Starting phenix.real_space_refine on Fri Sep 11 14:33:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.map" model { file = "/net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c14_7328/09_2026/6c14_7328.cif" } resolution = 4.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3678 atoms to isotropic. 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 46 5.16 5 C 4406 2.51 5 N 1100 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2110 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Conformer: "B" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} bond proxies already assigned to first conformer: 2142 Chain: "B" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1263 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain breaks: 2 Chain: "C" Number of atoms: 2110 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Conformer: "B" Number of residues, atoms: 266, 2107 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} bond proxies already assigned to first conformer: 2142 Chain: "D" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1263 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain breaks: 2 Time building chain proxies: 2.13, per 1000 atoms: 0.32 Number of scatterers: 6746 At special positions: 0 Unit cell: (73.84, 80.08, 139.36, 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 46 16.00 O 1194 8.00 N 1100 7.00 C 4406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 130 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 434.1 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 49.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.886A pdb=" N ALA A1183 " --> pdb=" O ASN A1180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A1184 " --> pdb=" O TYR A1181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1180 through 1184' Processing helix chain 'A' and resid 1193 through 1197 Processing helix chain 'A' and resid 1231 through 1235 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1261 through 1268 Processing helix chain 'A' and resid 1268 through 1280 Processing helix chain 'A' and resid 1327 through 1337 removed outlier: 4.074A pdb=" N LEU A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A1337 " --> pdb=" O LYS A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 3.889A pdb=" N ILE A1342 " --> pdb=" O LYS A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.835A pdb=" N LYS A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1372 " --> pdb=" O ILE A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1410 Proline residue: A1395 - end of helix Processing helix chain 'B' and resid 16 through 45 Processing helix chain 'B' and resid 91 through 117 Processing helix chain 'B' and resid 122 through 152 removed outlier: 3.593A pdb=" N LYS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 176 through 199 removed outlier: 4.125A pdb=" N MET B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1184 removed outlier: 3.882A pdb=" N ALA C1183 " --> pdb=" O ASN C1180 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C1184 " --> pdb=" O TYR C1181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1180 through 1184' Processing helix chain 'C' and resid 1193 through 1197 Processing helix chain 'C' and resid 1231 through 1235 Processing helix chain 'C' and resid 1249 through 1253 Processing helix chain 'C' and resid 1261 through 1268 Processing helix chain 'C' and resid 1268 through 1280 Processing helix chain 'C' and resid 1327 through 1337 removed outlier: 4.073A pdb=" N LEU C1335 " --> pdb=" O LEU C1331 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C1337 " --> pdb=" O LYS C1333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1344 removed outlier: 3.889A pdb=" N ILE C1342 " --> pdb=" O LYS C1338 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1372 removed outlier: 3.858A pdb=" N LYS C1370 " --> pdb=" O THR C1366 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C1372 " --> pdb=" O ILE C1368 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1410 Proline residue: C1395 - end of helix Processing helix chain 'D' and resid 16 through 45 Processing helix chain 'D' and resid 91 through 117 Processing helix chain 'D' and resid 122 through 152 removed outlier: 3.593A pdb=" N LYS D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 176 through 199 removed outlier: 4.125A pdb=" N MET D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1148 through 1149 Processing sheet with id=AA2, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 3.954A pdb=" N LEU A1244 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A1239 " --> pdb=" O ALA A1229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1229 " --> pdb=" O GLY A1239 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1243 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1225 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1158 through 1159 removed outlier: 7.252A pdb=" N VAL A1158 " --> pdb=" O VAL A1248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1202 removed outlier: 3.564A pdb=" N GLY A1199 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1311 through 1315 removed outlier: 3.818A pdb=" N SER A1258 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1315 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A1254 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 1148 through 1149 Processing sheet with id=AA9, first