Starting phenix.real_space_refine on Fri Sep 11 02:42:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpw_4616/09_2026/6qpw_4616.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4260 2.51 5 N 1187 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 6784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1486 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "C" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2987 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 7, 'TRANS': 369} Chain breaks: 2 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1610 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.71, per 1000 atoms: 0.25 Number of scatterers: 6784 At special positions: 0 Unit cell: (128.79, 103.68, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 6 15.00 Mg 2 11.99 O 1305 8.00 N 1187 7.00 C 4260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C1159 " - pdb=" SG CYS E1201 " distance=2.04 Simple disulfide: pdb=" SG CYS C1204 " - pdb=" SG CYS E1160 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 493.5 milliseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 48.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.718A pdb=" N LEU A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.822A pdb=" N LEU A 65 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.828A pdb=" N GLU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 204 through 234 Processing helix chain 'B' and resid 484 through 499 removed outlier: 4.046A pdb=" N GLU B 498 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 520 through 537 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.577A pdb=" N PHE B 560 " --> pdb=" O PRO B 557 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 561 " --> pdb=" O ALA B 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 561' Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 124 through 134 removed outlier: 4.052A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 176 through 204 removed outlier: 4.663A pdb=" N GLN C 195 " --> pdb=" O GLN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1060 removed outlier: 3.760A pdb=" N SER C1043 " --> pdb=" O ASN C1039 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C1050 " --> pdb=" O GLN C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1143 Processing helix chain 'C' and resid 1161 through 1176 Processing helix chain 'C' and resid 1187 through 1191 removed outlier: 3.978A pdb=" N MET C1190 " --> pdb=" O ARG C1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1221 Processing helix chain 'E' and resid 1070 through 1126 removed outlier: 3.970A pdb=" N ALA E1109 " --> pdb=" O LEU E1105 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR E1118 " --> pdb=" O GLN E1114 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS E1119 " --> pdb=" O GLU E1115 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1150 Processing helix chain 'E' and resid 1165 through 1169 removed outlier: 3.744A pdb=" N HIS E1168 " --> pdb=" O ASP E1165 " (cutoff:3.500A) Processing helix chain 'E' and resid 1170 through 1187 Processing helix chain 'E' and resid 1204 through 1219 removed outlier: 3.511A pdb=" N GLU E1217 " --> pdb=" O LYS E1213 " (cutoff:3.500A) Processing helix chain 'E' and resid 1231 through 1236 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 6.953A pdb=" N VAL A 122 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 7 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET A 120 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 9 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP A 118 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 145 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.496A pdb=" N PHE E1194 " --> pdb=" O ILE E1226 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE E1228 " --> pdb=" O PHE E1194 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU E1196 " --> pdb=" O ILE E1228 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 28 " --> pdb=" O SER E1240 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E1242 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 30 " --> pdb=" O ILE E1242 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL E1244 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 32 " --> pdb=" O VAL E1244 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ARG E1246 