Starting phenix.real_space_refine on Tue Aug 4 17:44:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uvb_64530/08_2026/9uvb_64530.map" } resolution = 3.23 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= 0.032 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3451 2.51 5 N 925 2.21 5 O 1043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5442 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2739 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Chain: "F" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2703 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Time building chain proxies: 1.24, per 1000 atoms: 0.23 Number of scatterers: 5442 At special positions: 0 Unit cell: (60.68, 90.2, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1043 8.00 N 925 7.00 C 3451 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: 0.42 Conformation dependent library (CDL) restraints added in 219.7 milliseconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 37.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'E' and resid 1019 through 1028 Processing helix chain 'E' and resid 1040 through 1044 removed outlier: 3.535A pdb=" N SER E1044 " --> pdb=" O GLN E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1053 removed outlier: 3.548A pdb=" N PHE E1050 " --> pdb=" O ASP E1046 " (cutoff:3.500A) Processing helix chain 'E' and resid 1059 through 1065 removed outlier: 4.441A pdb=" N SER E1062 " --> pdb=" O GLU E1059 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL E1063 " --> pdb=" O GLY E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1105 through 1109 Processing helix chain 'E' and resid 1121 through 1127 removed outlier: 4.177A pdb=" N SER E1126 " --> pdb=" O ARG E1123 " (cutoff:3.500A) Processing helix chain 'E' and resid 1128 through 1149 removed outlier: 3.558A pdb=" N ILE E1142 " --> pdb=" O GLY E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1177 through 1188 Processing helix chain 'E' and resid 1200 through 1205 Processing helix chain 'E' and resid 1224 through 1229 removed outlier: 3.553A pdb=" N VAL E1229 " --> pdb=" O GLY E1225 " (cutoff:3.500A) Processing helix chain 'E' and resid 1232 through 1249 removed outlier: 4.260A pdb=" N LYS E1236 " --> pdb=" O ASP E1232 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E1243 " --> pdb=" O MET E1239 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA E1246 " --> pdb=" O PHE E1242 " (cutoff:3.500A) Processing helix chain 'E' and resid 1315 through 1318 Processing helix chain 'E' and resid 1319 through 1324 Processing helix chain 'E' and resid 1327 through 1339 removed outlier: 3.562A pdb=" N ASN E1333 " --> pdb=" O THR E1329 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E1337 " --> pdb=" O ASN E1333 " (cutoff:3.500A) Processing helix chain 'E' and resid 1353 through 1359 Processing helix chain 'E' and resid 1361 through 1365 Processing helix chain 'F' and resid 1019 through 1029 removed outlier: 3.636A pdb=" N GLN F1025 " --> pdb=" O LYS F1021 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1043 removed outlier: 4.446A pdb=" N LEU F1042 " --> pdb=" O ALA F1039 " (cutoff:3.500A) Processing helix chain 'F' and resid 1046 through 1054 removed outlier: 3.626A pdb=" N GLY F1054 " --> pdb=" O PHE F1050 " (cutoff:3.500A) Processing helix chain 'F' and resid 1059 through 1063 removed outlier: 4.288A pdb=" N VAL F1063 " --> pdb=" O GLY F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1078 through 1083 Processing helix chain 'F' and resid 1100 through 1108 Processing helix chain 'F' and resid 1129 through 1146 removed outlier: 3.582A pdb=" N TYR F1139 " --> pdb=" O ASN F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1174 through 1187 removed outlier: 3.518A pdb=" N LEU F1178 " --> pdb=" O GLY F1174 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F1182 " --> pdb=" O LEU F1178 " (cutoff:3.500A) Processing helix chain 'F' and resid 1203 through 1208 Processing helix chain 'F' and resid 1231 through 1235 Processing helix chain 'F' and resid 1237 through 1242 removed outlier: 4.180A pdb=" N LEU F1241 " --> pdb=" O ALA F1237 " (cutoff:3.500A) Processing helix chain 'F' and resid 1242 through 1247 Processing helix chain 'F' and resid 1285 through 1287 No H-bonds generated for 'chain 'F' and resid 1285 through 1287' Processing helix chain 'F' and resid 1315 through 1319 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 1004 through 1005 Processing sheet with id=AA2, first strand: chain 'E' and resid 1068 through 1070 Processing