strand: chain 'C' and resid 1153 through 1155 removed outlier: 3.955A pdb=" N LEU C1244 " --> pdb=" O TYR C1154 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY C1239 " --> pdb=" O ALA C1229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1229 " --> pdb=" O GLY C1239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1243 " --> pdb=" O PHE C1225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C1225 " --> pdb=" O VAL C1243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1158 through 1159 removed outlier: 7.252A pdb=" N VAL C1158 " --> pdb=" O VAL C1248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 1199 through 1202 removed outlier: 3.580A pdb=" N GLY C1199 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1311 through 1315 removed outlier: 3.819A pdb=" N SER C1258 " --> pdb=" O CYS C1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1315 " --> pdb=" O GLN C1254 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C1254 " --> pdb=" O VAL C1315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1297 through 1299 Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 60 344 hydrogen bonds defined for protein. 966 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: 0.79 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2088 1.35 - 1.47: 1769 1.47 - 1.60: 2967 1.60 - 1.72: 0 1.72 - 1.85: 70 Bond restraints: 6894 Sorted by residual: bond pdb=" CB MET D 28 " pdb=" CG MET D 28 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" CB MET B 28 " pdb=" CG MET B 28 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB TRP B 29 " pdb=" CG TRP B 29 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.82e+00 bond pdb=" CB TRP D 29 " pdb=" CG TRP D 29 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.81e+00 bond pdb=" C ILE C1394 " pdb=" N PRO C1395 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.77e+00 ... (remaining 6889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 9211 3.55 - 7.10: 113 7.10 - 10.65: 10 10.65 - 14.21: 0 14.21 - 17.76: 2 Bond angle restraints: 9336 Sorted by residual: angle pdb=" C ARG C1360 " pdb=" N THR C1361 " pdb=" CA THR C1361 " ideal model delta sigma weight residual 120.94 138.70 -17.76 1.90e+00 2.77e-01 8.73e+01 angle pdb=" C ARG A1360 " pdb=" N THR A1361 " pdb=" CA THR A1361 " ideal model delta sigma weight residual 120.94 138.36 -17.42 1.90e+00 2.77e-01 8.41e+01 angle pdb=" CA ARG B 20 " pdb=" CB ARG B 20 " pdb=" CG ARG B 20 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA ARG D 20 " pdb=" CB ARG D 20 " pdb=" CG ARG D 20 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" N SER C1374 " pdb=" CA SER C1374 " pdb=" C SER C1374 " ideal model delta sigma weight residual 108.34 113.08 -4.74 1.31e+00 5.83e-01 1.31e+01 ... (remaining 9331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.34: 3814 13.34 - 26.69: 200 26.69 - 40.03: 56 40.03 - 53.37: 10 53.37 - 66.71: 2 Dihedral angle restraints: 4082 sinusoidal: 1594 harmonic: 2488 Sorted by residual: dihedral pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " pdb=" SG CYS B 130 " pdb=" CB CYS B 130 " ideal model delta sinusoidal sigma weight residual 93.00 140.28 -47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS D 114 " pdb=" SG CYS D 114 " pdb=" SG CYS D 130 " pdb=" CB CYS D 130 " ideal model delta sinusoidal sigma weight residual 93.00 140.28 -47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CA LYS C1344 " pdb=" C LYS C1344 " pdb=" N ASP C1345 " pdb=" CA ASP C1345 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 819 0.061 - 0.122: 203 0.122 - 0.183: 40 0.183 - 0.243: 9 0.243 - 0.304: 3 Chirality restraints: 1074 Sorted by residual: chirality pdb=" CB ILE D 45 " pdb=" CA ILE D 45 " pdb=" CG1 ILE D 45 " pdb=" CG2 ILE D 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE C1388 " pdb=" CA ILE C1388 " pdb=" CG1 ILE C1388 " pdb=" CG2 ILE C1388 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1071 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 46 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO D 47 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 47 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 47 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 46 " -0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO B 47 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1347 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO C1348 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C1348 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1348 " -0.034 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1611 2.79 - 3.32: 6290 3.32 - 3.84: 11324 3.84 - 4.37: 12852 4.37 - 4.90: 20646 Nonbonded interactions: 52723 Sorted by model distance: nonbonded pdb=" OD2 ASP A1319 " pdb=" OG1 THR A1322 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C1319 " pdb=" OG1 THR C1322 " model vdw 2.264 3.040 nonbonded pdb=" O TRP D 29 " pdb=" OG1 THR D 33 " model vdw 2.322 3.040 nonbonded pdb=" O TRP B 29 " pdb=" OG1 THR B 33 " model vdw 2.323 3.040 nonbonded pdb=" OE1 GLU A1203 " pdb=" OG1 THR A1206 " model vdw 2.329 3.040 ... (remaining 52718 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 0.005 0.055 6898 Z= 0.256 Angle : 1.038 17.757 9344 Z= 0.585 Chirality : 0.059 0.304 1074 Planarity : 0.008 0.075 1160 Dihedral : 9.458 66.714 2478 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.27 % Allowed : 0.82 % Favored : 98.90 % 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: -4.44 (0.22), residues: 846 helix: -2.47 (0.20), residues: 358 sheet: -3.92 (0.33), residues: 112 loop : -3.00 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1371 TYR 0.024 0.003 TYR D 148 PHE 0.031 0.003 PHE B 100 TRP 0.020 0.004 TRP D 49 HIS 0.007 0.002 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.26 ( 6894) covalent geometry : angle 1.03575 / 0.58 ( 9336) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 2.59134 / 2.29 ( 8) hydrogen bonds : bond 0.16525 / 11.17 ( 344) hydrogen bonds : angle 7.90256 / 5.38 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 1149 PHE cc_start: 0.8145 (m-80) cc_final: 0.7934 (m-80) REVERT: A 1160 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6129 (tp30) REVERT: A 1186 TYR cc_start: 0.8093 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1203 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8336 (tm-30) REVERT: A 1240 LYS cc_start: 0.8893 (pttt) cc_final: 0.8336 (ptmt) REVERT: A 1249 ASN cc_start: 0.7587 (p0) cc_final: 0.6409 (t0) REVERT: A 1270 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8697 (pm20) REVERT: A 1271 ASP cc_start: 0.9376 (m-30) cc_final: 0.9134 (m-30) REVERT: A 1274 GLU cc_start: 0.9366 (tt0) cc_final: 0.8850 (mt-10) REVERT: A 1389 ILE cc_start: 0.9392 (mt) cc_final: 0.9080 (tt) REVERT: A 1393 CYS cc_start: 0.9577 (m) cc_final: 0.9117 (m) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0740 time to fit residues: 7.6903 Evaluate side-chains 56 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.086 Evaluate side-chains 76 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6497 (mmp80) cc_final: 0.6060 (tpt170) REVERT: B 32 LEU cc_start: 0.9639 (mt) cc_final: 0.9127 (mm) REVERT: B 66 SER cc_start: 0.8171 (p) cc_final: 0.7953 (t) REVERT: B 123 THR cc_start: 0.8842 (p) cc_final: 0.8601 (p) REVERT: B 127 TYR cc_start: 0.8919 (m-10) cc_final: 0.8577 (m-80) REVERT: B 133 MET cc_start: 0.9448 (mmp) cc_final: 0.9235 (mmm) REVERT: B 180 MET cc_start: 0.7823 (ttp) cc_final: 0.7174 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0398 time to fit residues: 3.4876 Evaluate side-chains 52 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.3980 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1254 GLN B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.062073 restraints weight = 20861.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064722 restraints weight = 11263.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066722 restraints weight = 7387.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068254 restraints weight = 5350.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069422 restraints weight = 4152.937| |-----------------------------------------------------------------------------| r_work (final): 0.3341 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095707 restraints weight = 4712.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097993 restraints weight = 3369.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099946 restraints weight = 2599.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101434 restraints weight = 2062.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.102774 restraints weight = 1677.158| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6898 Z= 0.192 Angle : 0.793 9.081 9344 Z= 0.427 Chirality : 0.049 0.183 1074 Planarity : 0.006 0.047 1160 Dihedral : 6.311 23.502 936 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.37 % Allowed : 1.37 % Favored : 97.25 % 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: -3.34 (0.26), residues: 846 helix: -1.33 (0.23), residues: 368 sheet: -3.34 (0.35), residues: 142 loop : -2.54 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1219 TYR 0.022 0.003 TYR C1308 PHE 0.045 0.002 PHE D 100 TRP 0.009 0.002 TRP B 29 HIS 0.002 0.000 HIS C1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 6894) covalent geometry : angle 0.78724 / 0.42 ( 9336) SS BOND : bond 0.01845 / 0.94 ( 4) SS BOND : angle 3.31986 / 2.39 ( 8) hydrogen bonds : bond 0.05592 / 3.71 ( 344) hydrogen bonds : angle 6.42064 / 4.40 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 PHE cc_start: 0.8255 (m-80) cc_final: 0.7955 (m-80) REVERT: A 1184 MET cc_start: 0.8428 (mmp) cc_final: 0.8114 (mmm) REVERT: A 1186 TYR cc_start: 0.7965 (m-80) cc_final: 0.7662 (m-80) REVERT: A 1203 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8455 (tm-30) REVERT: A 1267 LYS cc_start: 0.9527 (tttt) cc_final: 0.9311 (ttpp) REVERT: A 1271 ASP cc_start: 0.9381 (m-30) cc_final: 0.9044 (m-30) REVERT: A 1275 ILE cc_start: 0.9472 (mm) cc_final: 0.8894 (mm) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.0712 time to fit residues: 5.3317 Evaluate side-chains 52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.083 Evaluate side-chains 72 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6466 (mmp80) cc_final: 0.6130 (tpt170) REVERT: B 32 LEU cc_start: 0.9485 (mt) cc_final: 0.9181 (mm) REVERT: B 98 MET cc_start: 0.8945 (ttp) cc_final: 0.8681 (tmm) REVERT: B 180 MET cc_start: 0.7867 (ttp) cc_final: 0.7165 (tpp) outliers start: 3 outliers final: 0 residues processed: 70 average time/residue: 0.0398 time to fit residues: 3.2171 Evaluate side-chains 49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 0.0470 chunk 39 optimal weight: 0.0030 chunk 11 optimal weight: 0.0010 overall best weight: 0.6274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062545 restraints weight = 26678.