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 501 through 503 Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.587A pdb=" N VAL C 81 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 6 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU C 79 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 8 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 77 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1150 through 1154 removed outlier: 5.820A pdb=" N TYR C1151 " --> pdb=" O ILE C1182 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C1184 " --> pdb=" O TYR C1151 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE C1153 " --> pdb=" O THR C1184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C1196 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C1208 " --> pdb=" O LYS C1201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1135 through 1140 348 hydrogen bonds defined for protein. 996 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: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 2313 1.37 - 1.52: 2354 1.52 - 1.66: 2181 1.66 - 1.81: 36 1.81 - 1.96: 3 Bond restraints: 6887 Sorted by residual: bond pdb=" C LEU C 91 " pdb=" N PRO C 92 " ideal model delta sigma weight residual 1.335 1.370 -0.034 1.30e-02 5.92e+03 6.97e+00 bond pdb=" CA THR B 514 " pdb=" CB THR B 514 " ideal model delta sigma weight residual 1.533 1.564 -0.031 1.82e-02 3.02e+03 2.96e+00 bond pdb=" N ASN C 119 " pdb=" CA ASN C 119 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.23e+00 bond pdb=" CG1 ILE E1113 " pdb=" CD1 ILE E1113 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C PRO E1190 " pdb=" N SER E1191 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.47e-02 4.63e+03 1.64e+00 ... (remaining 6882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 9003 2.56 - 5.11: 230 5.11 - 7.67: 24 7.67 - 10.23: 5 10.23 - 12.78: 4 Bond angle restraints: 9266 Sorted by residual: angle pdb=" N ALA C1141 " pdb=" CA ALA C1141 " pdb=" C ALA C1141 " ideal model delta sigma weight residual 113.12 105.66 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" CA CYS E1160 " pdb=" CB CYS E1160 " pdb=" SG CYS E1160 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" CA CYS C1204 " pdb=" CB CYS C1204 " pdb=" SG CYS C1204 " ideal model delta sigma weight residual 114.40 123.56 -9.16 2.30e+00 1.89e-01 1.58e+01 angle pdb=" N PHE A 12 " pdb=" CA PHE A 12 " pdb=" C PHE A 12 " ideal model delta sigma weight residual 110.53 105.83 4.70 1.29e+00 6.01e-01 1.33e+01 angle pdb=" C GLU C1203 " pdb=" N CYS C1204 " pdb=" CA CYS C1204 " ideal model delta sigma weight residual 122.06 115.41 6.65 1.86e+00 2.89e-01 1.28e+01 ... (remaining 9261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.50: 3725 18.50 - 36.99: 386 36.99 - 55.49: 81 55.49 - 73.98: 15 73.98 - 92.48: 8 Dihedral angle restraints: 4215 sinusoidal: 1769 harmonic: 2446 Sorted by residual: dihedral pdb=" CB CYS C1159 " pdb=" SG CYS C1159 " pdb=" SG CYS E1201 " pdb=" CB CYS E1201 " ideal model delta sinusoidal sigma weight residual -86.00 -21.71 -64.29 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA PHE A 12 " pdb=" C PHE A 12 " pdb=" N LYS A 13 " pdb=" CA LYS A 13 " ideal model delta harmonic sigma weight residual 180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CB CYS C1204 " pdb=" SG CYS C1204 " pdb=" SG CYS E1160 " pdb=" CB CYS E1160 " ideal model delta sinusoidal sigma weight residual -86.00 -41.47 -44.53 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 4212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 675 0.046 - 0.093: 239 0.093 - 0.139: 88 0.139 - 0.186: 25 0.186 - 0.232: 7 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CB ILE C1221 " pdb=" CA ILE C1221 " pdb=" CG1 ILE C1221 " pdb=" CG2 ILE C1221 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA CYS C1204 " pdb=" N CYS C1204 " pdb=" C CYS C1204 " pdb=" CB CYS C1204 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE E1185 " pdb=" CA ILE E1185 " pdb=" CG1 ILE E1185 " pdb=" CG2 ILE E1185 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1031 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 493 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ARG B 493 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG B 493 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B 494 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E1158 