sheet with id=AA3, first strand: chain 'E' and resid 1210 through 1211 removed outlier: 6.424A pdb=" N ILE E1252 " --> pdb=" O VAL E1282 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E1281 " --> pdb=" O ILE E1310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E1307 " --> pdb=" O THR E1303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E1303 " --> pdb=" O VAL E1307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 1002 through 1003 Processing sheet with id=AA5, first strand: chain 'F' and resid 1156 through 1158 removed outlier: 3.736A pdb=" N GLY F1161 " --> pdb=" O THR F1158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 1210 through 1211 removed outlier: 6.673A pdb=" N VAL F1191 " --> pdb=" O GLU F1210 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F1168 " --> pdb=" O ARG F1192 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 432 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: 0.68 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 955 1.28 - 1.41: 1173 1.41 - 1.55: 3354 1.55 - 1.68: 3 1.68 - 1.81: 42 Bond restraints: 5527 Sorted by residual: bond pdb=" CG LEU F1212 " pdb=" CD1 LEU F1212 " ideal model delta sigma weight residual 1.521 1.273 0.248 3.30e-02 9.18e+02 5.67e+01 bond pdb=" CG ASP E1250 " pdb=" OD2 ASP E1250 " ideal model delta sigma weight residual 1.249 1.146 0.103 1.90e-02 2.77e+03 2.92e+01 bond pdb=" C GLY F1174 " pdb=" O GLY F1174 " ideal model delta sigma weight residual 1.235 1.181 0.053 1.35e-02 5.49e+03 1.56e+01 bond pdb=" CA PRO F1165 " pdb=" C PRO F1165 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.16e-02 7.43e+03 1.26e+01 bond pdb=" CA LYS F1167 " pdb=" C LYS F1167 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.15e+01 ... (remaining 5522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 7364 3.20 - 6.40: 124 6.40 - 9.59: 17 9.59 - 12.79: 2 12.79 - 15.99: 1 Bond angle restraints: 7508 Sorted by residual: angle pdb=" N VAL F1072 " pdb=" CA VAL F1072 " pdb=" C VAL F1072 " ideal model delta sigma weight residual 113.47 107.04 6.43 1.01e+00 9.80e-01 4.05e+01 angle pdb=" N ARG F1007 " pdb=" CA ARG F1007 " pdb=" C ARG F1007 " ideal model delta sigma weight residual 110.32 100.66 9.66 1.59e+00 3.96e-01 3.69e+01 angle pdb=" N SER E1206 " pdb=" CA SER E1206 " pdb=" C SER E1206 " ideal model delta sigma weight residual 114.56 107.63 6.93 1.27e+00 6.20e-01 2.98e+01 angle pdb=" CB LEU F1212 " pdb=" CG LEU F1212 " pdb=" CD1 LEU F1212 " ideal model delta sigma weight residual 110.70 94.71 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" N ALA E1243 " pdb=" CA ALA E1243 " pdb=" C ALA E1243 " ideal model delta sigma weight residual 113.43 107.11 6.32 1.26e+00 6.30e-01 2.51e+01 ... (remaining 7503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 2774 17.29 - 34.59: 427 34.59 - 51.88: 120 51.88 - 69.18: 31 69.18 - 86.47: 10 Dihedral angle restraints: 3362 sinusoidal: 1297 harmonic: 2065 Sorted by residual: dihedral pdb=" CA TRP E1368 " pdb=" C TRP E1368 " pdb=" N PRO E1369 " pdb=" CA PRO E1369 " ideal model delta harmonic sigma weight residual 180.00 117.24 62.76 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA LEU F1187 " pdb=" C LEU F1187 " pdb=" N GLY F1188 " pdb=" CA GLY F1188 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA VAL E1353 " pdb=" C VAL E1353 " pdb=" N VAL E1354 " pdb=" CA VAL E1354 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 3359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 622 0.048 - 0.096: 207 0.096 - 0.144: 54 0.144 - 0.192: 10 0.192 - 0.240: 3 Chirality restraints: 896 Sorted by residual: chirality pdb=" CB ILE F1069 " pdb=" CA ILE F1069 " pdb=" CG1 ILE F1069 " pdb=" CG2 ILE F1069 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE F1346 " pdb=" CA ILE F1346 " pdb=" CG1 ILE F1346 " pdb=" CG2 ILE F1346 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL E1016 " pdb=" CA VAL E1016 " pdb=" CG1 VAL E1016 " pdb=" CG2 VAL E1016 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 893 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E1098 " 0.094 5.00e-02 4.00e+02 1.42e-01 3.21e+01 pdb=" N PRO E1099 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO E1099 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO E1099 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E1149 " 0.028 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE E1149 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE E1149 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE E1149 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E1149 