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065544 restraints weight = 11635.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067744 restraints weight = 7006.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069366 restraints weight = 4858.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.070596 restraints weight = 3676.218| |-----------------------------------------------------------------------------| r_work (final): 0.3376 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.110995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095127 restraints weight = 4650.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097445 restraints weight = 3363.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099611 restraints weight = 2610.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101195 restraints weight = 2063.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.102355 restraints weight = 1670.249| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6898 Z= 0.174 Angle : 0.765 9.955 9344 Z= 0.408 Chirality : 0.051 0.209 1074 Planarity : 0.006 0.069 1160 Dihedral : 6.027 22.927 936 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.37 % Allowed : 3.02 % Favored : 95.60 % 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: -2.55 (0.27), residues: 846 helix: -0.74 (0.24), residues: 368 sheet: -2.62 (0.40), residues: 144 loop : -2.21 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 20 TYR 0.022 0.002 TYR B 67 PHE 0.064 0.002 PHE A1165 TRP 0.012 0.002 TRP D 29 HIS 0.001 0.000 HIS C1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 6894) covalent geometry : angle 0.75952 / 0.41 ( 9336) SS BOND : bond 0.01660 / 0.85 ( 4) SS BOND : angle 3.22944 / 2.31 ( 8) hydrogen bonds : bond 0.05178 / 3.38 ( 344) hydrogen bonds : angle 5.89454 / 4.03 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: C 1184 MET cc_start: 0.8392 (mmp) cc_final: 0.8090 (mmm) REVERT: C 1186 TYR cc_start: 0.7943 (m-80) cc_final: 0.7585 (m-80) REVERT: C 1211 THR cc_start: 0.8935 (p) cc_final: 0.8219 (t) REVERT: C 1225 PHE cc_start: 0.8863 (p90) cc_final: 0.8455 (p90) REVERT: C 1387 PHE cc_start: 0.9233 (m-80) cc_final: 0.9015 (m-80) REVERT: C 1407 PHE cc_start: 0.8571 (t80) cc_final: 0.8042 (m-80) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0594 time to fit residues: 4.0066 Evaluate side-chains 45 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.086 Evaluate side-chains 65 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6911 (mmt-90) cc_final: 0.6257 (tpt170) REVERT: B 98 MET cc_start: 0.8946 (ttp) cc_final: 0.8731 (tmm) REVERT: B 99 PHE cc_start: 0.8803 (t80) cc_final: 0.8578 (t80) REVERT: B 118 PHE cc_start: 0.6884 (t80) cc_final: 0.6496 (t80) REVERT: B 180 MET cc_start: 0.8156 (ttp) cc_final: 0.7525 (tpp) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 0.0416 time to fit residues: 3.0862 Evaluate side-chains 46 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.0050 chunk 66 optimal weight: 0.3980 chunk 60 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063396 restraints weight = 20467.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066193 restraints weight = 10214.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068184 restraints weight = 6443.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069693 restraints weight = 4589.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070861 restraints weight = 3522.045| |-----------------------------------------------------------------------------| r_work (final): 0.3381 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.112891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096563 restraints weight = 4416.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098843 restraints weight = 3286.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100901 restraints weight = 2576.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.102509 restraints weight = 2072.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.103749 restraints weight = 1692.901| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6898 Z= 0.168 Angle : 0.754 8.799 9344 Z= 0.397 Chirality : 0.050 0.204 1074 Planarity : 0.005 0.041 1160 Dihedral : 5.829 22.782 936 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.82 % Allowed : 2.75 % Favored : 96.43 % 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: -2.33 (0.26), residues: 846 helix: -0.40 (0.24), residues: 372 sheet: -2.87 (0.47), residues: 96 loop : -2.35 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1163 TYR 0.023 0.002 TYR B 67 PHE 0.026 0.002 PHE D 100 TRP 0.006 0.001 TRP D 29 HIS 0.001 0.000 HIS C1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6894) covalent geometry : angle 0.74829 / 0.39 ( 9336) SS BOND : bond 0.01690 / 0.85 ( 4) SS BOND : angle 3.17124 / 2.43 ( 8) hydrogen bonds : bond 0.04837 / 3.11 ( 344) hydrogen bonds : angle 5.50512 / 3.75 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: C 1184 MET cc_start: 0.8340 (mmp) cc_final: 0.7375 (mmp) REVERT: C 1211 THR cc_start: 0.9112 (p) cc_final: 0.8571 (t) REVERT: C 1225 PHE cc_start: 0.8559 (p90) cc_final: 0.8154 (p90) REVERT: C 1271 ASP cc_start: 0.9224 (m-30) cc_final: 0.8838 (m-30) REVERT: C 1407 PHE cc_start: 0.8549 (t80) cc_final: 0.8041 