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO E1159 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E1159 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E1159 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E1235 " -0.020 2.00e-02 2.50e+03 1.91e-02 6.38e+00 pdb=" CG PHE E1235 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E1235 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E1235 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE E1235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E1235 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E1235 " 0.000 2.00e-02 2.50e+03 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 143 2.68 - 3.23: 6111 3.23 - 3.79: 10669 3.79 - 4.34: 14120 4.34 - 4.90: 22982 Nonbonded interactions: 54025 Sorted by model distance: nonbonded pdb="MG MG E1301 " pdb=" O3B AGS E1302 " model vdw 2.122 2.170 nonbonded pdb=" OE1 GLN A 177 " pdb="MG MG A 301 " model vdw 2.180 2.170 nonbonded pdb="MG MG A 301 " pdb=" O3B AGS A 302 " model vdw 2.185 2.170 nonbonded pdb=" OG SER A 199 " pdb=" O LEU E1105 " model vdw 2.275 3.040 nonbonded pdb=" O1B AGS E1302 " pdb=" O2G AGS E1302 " model vdw 2.303 3.040 ... (remaining 54020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 0.050 6891 Z= 0.256 Angle : 1.000 12.782 9270 Z= 0.561 Chirality : 0.058 0.232 1034 Planarity : 0.006 0.070 1191 Dihedral : 16.013 92.477 2619 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.14 % Allowed : 11.75 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.55 (0.24), residues: 823 helix: -2.36 (0.19), residues: 390 sheet: -0.73 (0.44), residues: 125 loop : -2.85 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 135 TYR 0.018 0.002 TYR A 157 PHE 0.043 0.003 PHE E1235 TRP 0.014 0.003 TRP A 118 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 ( 6887) covalent geometry : angle 0.99492 / 0.56 ( 9266) SS BOND : bond 0.00606 / 0.35 ( 2) SS BOND : angle 4.79258 / 2.59 ( 4) hydrogen bonds : bond 0.12497 / 8.48 ( 348) hydrogen bonds : angle 6.37891 / 4.36 ( 996) Misc. bond : bond 0.00257 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8462 (m) cc_final: 0.8144 (m) REVERT: A 186 GLN cc_start: 0.8483 (mt0) cc_final: 0.8149 (mt0) REVERT: A 193 ARG cc_start: 0.7032 (tpt-90) cc_final: 0.6655 (ttp-110) REVERT: C 1034 LYS cc_start: 0.4682 (mttt) cc_final: 0.4249 (ptmt) REVERT: C 1037 LYS cc_start: 0.7486 (tmmt) cc_final: 0.7285 (pttp) REVERT: E 1216 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7651 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1120 time to fit residues: 25.4718 Evaluate side-chains 102 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 227 GLN B 513 ASN C 197 ASN C1125 GLN E1076 GLN E1248 GLN E1265 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.192620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.151501 restraints weight = 8876.007| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.83 r_work: 0.3870 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6891 Z= 0.169 Angle : 0.683 10.972 9270 Z= 0.363 Chirality : 0.046 0.193 1034 Planarity : 0.005 0.053 1191 Dihedral : 7.532 93.062 924 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.78 % Allowed : 18.58 % Favored : 79.64 % 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: -1.99 (0.27), residues: 823 helix: -0.62 (0.24), residues: 387 sheet: -0.52 (0.45), residues: 122 loop : -2.49 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 522 TYR 0.013 0.002 TYR C 2 PHE 0.026 0.002 PHE E1235 TRP 0.006 0.001 TRP A 133 HIS 0.004 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6887) covalent geometry : angle 0.67722 / 0.36 ( 9266) SS BOND : bond 0.00341 / 0.20 ( 2) SS BOND : angle 4.22239 / 2.25 ( 4) hydrogen bonds : bond 0.04295 / 2.85 ( 348) hydrogen bonds : angle 5.14836 / 3.52 ( 996) Misc. bond : bond 0.00183 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7442 (tpt-90) cc_final: 0.6794 (ttp-110) REVERT: B 515 GLU cc_start: 0.8031 (pm20) cc_final: 0.7536 (pt0) REVERT: C 1034 LYS cc_start: 0.4821 (mttt) cc_final: 0.4205 (ptmt) REVERT: C 1214 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.6141 (tpp-160) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 0.0998 time to fit residues: 15.3599 Evaluate side-chains 102 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS C1130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.190245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151176 restraints weight = 8800.493| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.60 r_work: 0.3871 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6891 Z= 0.170 Angle : 0.621 7.588 9270 Z= 0.331 Chirality : 0.045 0.139 1034 Planarity : 0.004 0.042 1191 Dihedral : 7.283 96.102 924 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.69 % Allowed : 18.99 % Favored : 77.32 % 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: -1.43 (0.28), residues: 823 helix: 0.05 (0.25), residues: 386 sheet: -0.84 (0.44), residues: 139 loop : -2.28 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1058 TYR 0.016 0.002 TYR C 2 PHE 0.028 0.002 PHE E1235 TRP 0.007 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6887) covalent geometry : angle 0.62012 / 0.33 ( 9266) SS BOND : bond 0.00168 / 0.10 ( 2) SS BOND : angle 1.76296 / 0.86 ( 4) hydrogen bonds : bond 0.04055 / 2.68 ( 348) hydrogen bonds : angle 4.90398 / 3.36 ( 996) Misc. bond : bond 0.00223 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.6900 (ttp-110) REVERT: B 515 GLU cc_start: 0.8072 (pm20) cc_final: 0.7648 (pt0) REVERT: C 30 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8444 (mp) REVERT: C 1064 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7295 (p) REVERT: C 1134 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6592 (m) REVERT: C 1214 ARG cc_start: 0.6278 (tpp-160) cc_final: 0.6074 (tpp-160) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.0913 time to fit residues: 14.6811 Evaluate side-chains 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1096 GLN Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1160 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.187594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.146020 restraints weight = 8962.161| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.90 r_work: 0.3860 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6891 Z= 0.157 Angle : 0.621 9.615 9270 Z= 0.329 Chirality : 0.044 0.156 1034 Planarity : 0.004 0.039 1191 Dihedral : 7.238 96.502 924 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.83 % Allowed : 20.36 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.13 (0.29), residues: 823 helix: 0.34 (0.25), residues: 383 sheet: -0.64 (0.44), residues: 142 loop : -2.21 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.015 0.002 TYR C 2 PHE 0.027 0.002 PHE E1235 TRP 0.009 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 6887) covalent geometry : angle 0.61863 / 0.33 ( 9266) SS BOND : bond 0.00478 / 0.30 ( 2) SS BOND : angle 2.70208 / 1.13 ( 4) hydrogen bonds : bond 0.03876 / 2.59 ( 348) hydrogen bonds : angle 4.80666 / 3.30 ( 996) Misc. bond : bond 0.00179 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7664 (ttt) REVERT: A 193 ARG cc_start: 0.7438 (tpt-90) cc_final: 0.6797 (ttp-110) REVERT: A 202 LEU cc_start: 0.7618 (tp) cc_final: 0.7353 (tp) REVERT: B 515 GLU cc_start: 0.8161 (pm20) cc_final: 0.7641 (pt0) REVERT: C 30 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (mp) REVERT: C 164 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7215 (tm-30) REVERT: C 1064 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7409 (p) REVERT: C 1134 CYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6569 (m) REVERT: C 1214 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6206 (tpp-160) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.1013 time to fit residues: 15.9788 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1160 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.190007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150319 restraints weight = 9001.548| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.64 r_work: 0.3860 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6891 Z= 0.162 Angle : 0.594 7.427 9270 Z= 0.318 Chirality : 0.044 0.157 1034 Planarity : 0.003 0.036 1191 Dihedral : 7.146 96.450 924 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.83 % Allowed : 22.54 % Favored : 73.63 % 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: -1.00 (0.29), residues: 823 helix: 0.49 (0.26), residues: 382 sheet: -0.67 (0.44), residues: 146 loop : -2.15 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.013 0.002 TYR C 2 PHE 0.027 0.002 PHE E1235 