F 1079 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7316 (mm-30) REVERT: F 1102 MET cc_start: 0.8430 (mpp) cc_final: 0.7930 (tpp) REVERT: F 1162 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7187 (tptt) REVERT: F 1169 MET cc_start: 0.9299 (tmm) cc_final: 0.9065 (tmm) REVERT: F 1213 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7811 (mm-30) REVERT: F 1287 GLN cc_start: 0.5735 (OUTLIER) cc_final: 0.5454 (pt0) outliers start: 32 outliers final: 24 residues processed: 136 average time/residue: 0.0671 time to fit residues: 12.1918 Evaluate side-chains 134 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1062 SER Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1287 GLN Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Chi-restraints excluded: chain F residue 1367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [72, 73, 9, 70, 18, 39, 43, 34, 37, 50, 6] chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114535 restraints weight = 7127.505| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.08 r_work: 0.3280 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5807 Z= 0.142 Angle : 0.739 12.006 7900 Z= 0.365 Chirality : 0.045 0.218 934 Planarity : 0.005 0.046 1019 Dihedral : 10.591 86.118 918 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.72 % Favored : 86.88 % Rotamer: Outliers : 5.88 % Allowed : 34.12 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.30), residues: 747 helix: -0.82 (0.32), residues: 271 sheet: -5.04 (0.43), residues: 67 loop : -2.62 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1197 TYR 0.013 0.001 TYR E1327 PHE 0.010 0.001 PHE E1031 TRP 0.030 0.002 TRP F1368 HIS 0.001 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 5807) covalent geometry : angle 0.73932 / 0.37 ( 7900) hydrogen bonds : bond 0.03651 / 2.26 ( 129) hydrogen bonds : angle 5.06371 / 3.72 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1045 PHE cc_start: 0.8230 (m-80) cc_final: 0.7964 (m-80) REVERT: E 1115 MET cc_start: 0.9100 (mmm) cc_final: 0.8733 (mmp) REVERT: E 1128 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7956 (t0) REVERT: E 1154 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8831 (p) REVERT: E 1234 PHE cc_start: 0.8044 (t80) cc_final: 0.7725 (t80) REVERT: E 1240 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7558 (tt0) REVERT: E 1261 LYS cc_start: 0.7417 (mmmt) cc_final: 0.7092 (mptt) REVERT: E 1299 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7882 (tt0) REVERT: F 1028 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7791 (mttt) REVERT: F 1042 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7853 (tt) REVERT: F 1068 ILE cc_start: 0.8643 (pt) cc_final: 0.8207 (mt) REVERT: F 1079 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7268 (mm-30) REVERT: F 1102 MET cc_start: 0.8459 (mpp) cc_final: 0.7925 (tpp) REVERT: F 1162 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7123 (tptt) REVERT: F 1169 MET cc_start: 0.9281 (tmm) cc_final: 0.9045 (tmm) REVERT: F 1213 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7675 (mm-30) REVERT: F 1287 GLN cc_start: 0.5718 (OUTLIER) cc_final: 0.5463 (pt0) outliers start: 35 outliers final: 24 residues processed: 139 average time/residue: 0.0703 time to fit residues: 12.7869 Evaluate side-chains 135 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1012 ASN Chi-restraints excluded: chain F residue 1019 THR Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1231 SER Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1287 GLN Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Chi-restraints excluded: chain F residue 1367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [53, 20, 29, 12, 9, 50, 17, 40, 21, 8, 51] chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114729 restraints weight = 7107.468| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.08 r_work: 0.3282 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5807 Z= 0.139 Angle : 0.749 11.840 7900 Z= 0.367 Chirality : 0.045 0.224 934 Planarity : 0.005 0.049 1019 Dihedral : 10.392 82.903 918 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.25 % Favored : 86.48 % Rotamer: Outliers : 4.54 % Allowed : 35.46 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.31), residues: 747 helix: -0.74 (0.32), residues: 266 sheet: -4.79 (0.47), residues: 61 loop : -2.53 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F1362 TYR 0.013 0.001 TYR E1327 PHE 0.017 0.001 PHE E1216 TRP 0.032 0.002 TRP F1368 HIS 0.002 0.001 HIS F1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5807) covalent geometry : angle 0.74920 / 0.37 ( 7900) hydrogen bonds : bond 0.03762 / 2.33 ( 129) hydrogen bonds : angle 5.02988 / 3.71 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1045 PHE cc_start: 0.8232 (m-80) cc_final: 0.7963 (m-80) REVERT: E 1056 GLU cc_start: 0.7248 (tt0) cc_final: 0.6506 (mp0) REVERT: E 1115 MET cc_start: 0.9069 (mmm) cc_final: 0.8736 (mmp) REVERT: E 1152 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: E 1199 GLU cc_start: 0.8193 (pm20) cc_final: 0.7831 (pm20) REVERT: E 1234 PHE cc_start: 0.7947 (t80) cc_final: 0.7680 (t80) REVERT: E 1240 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7555 (tt0) REVERT: E 1261 LYS cc_start: 0.7518 (mmmt) cc_final: 0.7191 (mptt) REVERT: E 1299 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7877 (tt0) REVERT: F 1009 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7588 (ttm-80) REVERT: F 1028 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7777 (mttt) REVERT: F 1042 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7860 (tt) REVERT: F 1068 ILE cc_start: 0.8646 (pt) cc_final: 0.8218 (mt) REVERT: F 1079 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7342 (mm-30) REVERT: F 1102 MET cc_start: 0.8395 (mpp) cc_final: 0.7800 (tpp) REVERT: F 1162 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7085 (tptt) REVERT: F 1169 MET cc_start: 0.9270 (tmm) cc_final: 0.9013 (tmm) REVERT: F 1213 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7694 (mm-30) outliers start: 27 outliers final: 21 residues processed: 134 average time/residue: 0.0734 time to fit residues: 12.8254 Evaluate side-chains 132 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 GLN Chi-restraints excluded: chain E residue 1071 LYS Chi-restraints excluded: chain E residue 1091 SER Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1123 ARG Chi-restraints excluded: chain E residue 1152 PHE Chi-restraints excluded: chain E residue 1153 PHE Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1323 SER Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1042 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1116 ASP Chi-restraints excluded: chain F residue 1142 ILE Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1187 LEU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1228 LYS Chi-restraints excluded: chain F residue 1231 SER Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1348 VAL Chi-restraints excluded: chain F residue 1360 VAL Chi-restraints excluded: chain F residue 1366 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [39, 37, 69, 49, 9, 65, 47, 33, 36, 27, 61] chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114779 restraints weight = 6942.982| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.02 r_work: 0.3291 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5807 Z= 0.139 Angle : 0.731 11.299 7900 Z= 0.361 Chirality : 0.044 0.219 934 Planarity : 0.005 0.048 1019 Dihedral : 10.138 79.035 918 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.85 % Favored : 86.88 % Rotamer: Outliers : 4.87 % Allowed : 35.29 % Favored : 59.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.31), residues: 747 helix: -0.69 (0.32), residues: 272 sheet: -4.82 (0.44), residues: 63 loop : -2.48 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1362 TYR 0.012 0.001 TYR E1327 PHE 0.012 0.001 PHE E1216 TRP 0.034 0.002 TRP F1368 HIS 0.002 0.001 HIS F1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5807) covalent geometry : angle 0.73130 / 0.36 ( 7900) hydrogen bonds : bond 0.03651 / 2.28 ( 129) hydrogen bonds : angle 4.89724 / 3.62 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.88 seconds wall clock time: 24 minutes 8.43 seconds (1448.43 seconds total)