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0551 time to fit residues: 3.6144 Evaluate side-chains 41 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.084 Evaluate side-chains 67 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.6937 (mmt-90) cc_final: 0.6412 (tpt170) REVERT: B 103 LEU cc_start: 0.9375 (tt) cc_final: 0.9157 (mt) REVERT: B 113 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8955 (mp) REVERT: B 118 PHE cc_start: 0.6860 (t80) cc_final: 0.6620 (t80) REVERT: B 133 MET cc_start: 0.9312 (mmm) cc_final: 0.9092 (mmm) REVERT: B 141 LEU cc_start: 0.9418 (mt) cc_final: 0.9174 (mt) REVERT: B 180 MET cc_start: 0.8149 (ttp) cc_final: 0.7712 (tpt) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.0415 time to fit residues: 3.1639 Evaluate side-chains 51 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 53 optimal weight: 0.1980 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.0670 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061553 restraints weight = 27299.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064536 restraints weight = 12886.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066766 restraints weight = 7993.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068399 restraints weight = 5613.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069635 restraints weight = 4277.641| |-----------------------------------------------------------------------------| r_work (final): 0.3358 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100483 restraints weight = 4654.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.102933 restraints weight = 3480.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.104844 restraints weight = 2731.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.106407 restraints weight = 2199.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.107540 restraints weight = 1809.126| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6898 Z= 0.154 Angle : 0.749 8.981 9344 Z= 0.391 Chirality : 0.049 0.212 1074 Planarity : 0.005 0.041 1160 Dihedral : 5.684 22.104 936 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.55 % Allowed : 3.02 % Favored : 96.43 % 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: -2.08 (0.27), residues: 846 helix: -0.14 (0.25), residues: 364 sheet: -2.37 (0.50), residues: 96 loop : -2.34 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1371 TYR 0.017 0.002 TYR D 67 PHE 0.031 0.002 PHE B 100 TRP 0.004 0.001 TRP B 152 HIS 0.002 0.000 HIS A1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 6894) covalent geometry : angle 0.74220 / 0.39 ( 9336) SS BOND : bond 0.00942 / 0.48 ( 4) SS BOND : angle 3.46162 / 2.53 ( 8) hydrogen bonds : bond 0.04906 / 3.13 ( 344) hydrogen bonds : angle 5.25887 / 3.58 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8174 (ppp) cc_final: 0.7870 (ppp) REVERT: A 1208 LEU cc_start: 0.9064 (mt) cc_final: 0.8787 (mt) REVERT: A 1211 THR cc_start: 0.9173 (p) cc_final: 0.8769 (t) REVERT: A 1213 MET cc_start: 0.8341 (ptm) cc_final: 0.7702 (ppp) REVERT: A 1225 PHE cc_start: 0.8711 (p90) cc_final: 0.8421 (p90) REVERT: A 1270 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8827 (pm20) REVERT: A 1327 ASP cc_start: 0.9187 (t0) cc_final: 0.8872 (t70) REVERT: A 1407 PHE cc_start: 0.8509 (t80) cc_final: 0.7912 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0512 time to fit residues: 3.7504 Evaluate side-chains 47 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.088 Evaluate side-chains 65 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6570 (tpt170) REVERT: B 80 LYS cc_start: 0.8640 (pttt) cc_final: 0.7725 (tppt) REVERT: B 123 THR cc_start: 0.8972 (p) cc_final: 0.8679 (p) REVERT: B 127 TYR cc_start: 0.8729 (m-80) cc_final: 0.8491 (m-80) REVERT: B 133 MET cc_start: 0.9342 (mmm) cc_final: 0.9122 (mmm) REVERT: B 180 MET cc_start: 0.8135 (ttp) cc_final: 0.7722 (tpt) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0403 time to fit residues: 3.0442 Evaluate side-chains 49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063922 restraints weight = 9737.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065587 restraints weight = 6659.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066850 restraints weight = 5017.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067801 restraints weight = 4028.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068503 restraints weight = 3382.745| |-----------------------------------------------------------------------------| r_work (final): 0.3319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.112943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097192 restraints weight = 4384.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099781 restraints weight = 3187.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101755 restraints weight = 2436.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.103318 restraints weight = 1943.