TRP 0.009 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6887) covalent geometry : angle 0.59333 / 0.32 ( 9266) SS BOND : bond 0.00331 / 0.20 ( 2) SS BOND : angle 1.68999 / 0.77 ( 4) hydrogen bonds : bond 0.03759 / 2.52 ( 348) hydrogen bonds : angle 4.66666 / 3.22 ( 996) Misc. bond : bond 0.00198 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7698 (ttt) REVERT: A 193 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.6865 (ttp-110) REVERT: A 202 LEU cc_start: 0.7640 (tp) cc_final: 0.7430 (tp) REVERT: B 515 GLU cc_start: 0.8091 (pm20) cc_final: 0.7534 (pt0) REVERT: C 30 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (mp) REVERT: C 164 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7240 (tm-30) REVERT: C 1064 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7526 (p) REVERT: C 1134 CYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6592 (m) REVERT: C 1175 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (mp) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 0.0892 time to fit residues: 14.5686 Evaluate side-chains 120 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.188168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.147651 restraints weight = 9040.387| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.79 r_work: 0.3829 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6891 Z= 0.180 Angle : 0.612 7.257 9270 Z= 0.327 Chirality : 0.044 0.156 1034 Planarity : 0.004 0.037 1191 Dihedral : 7.138 96.024 924 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.78 % Allowed : 22.40 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.89 (0.29), residues: 823 helix: 0.63 (0.26), residues: 381 sheet: -0.71 (0.46), residues: 139 loop : -2.11 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1165 TYR 0.014 0.002 TYR C 2 PHE 0.026 0.002 PHE E1235 TRP 0.009 0.002 TRP A 118 HIS 0.004 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6887) covalent geometry : angle 0.61152 / 0.33 ( 9266) SS BOND : bond 0.00380 / 0.23 ( 2) SS BOND : angle 1.45697 / 0.70 ( 4) hydrogen bonds : bond 0.03778 / 2.54 ( 348) hydrogen bonds : angle 4.73199 / 3.25 ( 996) Misc. bond : bond 0.00222 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7544 (ttt) REVERT: A 193 ARG cc_start: 0.7560 (tpt-90) cc_final: 0.6886 (ttp-110) REVERT: A 202 LEU cc_start: 0.7659 (tp) cc_final: 0.7420 (tp) REVERT: A 212 GLU cc_start: 0.8112 (tt0) cc_final: 0.7196 (tp30) REVERT: B 515 GLU cc_start: 0.8188 (pm20) cc_final: 0.7624 (pt0) REVERT: C 30 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 164 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7371 (tm-30) REVERT: C 168 ASP cc_start: 0.8435 (m-30) cc_final: 0.7915 (m-30) REVERT: C 1064 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7604 (p) REVERT: C 1134 CYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6577 (m) REVERT: C 1175 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 1214 ARG cc_start: 0.7020 (tpp-160) cc_final: 0.6451 (tpm170) REVERT: E 1197 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6518 (m-30) outliers start: 35 outliers final: 23 residues processed: 122 average time/residue: 0.0870 time to fit residues: 14.2506 Evaluate side-chains 124 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 ASN C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.188818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148527 restraints weight = 8841.072| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.76 r_work: 0.3838 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6891 Z= 0.152 Angle : 0.586 7.446 9270 Z= 0.316 Chirality : 0.043 0.150 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.040 96.740 924 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.83 % Allowed : 24.18 % Favored : 71.99 % 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: -0.80 (0.29), residues: 823 helix: 0.73 (0.26), residues: 381 sheet: -0.75 (0.46), residues: 137 loop : -2.02 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.011 0.002 TYR C 2 PHE 0.026 0.002 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6887) covalent geometry : angle 0.58504 / 0.32 ( 9266) SS BOND : bond 0.00376 / 0.23 ( 2) SS BOND : angle 1.42560 / 0.69 ( 4) hydrogen bonds : bond 0.03666 / 2.46 ( 348) hydrogen bonds : angle 4.61154 / 3.17 ( 996) Misc. bond : bond 0.00179 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7511 (ttt) REVERT: A 193 ARG cc_start: 0.7554 (tpt-90) cc_final: 0.6895 (ttp-110) REVERT: A 202 LEU cc_start: 0.7566 (tp) cc_final: 0.7330 (tp) REVERT: A 212 GLU cc_start: 0.8065 (tt0) cc_final: 0.7171 (tp30) REVERT: A 214 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7886 (mp0) REVERT: B 515 GLU cc_start: 0.8198 (pm20) cc_final: 0.7659 (pt0) REVERT: C 30 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 164 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7370 (tm-30) REVERT: C 168 ASP cc_start: 0.8432 (m-30) cc_final: 0.7910 (m-30) REVERT: C 200 MET cc_start: -0.1313 (ptp) cc_final: -0.1597 (ttp) REVERT: C 1130 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: C 1134 CYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6615 (m) REVERT: C 1175 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7831 (mp) REVERT: C 1214 ARG cc_start: 0.6828 (tpp-160) cc_final: 0.6299 (tpm170) outliers start: 28 outliers final: 20 residues processed: 120 average time/residue: 0.0853 time to fit residues: 13.8834 Evaluate side-chains 122 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1130 GLN Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.190015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149450 restraints weight = 9039.038| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.79 r_work: 0.3851 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6891 Z= 0.139 Angle : 0.585 7.388 9270 Z= 0.314 Chirality : 0.043 0.149 1034 Planarity : 0.003 0.035 1191 Dihedral : 6.960 97.167 924 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.10 % Allowed : 24.32 % Favored : 71.58 % 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: -0.69 (0.29), residues: 823 helix: 0.83 (0.26), residues: 382 sheet: -0.65 (0.46), residues: 137 loop : -2.03 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.010 0.002 TYR E1137 PHE 0.026 0.001 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6887) covalent geometry : angle 0.58428 / 0.31 ( 9266) SS BOND : bond 0.00412 / 0.25 ( 2) SS BOND : angle 1.35979 / 0.66 ( 4) hydrogen bonds : bond 0.03567 / 2.39 ( 348) hydrogen bonds : angle 4.56227 / 3.14 ( 996) Misc. bond : bond 0.00158 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: A 193 ARG cc_start: 0.7519 (tpt-90) cc_final: 0.6899 (ttp-110) REVERT: A 202 LEU cc_start: 0.7516 (tp) cc_final: 0.7284 (tp) REVERT: B 515 GLU cc_start: 0.8163 (pm20) cc_final: 0.7665 (pt0) REVERT: C 30 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 164 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7408 (tm-30) REVERT: C 168 ASP cc_start: 0.8416 (m-30) cc_final: 0.7770 (m-30) REVERT: C 200 MET cc_start: -0.1321 (ptp) cc_final: -0.1621 (ttp) REVERT: C 1114 ASN cc_start: 0.7802 (p0) cc_final: 0.7349 (p0) REVERT: C 1134 CYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6599 (m) REVERT: C 1175 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7813 (mp) REVERT: C 1214 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6181 (tpm170) outliers start: 30 outliers final: 22 residues processed: 122 average time/residue: 0.0857 time to fit residues: 14.2140 Evaluate side-chains 124 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.189276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149128 restraints weight = 8973.052| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.78 r_work: 0.3840 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6891 Z= 0.151 Angle : 0.610 9.729 9270 Z= 0.324 Chirality : 0.045 0.204 1034 Planarity : 0.003 0.035 1191 Dihedral : 6.909 96.269 924 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.96 % Allowed : 25.41 % Favored : 70.63 % 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: -0.65 (0.29), residues: 823 helix: 0.88 (0.26), residues: 382 sheet: -0.64 (0.46), residues: 137 loop : -2.03 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.011 0.002 TYR C 2 PHE 0.026 0.002 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6887) covalent geometry : angle 0.60972 / 0.32 ( 9266) SS BOND : bond 0.00421 / 0.25 ( 2) SS BOND : angle 1.40541 / 0.68 ( 4) hydrogen bonds : bond 0.03611 / 2.42 ( 348) hydrogen bonds : angle 4.51888 / 3.10 ( 996) Misc. bond : bond 0.00191 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7603 (ttt) REVERT: A 193 ARG cc_start: 0.7534 (tpt-90) cc_final: 0.6893 (ttp-110) REVERT: A 202 LEU cc_start: 0.7532 (tp) cc_final: 0.7300 (tp) REVERT: B 515 GLU cc_start: 0.8131 (pm20) cc_final: 0.7634 (pt0) REVERT: C 30 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 102 GLU cc_start: 0.3911 (OUTLIER) cc_final: 0.3640 (pm20) REVERT: C 164 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7407 (tm-30) REVERT: C 168 ASP cc_start: 0.8405 (m-30) cc_final: 0.7797 (m-30) REVERT: C 1114 ASN cc_start: 0.7836 (p0) cc_final: 0.7390 (p0) REVERT: C 1134 CYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6600 (m) REVERT: C 1175 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7819 (mp) REVERT: C 1214 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6098 (tpm170) outliers start: 29 outliers final: 21 residues processed: 119 average time/residue: 0.0925 time to fit residues: 14.6721 Evaluate side-chains 121 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.186394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147550 restraints weight = 8991.685| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.58 r_work: 0.3826 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6891 Z= 0.180 Angle : 0.632 10.137 9270 Z= 0.336 Chirality : 0.045 0.196 1034 Planarity : 0.004 0.035 1191 Dihedral : 6.973 96.004 924 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.55 % Allowed : 25.96 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.29), residues: 823 helix: 0.86 (0.26), residues: 382 sheet: -0.71 (0.45), residues: 138 loop : -2.07 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.012 0.002 TYR C 2 PHE 0.027 0.002 PHE E1235 TRP 0.009 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6887) covalent geometry : angle 0.63104 / 0.34 ( 9266) SS BOND : bond 0.00467 / 0.27 ( 2) SS BOND : angle 1.53053 / 0.78 ( 4) hydrogen bonds : bond 0.03694 / 2.48 ( 348) hydrogen bonds : angle 4.55545 / 3.13 ( 996) Misc. bond : bond 0.00214 / 0.12 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7707 (ttt) REVERT: A 193 ARG cc_start: 0.7599 (tpt-90) cc_final: 0.7000 (ttp-110) REVERT: A 202 LEU cc_start: 0.7617 (tp) cc_final: 0.7382 (tp) REVERT: B 515 GLU cc_start: 0.8127 (pm20) cc_final: 0.7681 (pt0) REVERT: C 30 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8396 (mp) REVERT: C 57 LYS cc_start: 0.6352 (pttp) cc_final: 0.6146 (mptt) REVERT: C 164 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7473 (tm-30) REVERT: C 168 ASP cc_start: 0.8434 (m-30) cc_final: 0.7806 (m-30) REVERT: C 200 MET cc_start: -0.1564 (ptp) cc_final: -0.1766 (ttp) REVERT: C 1114 ASN cc_start: 0.7860 (p0) cc_final: 0.7455 (p0) REVERT: C 1134 CYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6637 (m) REVERT: C 1175 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7883 (mp) outliers start: 26 outliers final: 20 residues processed: 113 average time/residue: 0.0828 time to fit residues: 12.6514 Evaluate side-chains 121 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1134 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.0040 chunk 60 optimal weight: 0.0470 chunk 32 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.1688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.192858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153204 restraints weight = 8862.435| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.74 r_work: 0.3898 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6891 Z= 0.114 Angle : 0.584 10.246 9270 Z= 0.312 Chirality : 0.043 0.191 1034 Planarity : 0.003 0.035 1191 Dihedral : 6.713 99.763 924 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.60 % Allowed : 27.46 % Favored : 69.95 % 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: -0.44 (0.30), residues: 823 helix: 1.06 (0.26), residues: 384 sheet: -0.40 (0.46), residues: 137 loop : -2.03 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1126 TYR 0.009 0.001 TYR C 116 PHE 0.023 0.001 PHE E1235 TRP 0.013 0.002 TRP A 118 HIS 0.004 0.001 HIS E1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6887) covalent geometry : angle 0.58373 / 0.31 ( 9266) SS BOND : bond 0.00428 / 0.26 ( 2) SS BOND : angle 1.26716 / 0.58 ( 4) hydrogen bonds : bond 0.03362 / 2.24 ( 348) hydrogen bonds : angle 4.36187 / 2.99 ( 996) Misc. bond : bond 0.00081 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1904.23 seconds wall clock time: 33 minutes 25.15 seconds (2005.15 seconds total)