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE E1149 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E1149 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E1056 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU E1056 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU E1056 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE E1057 " -0.019 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 94 2.59 - 3.17: 4978 3.17 - 3.74: 8829 3.74 - 4.32: 12677 4.32 - 4.90: 20598 Nonbonded interactions: 47176 Sorted by model distance: nonbonded pdb=" O GLU E1056 " pdb=" OE1 GLU E1056 " model vdw 2.011 3.040 nonbonded pdb=" O ASP E1250 " pdb=" OD1 ASP E1250 " model vdw 2.093 3.040 nonbonded pdb=" O ILE F1355 " pdb=" OG1 THR F1359 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG F1123 " pdb=" OD1 ASP F1352 " model vdw 2.201 3.120 nonbonded pdb=" O VAL F1063 " pdb=" OG SER F1066 " model vdw 2.203 3.040 ... (remaining 47171 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 1214 or resid 1224 or resid 1231 through 1374 \ )) selection = (chain 'F' and resid 1001 through 1374) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.008 0.248 5527 Z= 0.354 Angle : 1.067 15.988 7508 Z= 0.638 Chirality : 0.053 0.240 896 Planarity : 0.008 0.142 979 Dihedral : 18.948 86.472 2030 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 35.66 Ramachandran Plot: Outliers : 1.25 % Allowed : 15.00 % Favored : 83.75 % Rotamer: Outliers : 0.69 % Allowed : 33.28 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -5.22 (0.25), residues: 720 helix: -3.18 (0.25), residues: 231 sheet: -3.87 (0.59), residues: 57 loop : -3.76 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F1356 TYR 0.013 0.002 TYR E1294 PHE 0.049 0.003 PHE E1149 TRP 0.006 0.001 TRP E1368 HIS 0.002 0.001 HIS F1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.35 ( 5527) covalent geometry : angle 1.06714 / 0.64 ( 7508) hydrogen bonds : bond 0.21574 / 14.71 ( 165) hydrogen bonds : angle 8.83931 / 5.92 ( 432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.140 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.0579 time to fit residues: 7.5090 Evaluate side-chains 96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1321 THR Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1185 ASN F 999 HIS F1288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.220944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.196382 restraints weight = 5877.614| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.80 r_work: 0.4134 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5527 Z= 0.176 Angle : 0.741 7.378 7508 Z= 0.390 Chirality : 0.050 0.256 896 Planarity : 0.006 0.061 979 Dihedral : 6.979 57.709 768 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.97 % Allowed : 12.78 % Favored : 86.25 % Rotamer: Outliers : 6.41 % Allowed : 28.77 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -4.49 (0.27), residues: 720 helix: -2.29 (0.28), residues: 246 sheet: -4.08 (0.50), residues: 77 loop : -3.29 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E1356 TYR 0.006 0.001 TYR E1294 PHE 0.015 0.002 PHE E1149 TRP 0.008 0.001 TRP F1064 HIS 0.001 0.001 HIS F 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5527) covalent geometry : angle 0.74108 / 0.39 ( 7508) hydrogen bonds : bond 0.04269 / 2.87 ( 165) hydrogen bonds : angle 6.18612 / 4.09 ( 432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: E 1293 GLU cc_start: 0.7247 (pm20) cc_final: 0.7032 (pm20) REVERT: E 1295 THR cc_start: 0.8201 (m) cc_final: 0.7906 (p) REVERT: E 1314 ASP cc_start: 0.6573 (t70) cc_final: 0.5801 (p0) REVERT: E 1326 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6984 (mt) REVERT: E 1361 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7372 (mt) REVERT: E 1362 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7024 (ttt90) REVERT: F 1207 MET cc_start: 0.3074 (mtt) cc_final: 0.2841 (mmp) REVERT: F 1234 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 37 outliers final: 9 residues processed: 131 average time/residue: 0.0521 time to fit residues: 9.2246 Evaluate side-chains 105 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1321 THR Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain E residue 1361 ILE Chi-restraints excluded: chain E residue 1362 ARG Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1012 ASN E1185 ASN ** F1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.221249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.197387 