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.104650 restraints weight = 1578.648| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6898 Z= 0.183 Angle : 0.750 10.817 9344 Z= 0.395 Chirality : 0.051 0.279 1074 Planarity : 0.005 0.039 1160 Dihedral : 5.566 21.057 936 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.27 % Allowed : 1.65 % Favored : 98.08 % 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: -1.88 (0.27), residues: 846 helix: -0.03 (0.24), residues: 364 sheet: -2.27 (0.50), residues: 96 loop : -2.17 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1371 TYR 0.015 0.002 TYR D 67 PHE 0.027 0.002 PHE D 100 TRP 0.009 0.001 TRP B 29 HIS 0.002 0.001 HIS C1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 6894) covalent geometry : angle 0.73773 / 0.39 ( 9336) SS BOND : bond 0.02520 / 1.29 ( 4) SS BOND : angle 4.60304 / 3.23 ( 8) hydrogen bonds : bond 0.04964 / 3.20 ( 344) hydrogen bonds : angle 5.40791 / 3.70 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1164 MET cc_start: 0.8215 (ppp) cc_final: 0.8010 (ppp) REVERT: C 1208 LEU cc_start: 0.9028 (mt) cc_final: 0.8728 (mt) REVERT: C 1225 PHE cc_start: 0.8651 (p90) cc_final: 0.8349 (p90) REVERT: C 1270 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8749 (pm20) REVERT: C 1271 ASP cc_start: 0.9353 (m-30) cc_final: 0.9112 (m-30) REVERT: C 1407 PHE cc_start: 0.8552 (t80) cc_final: 0.7932 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0553 time to fit residues: 3.3106 Evaluate side-chains 42 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.088 Evaluate side-chains 58 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6624 (tpt170) REVERT: B 80 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7657 (tppt) REVERT: B 99 PHE cc_start: 0.9023 (t80) cc_final: 0.8802 (t80) REVERT: B 105 MET cc_start: 0.8854 (tmm) cc_final: 0.8591 (tmm) REVERT: B 180 MET cc_start: 0.8186 (ttp) cc_final: 0.7799 (tpt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0412 time to fit residues: 2.7551 Evaluate side-chains 45 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 0.0060 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1216 HIS C1281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061691 restraints weight = 30702.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064948 restraints weight = 13861.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067336 restraints weight = 8498.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069075 restraints weight = 5956.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070188 restraints weight = 4544.568| |-----------------------------------------------------------------------------| r_work (final): 0.3366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.100628 restraints weight = 4583.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.102887 restraints weight = 3504.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.104886 restraints weight = 2790.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106358 restraints weight = 2271.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107402 restraints weight = 1891.066| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6898 Z= 0.139 Angle : 0.755 11.347 9344 Z= 0.381 Chirality : 0.050 0.235 1074 Planarity : 0.004 0.039 1160 Dihedral : 5.452 18.393 936 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.27 % Allowed : 1.37 % Favored : 98.35 % 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: -1.61 (0.27), residues: 846 helix: 0.21 (0.24), residues: 376 sheet: -1.75 (0.56), residues: 82 loop : -2.24 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1371 TYR 0.018 0.002 TYR A1205 PHE 0.026 0.002 PHE D 100 TRP 0.004 0.001 TRP B 177 HIS 0.001 0.000 HIS C1216 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6894) covalent geometry : angle 0.74589 / 0.38 ( 9336) SS BOND : bond 0.00833 / 0.42 ( 4) SS BOND : angle 4.01151 / 2.83 ( 8) hydrogen bonds : bond 0.04698 / 3.03 ( 344) hydrogen bonds : angle 5.12838 / 3.47 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: C 1160 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6644 (mm-30) REVERT: C 1164 MET cc_start: 0.8505 (ppp) cc_final: 0.8302 (ppp) REVERT: C 1208 LEU cc_start: 0.9098 (mt) cc_final: 0.8815 (mt) REVERT: C 1211 THR cc_start: 0.9085 (p) cc_final: 0.8687 (t) REVERT: C 1327 ASP cc_start: 0.9257 (t0) cc_final: 0.8914 (t70) REVERT: C 1358 GLU cc_start: 0.7221 (pt0) cc_final: 0.6962 (pp20) REVERT: C 1407 PHE cc_start: 0.8517 (t80) cc_final: 0.7896 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0585 time to fit residues: 4.1148 Evaluate side-chains 44 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.091 Evaluate side-chains 57 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.6706 (tpt170) REVERT: B 99 PHE cc_start: 0.8954 (t80) cc_final: 0.8709 (t80) REVERT: B 134 GLN cc_start: 0.9118 (mp10) cc_final: 0.8535 (mp10) REVERT: B 141 LEU cc_start: 0.9418 (mt) cc_final: 0.9108 (mt) REVERT: B 180 MET cc_start: 0.8185 (ttp) cc_final: 0.7779 (tpt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0375 time to fit residues: 2.4650 Evaluate side-chains 46 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.079162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062438 restraints weight = 15758.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064830 restraints weight = 9322.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066595 restraints weight = 6421.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.067731 restraints weight = 4804.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068861 restraints weight = 3896.100| |-----------------------------------------------------------------------------| r_work (final): 0.3340 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.111020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095175 restraints weight = 4725.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096919 restraints weight = 3522.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098376 restraints weight = 2817.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099827 restraints weight = 2335.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100814 restraints weight = 1998.173| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6898 Z= 0.163 Angle : 0.754 11.185 9344 Z= 0.388 Chirality : 0.049 0.204 1074 Planarity : 0.005 0.042 1160 Dihedral : 5.468 20.331 936 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.27 % Allowed : 1.65 % Favored : 98.08 % 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: -1.63 (0.27), residues: 846 helix: 0.13 (0.24), residues: 376 sheet: -2.03 (0.49), residues: 92 loop : -2.08 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1371 TYR 0.034 0.002 TYR A1308 PHE 0.030 0.002 PHE D 100 TRP 0.005 0.001 TRP D 49 HIS 0.002 0.001 HIS D 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6894) covalent geometry : angle 0.74097 / 0.38 ( 9336) SS BOND : bond 0.01236 / 0.63 ( 4) SS BOND : angle 4.91159 / 3.60 ( 8) hydrogen bonds : bond 0.04917 / 3.18 ( 344) hydrogen bonds : angle 5.21586 / 3.54 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: C 1164 MET cc_start: 0.8492 (ppp) cc_final: 0.8292 (pmm) REVERT: C 1208 LEU cc_start: 0.9078 (mt) cc_final: 0.8743 (mt) REVERT: C 1225 PHE cc_start: 0.8855 (p90) cc_final: 0.8388 (p90) REVERT: C 1253 MET cc_start: 0.8295 (ptp) cc_final: 0.6656 (tpp) REVERT: C 1271 ASP cc_start: 0.9398 (m-30) cc_final: 0.9170 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0563 time to fit residues: 3.5755 Evaluate side-chains 39 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.082 Evaluate side-chains 52 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7266 (mmt-90) cc_final: 0.6699 (tpt170) REVERT: B 99 PHE cc_start: 0.8988 (t80) cc_final: 0.8741 (t80) REVERT: B 133 MET cc_start: 0.9073 (mtp) cc_final: 0.8295 (ttt) REVERT: B 180 MET cc_start: 0.8188 (ttp) cc_final: 0.7758 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0442 time to fit residues: 2.6411 Evaluate side-chains 49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 21 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061050 restraints weight = 30732.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064152 restraints weight = 14138.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066454 restraints weight = 8873.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068197 restraints weight = 6276.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069528 restraints weight = 4800.636| |-----------------------------------------------------------------------------| r_work (final): 0.3354 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.111800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095492 restraints weight = 4455.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097736 restraints weight = 3256.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099551 restraints weight = 2532.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100945 restraints weight = 2039.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101932 restraints weight = 1682.633| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6898 Z= 0.145 Angle : 0.755 10.864 9344 Z= 0.382 Chirality : 0.049 0.225 1074 Planarity : 0.005 0.038 1160 Dihedral : 5.461 23.423 936 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.27 % Allowed : 0.55 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.27), residues: 846 helix: 0.27 (0.25), residues: 376 sheet: -1.96 (0.47), residues: 92 loop : -2.16 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1371 TYR 0.023 0.002 TYR A1308 PHE 0.027 0.002 PHE D 100 TRP 0.009 0.001 TRP D 177 HIS 0.001 0.000 HIS C1299 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6894) covalent geometry : angle 0.74484 / 0.38 ( 9336) SS BOND : bond 0.00906 / 0.45 ( 4) SS BOND : angle 4.23228 / 3.18 ( 8) hydrogen bonds : bond 0.04643 / 3.00 ( 344) hydrogen bonds : angle 5.19622 / 3.54 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: C 1160 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6688 (mm-30) REVERT: C 1164 MET cc_start: 0.8306 (ppp) cc_final: 0.7947 (ppp) REVERT: C 1205 TYR cc_start: 0.8640 (m-80) cc_final: 0.8160 (m-10) REVERT: C 1208 LEU cc_start: 0.9119 (mt) cc_final: 0.8763 (mt) REVERT: C 1211 THR cc_start: 0.9040 (p) cc_final: 0.8395 (p) REVERT: C 1213 MET cc_start: 0.8078 (ptm) cc_final: 0.7562 (ppp) REVERT: C 1253 MET cc_start: 0.8257 (ptp) cc_final: 0.6762 (tpp) REVERT: C 1407 PHE cc_start: 0.8338 (t80) cc_final: 0.8102 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0745 time to fit residues: 4.6854 Evaluate side-chains 41 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.092 Evaluate side-chains 54 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7194 (mmt-90) cc_final: 0.6673 (tpt170) REVERT: B 99 PHE cc_start: 0.8943 (t80) cc_final: 0.8694 (t80) REVERT: B 105 MET cc_start: 0.8801 (tmm) cc_final: 0.8554 (tmm) REVERT: B 134 GLN cc_start: 0.9090 (mp10) cc_final: 0.8720 (mp10) REVERT: B 141 LEU cc_start: 0.9511 (mt) cc_final: 0.9261 (mt) REVERT: B 145 CYS cc_start: 0.8286 (t) cc_final: 0.7989 (p) REVERT: B 180 MET cc_start: 0.8249 (ttp) cc_final: 0.7819 (tpt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0356 time to fit residues: 2.2303 Evaluate side-chains 48 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 5 optimal weight: 0.0470 chunk 57 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063913 restraints weight = 16573.