restraints weight = 5821.318| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 1.70 r_work: 0.4153 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5527 Z= 0.156 Angle : 0.700 7.387 7508 Z= 0.363 Chirality : 0.049 0.253 896 Planarity : 0.006 0.048 979 Dihedral : 6.481 56.396 766 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.97 % Allowed : 12.22 % Favored : 86.81 % Rotamer: Outliers : 5.89 % Allowed : 28.25 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -4.03 (0.28), residues: 720 helix: -1.85 (0.30), residues: 245 sheet: -3.89 (0.47), residues: 87 loop : -2.99 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1123 TYR 0.006 0.001 TYR E1312 PHE 0.010 0.002 PHE F1242 TRP 0.010 0.001 TRP E1368 HIS 0.002 0.001 HIS F 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5527) covalent geometry : angle 0.69958 / 0.36 ( 7508) hydrogen bonds : bond 0.03960 / 2.69 ( 165) hydrogen bonds : angle 5.87984 / 3.85 ( 432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.161 Fit side-chains REVERT: E 1059 GLU cc_start: 0.6934 (tp30) cc_final: 0.6639 (tp30) REVERT: E 1272 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7315 (t) REVERT: E 1314 ASP cc_start: 0.6602 (t70) cc_final: 0.5871 (p0) REVERT: E 1326 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6918 (mt) REVERT: E 1361 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7358 (mt) REVERT: E 1366 ILE cc_start: 0.8273 (mp) cc_final: 0.8046 (mm) REVERT: F 1162 LYS cc_start: 0.7939 (tttt) cc_final: 0.7657 (tttp) outliers start: 34 outliers final: 18 residues processed: 121 average time/residue: 0.0637 time to fit residues: 10.2648 Evaluate side-chains 107 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1078 ASP Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1185 ASN Chi-restraints excluded: chain E residue 1272 VAL Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain E residue 1361 ILE Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1069 ILE Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1214 LEU Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.220656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.195668 restraints weight = 5831.011| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 1.80 r_work: 0.4127 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5527 Z= 0.165 Angle : 0.704 8.369 7508 Z= 0.362 Chirality : 0.050 0.268 896 Planarity : 0.005 0.048 979 Dihedral : 6.111 54.740 765 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.67 % Favored : 87.22 % Rotamer: Outliers : 6.41 % Allowed : 29.98 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.79 (0.28), residues: 720 helix: -1.84 (0.30), residues: 256 sheet: -3.61 (0.50), residues: 79 loop : -2.80 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1123 TYR 0.012 0.001 TYR E1294 PHE 0.009 0.002 PHE F1149 TRP 0.012 0.002 TRP E1368 HIS 0.002 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 5527) covalent geometry : angle 0.70374 / 0.36 ( 7508) hydrogen bonds : bond 0.03932 / 2.67 ( 165) hydrogen bonds : angle 5.73914 / 3.80 ( 432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.167 Fit side-chains REVERT: E 1314 ASP cc_start: 0.6456 (t70) cc_final: 0.5830 (p0) REVERT: E 1326 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6600 (tp) REVERT: E 1362 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7010 (ttt90) REVERT: E 1366 ILE cc_start: 0.8212 (mp) cc_final: 0.7993 (mm) REVERT: F 1027 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6686 (tp) REVERT: F 1144 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: F 1162 LYS cc_start: 0.7912 (tttt) cc_final: 0.7640 (tttp) outliers start: 37 outliers final: 19 residues processed: 122 average time/residue: 0.0534 time to fit residues: 8.8710 Evaluate side-chains 105 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1080 ILE Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1112 VAL Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1348 VAL Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain E residue 1362 ARG Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1214 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 0.0060 chunk 9 optimal weight: 0.9980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180190 restraints weight = 5554.787| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.69 r_work: 0.4145 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5527 Z= 0.126 Angle : 0.669 7.638 7508 Z= 0.343 Chirality : 0.047 0.222 896 Planarity : 0.005 0.047 979 Dihedral : 5.725 56.210 765 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.86 % Favored : 89.03 % Rotamer: Outliers : 4.51 % Allowed : 32.76 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.48 (0.29), residues: 720 helix: -1.53 (0.31), residues: 257 sheet: -3.77 (0.46), residues: 89 loop : -2.50 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1123 TYR 0.012 0.001 TYR E1294 PHE 0.010 0.001 PHE E1242 TRP 0.008 0.001 TRP F1064 HIS 0.002 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5527) covalent geometry : angle 0.66927 / 0.34 ( 7508) hydrogen bonds : bond 0.03508 / 2.35 ( 165) hydrogen bonds : angle 5.40012 / 3.57 ( 432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.139 Fit side-chains REVERT: E 1248 GLU cc_start: 0.7309 (tt0) cc_final: 0.7029 (tt0) REVERT: E 1314 ASP cc_start: 0.6431 (t70) cc_final: 0.5867 (p0) REVERT: E 1326 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7069 (mt) REVERT: F 1027 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6689 (tp) REVERT: F 1162 LYS cc_start: 0.7747 (tttt) cc_final: 0.7536 (tttp) REVERT: F 1204 VAL cc_start: 0.5256 (OUTLIER) cc_final: 0.4445 (p) REVERT: F 1276 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7486 (ttpt) outliers start: 26 outliers final: 14 residues processed: 120 average time/residue: 0.0618 time to fit residues: 9.9721 Evaluate side-chains 106 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1066 SER Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1112 VAL Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1214 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1276 LYS Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN E1185 ASN F1084 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.200229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175841 restraints weight = 5543.521| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.67 r_work: 0.4098 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5527 Z= 0.151 Angle : 0.682 8.447 7508 Z= 0.350 Chirality : 0.048 0.236 896 Planarity : 0.005 0.047 979 Dihedral : 5.685 53.821 765 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.25 % Favored : 87.64 % Rotamer: Outliers : 6.24 % Allowed : 33.10 % Favored : 60.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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 (0.29), residues: 720 helix: -1.51 (0.30), residues: 257 sheet: -3.49 (0.51), residues: 84 loop : -2.47 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1123 TYR 0.006 0.001 TYR E1294 PHE 0.008 0.001 PHE F1153 TRP 0.009 0.001 TRP E1368 HIS 0.002 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 5527) covalent geometry : angle 0.68237 / 0.35 ( 7508) hydrogen bonds : bond 0.03689 / 2.51 ( 165) hydrogen bonds : angle 5.49066 / 3.61 ( 432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.133 Fit side-chains REVERT: E 1207 MET cc_start: 0.7353 (ttm) cc_final: 0.7083 (mtt) REVERT: E 1314 ASP cc_start: 0.6497 (t70) cc_final: 0.6000 (p0) REVERT: E 1326 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7113 (mt) REVERT: F 1027 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6702 (tp) REVERT: F 1144 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: F 1151 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8341 (mtm-85) REVERT: F 1162 LYS cc_start: 0.7751 (tttt) cc_final: 0.7539 (tttp) outliers start: 36 outliers final: 20 residues processed: 125 average time/residue: 0.0682 time to fit residues: 11.1198 Evaluate side-chains 114 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1112 VAL Chi-restraints excluded: chain E residue 1185 ASN Chi-restraints excluded: chain E residue 1212 LEU Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.205108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181106 restraints weight = 5584.616| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.67 r_work: 0.4137 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5527 Z= 0.130 Angle : 0.667 8.643 7508 Z= 0.342 Chirality : 0.047 0.241 896 Planarity : 0.005 0.049 979 Dihedral : 5.552 55.076 765 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.31 % Favored : 89.58 % Rotamer: Outliers : 4.68 % Allowed : 35.36 % Favored : 59.