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066497 restraints weight = 9645.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.068487 restraints weight = 6557.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069956 restraints weight = 4898.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071093 restraints weight = 3875.455| |-----------------------------------------------------------------------------| r_work (final): 0.3393 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.112261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095819 restraints weight = 4554.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098234 restraints weight = 3334.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099942 restraints weight = 2589.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.101335 restraints weight = 2099.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102499 restraints weight = 1741.588| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6898 Z= 0.164 Angle : 0.804 11.037 9344 Z= 0.412 Chirality : 0.049 0.218 1074 Planarity : 0.005 0.038 1160 Dihedral : 5.437 22.445 936 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.27 % Allowed : 0.55 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 846 helix: 0.36 (0.25), residues: 374 sheet: -1.73 (0.47), residues: 92 loop : -2.09 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1371 TYR 0.019 0.002 TYR A1308 PHE 0.067 0.002 PHE C1165 TRP 0.011 0.001 TRP D 177 HIS 0.001 0.000 HIS D 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 6894) covalent geometry : angle 0.79081 / 0.41 ( 9336) SS BOND : bond 0.01176 / 0.59 ( 4) SS BOND : angle 4.95420 / 3.66 ( 8) hydrogen bonds : bond 0.05153 / 3.44 ( 344) hydrogen bonds : angle 5.50667 / 3.77 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: C 1160 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6601 (mm-30) REVERT: C 1205 TYR cc_start: 0.8597 (m-80) cc_final: 0.8136 (m-10) REVERT: C 1208 LEU cc_start: 0.9157 (mt) cc_final: 0.8775 (mt) REVERT: C 1211 THR cc_start: 0.8873 (p) cc_final: 0.8451 (p) REVERT: C 1213 MET cc_start: 0.8020 (ptm) cc_final: 0.7598 (ppp) REVERT: C 1253 MET cc_start: 0.8261 (ptp) cc_final: 0.7031 (mmt) REVERT: C 1358 GLU cc_start: 0.7194 (pt0) cc_final: 0.6990 (pm20) REVERT: C 1387 PHE cc_start: 0.9051 (m-80) cc_final: 0.8311 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0492 time to fit residues: 3.3822 Evaluate side-chains 44 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.086 Evaluate side-chains 50 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6714 (tpt170) REVERT: B 99 PHE cc_start: 0.8962 (t80) cc_final: 0.8715 (t80) REVERT: B 133 MET cc_start: 0.9011 (mtp) cc_final: 0.8373 (ttt) REVERT: B 141 LEU cc_start: 0.9473 (mt) cc_final: 0.9227 (mt) REVERT: B 145 CYS cc_start: 0.8221 (t) cc_final: 0.8007 (p) REVERT: B 180 MET cc_start: 0.8173 (ttp) cc_final: 0.7722 (tpt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0396 time to fit residues: 2.2649 Evaluate side-chains 48 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.0770 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.0470 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063719 restraints weight = 20695.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066827 restraints weight = 10714.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068994 restraints weight = 6927.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.070699 restraints weight = 5045.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071949 restraints weight = 3937.287| |-----------------------------------------------------------------------------| r_work (final): 0.3413 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.113669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096849 restraints weight = 4483.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099175 restraints weight = 3271.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.101184 restraints weight = 2550.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.102743 restraints weight = 2046.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.103874 restraints weight = 1697.963| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6898 Z= 0.157 Angle : 0.776 9.953 9344 Z= 0.397 Chirality : 0.049 0.235 1074 Planarity : 0.005 0.036 1160 Dihedral : 5.288 19.611 936 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % 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: -1.30 (0.27), residues: 846 helix: 0.48 (0.25), residues: 374 sheet: -1.57 (0.49), residues: 92 loop : -2.07 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1371 TYR 0.015 0.001 TYR C1308 PHE 0.053 0.002 PHE A1165 TRP 0.008 0.001 TRP B 29 HIS 0.001 0.000 HIS A1299 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 6894) covalent geometry : angle 0.76608 / 0.39 ( 9336) SS BOND : bond 0.00732 / 0.36 ( 4) SS BOND : angle 4.37479 / 3.24 ( 8) hydrogen bonds : bond 0.05093 / 3.38 ( 344) hydrogen bonds : angle 5.31914 / 3.68 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.59 seconds wall clock time: 18 minutes 16.30 seconds (1096.30 seconds total)