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.21 (0.29), residues: 720 helix: -1.40 (0.30), residues: 258 sheet: -3.51 (0.49), residues: 89 loop : -2.29 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1123 TYR 0.006 0.001 TYR E1294 PHE 0.009 0.001 PHE F1031 TRP 0.008 0.001 TRP E1368 HIS 0.002 0.000 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5527) covalent geometry : angle 0.66713 / 0.34 ( 7508) hydrogen bonds : bond 0.03545 / 2.40 ( 165) hydrogen bonds : angle 5.30570 / 3.46 ( 432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.160 Fit side-chains REVERT: E 1314 ASP cc_start: 0.6596 (t70) cc_final: 0.6078 (p0) REVERT: E 1326 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7066 (mt) REVERT: F 1027 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6690 (tp) REVERT: F 1107 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7602 (tt0) REVERT: F 1113 MET cc_start: 0.8197 (mtt) cc_final: 0.7893 (mtp) REVERT: F 1144 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: F 1151 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8205 (mtm-85) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.0644 time to fit residues: 9.4502 Evaluate side-chains 103 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER 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 1154 THR Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN ** E1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.205652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.182248 restraints weight = 5500.852| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.63 r_work: 0.4143 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5527 Z= 0.128 Angle : 0.665 7.952 7508 Z= 0.340 Chirality : 0.047 0.218 896 Planarity : 0.005 0.049 979 Dihedral : 5.446 54.795 765 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.58 % Favored : 89.31 % Rotamer: Outliers : 3.99 % Allowed : 35.70 % Favored : 60.31 % 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: -3.10 (0.30), residues: 720 helix: -1.27 (0.31), residues: 258 sheet: -3.10 (0.45), residues: 104 loop : -2.29 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1123 TYR 0.005 0.001 TYR E1294 PHE 0.010 0.001 PHE F1031 TRP 0.009 0.001 TRP E1368 HIS 0.002 0.000 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5527) covalent geometry : angle 0.66533 / 0.34 ( 7508) hydrogen bonds : bond 0.03487 / 2.36 ( 165) hydrogen bonds : angle 5.23671 / 3.42 ( 432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.207 Fit side-chains REVERT: E 1052 GLN cc_start: 0.7844 (mt0) cc_final: 0.7642 (mp10) REVERT: E 1195 ASP cc_start: 0.6952 (t70) cc_final: 0.6733 (t70) REVERT: E 1229 VAL cc_start: 0.4969 (OUTLIER) cc_final: 0.4767 (t) REVERT: E 1314 ASP cc_start: 0.6615 (t70) cc_final: 0.6139 (p0) REVERT: E 1326 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7168 (mt) REVERT: E 1350 PHE cc_start: 0.6516 (m-10) cc_final: 0.6072 (m-10) REVERT: F 1027 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6619 (tp) REVERT: F 1113 MET cc_start: 0.8165 (mtt) cc_final: 0.7799 (mtp) REVERT: F 1151 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8184 (mtm-85) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.0742 time to fit residues: 10.6858 Evaluate side-chains 107 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER 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 1154 THR Chi-restraints excluded: chain E residue 1229 VAL Chi-restraints excluded: chain E residue 1326 LEU Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.0370 chunk 33 optimal weight: 0.0470 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.233131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.209815 restraints weight = 5853.634| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 1.73 r_work: 0.4338 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5527 Z= 0.117 Angle : 0.657 7.899 7508 Z= 0.337 Chirality : 0.046 0.227 896 Planarity : 0.005 0.053 979 Dihedral : 5.241 55.067 765 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.89 % Favored : 90.00 % Rotamer: Outliers : 4.33 % Allowed : 34.84 % Favored : 60.83 % 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: -2.77 (0.30), residues: 720 helix: -0.93 (0.32), residues: 249 sheet: -2.95 (0.45), residues: 105 loop : -2.12 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1123 TYR 0.006 0.001 TYR E1312 PHE 0.009 0.001 PHE F1031 TRP 0.009 0.001 TRP E1368 HIS 0.002 0.000 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 5527) covalent geometry : angle 0.65668 / 0.34 ( 7508) hydrogen bonds : bond 0.03221 / 2.18 ( 165) hydrogen bonds : angle 5.09710 / 3.32 ( 432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.190 Fit side-chains REVERT: E 1009 ARG cc_start: 0.7113 (mtp180) cc_final: 0.6844 (mtm180) REVERT: E 1314 ASP cc_start: 0.6762 (t70) cc_final: 0.6151 (p0) REVERT: E 1350 PHE cc_start: 0.6379 (m-10) cc_final: 0.5862 (m-10) REVERT: F 1027 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6771 (tp) REVERT: F 1107 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7720 (tt0) REVERT: F 1144 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: F 1362 ARG cc_start: 0.8036 (tpt-90) cc_final: 0.7748 (tpt-90) outliers start: 25 outliers final: 19 residues processed: 111 average time/residue: 0.0746 time to fit residues: 10.6134 Evaluate side-chains 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1110 VAL Chi-restraints excluded: chain F residue 1144 GLU Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1241 LEU Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN ** E1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.229797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.205825 restraints weight = 5834.282| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 1.75 r_work: 0.4297 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5527 Z= 0.133 Angle : 0.671 7.990 7508 Z= 0.343 Chirality : 0.047 0.228 896 Planarity : 0.005 0.055 979 Dihedral : 4.880 23.451 763 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 1.11 % Allowed : 10.14 % Favored : 88.75 % Rotamer: Outliers : 3.99 % Allowed : 33.62 % Favored : 62.39 % 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: -2.83 (0.30), residues: 720 helix: -1.13 (0.31), residues: 258 sheet: -2.87 (0.45), residues: 105 loop : -2.08 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1151 TYR 0.004 0.001 TYR E1294 PHE 0.010 0.001 PHE F1031 TRP 0.009 0.001 TRP E1368 HIS 0.001 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5527) covalent geometry : angle 0.67125 / 0.34 ( 7508) hydrogen bonds : bond 0.03333 / 2.27 ( 165) hydrogen bonds : angle 5.20437 / 3.39 ( 432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: E 1151 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7043 (mtm180) REVERT: E 1195 ASP cc_start: 0.6996 (t70) cc_final: 0.6431 (t70) REVERT: E 1314 ASP cc_start: 0.6817 (t70) cc_final: 0.6190 (p0) REVERT: F 1107 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7735 (tt0) REVERT: F 1113 MET cc_start: 0.8054 (mtt) cc_final: 0.7688 (mtp) outliers start: 23 outliers final: 21 residues processed: 105 average time/residue: 0.0623 time to fit residues: 8.7160 Evaluate side-chains 106 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1058 VAL Chi-restraints excluded: chain E residue 1066 SER Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1092 PHE Chi-restraints excluded: chain E residue 1112 VAL Chi-restraints excluded: chain E residue 1154 THR Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain F residue 1016 VAL Chi-restraints excluded: chain F residue 1027 LEU Chi-restraints excluded: chain F residue 1063 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1168 VAL Chi-restraints excluded: chain F residue 1191 VAL Chi-restraints excluded: chain F residue 1204 VAL Chi-restraints excluded: chain F residue 1212 LEU Chi-restraints excluded: chain F residue 1234 PHE Chi-restraints excluded: chain F residue 1241 LEU Chi-restraints excluded: chain F residue 1251 ILE Chi-restraints excluded: chain F residue 1283 ASP Chi-restraints excluded: chain F residue 1323 SER Chi-restraints excluded: chain F residue 1337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E1156 GLN ** E1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.229655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.205753 restraints weight = 5877.348| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.76 r_work: 0.4245 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5527 Z= 0.133 Angle : 0.671 7.326 7508 Z= 0.343 Chirality : 0.048 0.226 896 Planarity : 0.005 0.055 979 Dihedral : 4.906 22.337 763 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.44 % Favored : 89.72 % Rotamer: Outliers : 3.81 % Allowed : 32.93 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.85 (0.30), residues: 720 helix: -1.19 (0.30), residues: 266 sheet: -2.73 (0.48), residues: 100 loop : -2.15 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1151 TYR 0.005 0.001 TYR E1312 PHE 0.009 0.001 PHE F1031 TRP 0.008 0.001 TRP E1368 HIS 0.002 0.001 HIS E1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5527) covalent geometry : angle 0.67084 / 0.34 ( 7508) hydrogen bonds : bond 0.03362 / 2.27 ( 165) hydrogen bonds : angle 5.24649 / 3.43 ( 432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.52 seconds wall clock time: 23 minutes 2.10 seconds (1382.10 seconds total)