Starting phenix.real_space_refine on Tue Mar 3 16:13:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qpw_4616/03_2026/6qpw_4616.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpw_4616/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qpw_4616/03_2026/6qpw_4616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpw_4616/03_2026/6qpw_4616.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpw_4616/03_2026/6qpw_4616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpw_4616/03_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-dev-5986/lib/python3.9/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: 0.68 Conformation dependent library (CDL) restraints added in 255.1 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: 0.18 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: 0.93 Time building geometry restraints manager: 0.87 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: 3739 18.50 - 36.99: 388 36.99 - 55.49: 87 55.49 - 73.98: 15 73.98 - 92.48: 8 Dihedral angle restraints: 4237 sinusoidal: 1791 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 4234 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.860 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 16.131 92.477 2641 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 covalent geometry : bond 0.00540 ( 6887) covalent geometry : angle 0.99492 ( 9266) SS BOND : bond 0.00606 ( 2) SS BOND : angle 4.79258 ( 4) hydrogen bonds : bond 0.12497 ( 348) hydrogen bonds : angle 6.37891 ( 996) Misc. bond : bond 0.00257 ( 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 : 0.228 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: 0.1158 time to fit residues: 26.1030 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 : 0.280 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.192645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.151493 restraints weight = 8869.214| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.83 r_work: 0.3880 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1892 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= 0.169 Angle : 0.686 11.206 9270 Z= 0.367 Chirality : 0.046 0.183 1034 Planarity : 0.004 0.052 1191 Dihedral : 8.224 94.335 946 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.05 % Allowed : 18.58 % Favored : 79.37 % 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: -2.02 (0.26), residues: 823 helix: -0.64 (0.24), residues: 387 sheet: -0.54 (0.45), residues: 122 loop : -2.50 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1126 TYR 0.012 0.002 TYR C 2 PHE 0.026 0.002 PHE E1235 TRP 0.006 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6887) covalent geometry : angle 0.68048 ( 9266) SS BOND : bond 0.00333 ( 2) SS BOND : angle 4.05394 ( 4) hydrogen bonds : bond 0.04320 ( 348) hydrogen bonds : angle 5.15200 ( 996) Misc. bond : bond 0.00170 ( 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 125 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7392 (tpt-90) cc_final: 0.6758 (ttp-110) REVERT: B 515 GLU cc_start: 0.8049 (pm20) cc_final: 0.7523 (pt0) REVERT: C 1034 LYS cc_start: 0.4797 (mttt) cc_final: 0.4156 (ptmt) REVERT: C 1214 ARG cc_start: 0.6366 (tpp-160) cc_final: 0.6158 (tpp-160) outliers start: 15 outliers final: 6 residues processed: 119 average time/residue: 0.0951 time to fit residues: 14.5541 Evaluate side-chains 102 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 74 MET 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: 0.2980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN C1130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.186797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148110 restraints weight = 8900.776| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.58 r_work: 0.3837 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6891 Z= 0.232 Angle : 0.689 9.127 9270 Z= 0.363 Chirality : 0.047 0.144 1034 Planarity : 0.004 0.043 1191 Dihedral : 8.024 95.711 946 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.10 % Allowed : 19.81 % Favored : 76.09 % 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 (0.28), residues: 823 helix: -0.10 (0.25), residues: 386 sheet: -0.96 (0.43), residues: 139 loop : -2.33 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1058 TYR 0.019 0.002 TYR C 2 PHE 0.029 0.002 PHE E1235 TRP 0.007 0.002 TRP A 118 HIS 0.006 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6887) covalent geometry : angle 0.68896 ( 9266) SS BOND : bond 0.00460 ( 2) SS BOND : angle 1.36754 ( 4) hydrogen bonds : bond 0.04328 ( 348) hydrogen bonds : angle 5.05073 ( 996) Misc. bond : bond 0.00291 ( 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: 30 poor density : 102 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7531 (tpt-90) cc_final: 0.6957 (ttp-110) REVERT: B 515 GLU cc_start: 0.8051 (pm20) cc_final: 0.7635 (pt0) REVERT: C 30 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 164 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7343 (tm-30) REVERT: C 1064 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7408 (p) REVERT: C 1134 CYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6724 (m) outliers start: 30 outliers final: 17 residues processed: 120 average time/residue: 0.0842 time to fit residues: 13.3672 Evaluate side-chains 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 B residue 505 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 1064 THR 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 Chi-restraints excluded: chain E residue 1226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.3980 chunk 9 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 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 = 0.4460 r_free = 0.4460 target = 0.191415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150424 restraints weight = 8889.049| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.82 r_work: 0.3868 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6891 Z= 0.136 Angle : 0.606 7.332 9270 Z= 0.324 Chirality : 0.044 0.172 1034 Planarity : 0.004 0.039 1191 Dihedral : 7.698 98.681 946 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.55 % Allowed : 21.04 % Favored : 75.41 % 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: -1.18 (0.28), residues: 823 helix: 0.33 (0.25), residues: 382 sheet: -0.75 (0.45), residues: 137 loop : -2.21 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.013 0.001 TYR C 2 PHE 0.027 0.001 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6887) covalent geometry : angle 0.60286 ( 9266) SS BOND : bond 0.01092 ( 2) SS BOND : angle 2.84862 ( 4) hydrogen bonds : bond 0.03845 ( 348) hydrogen bonds : angle 4.82871 ( 996) Misc. bond : bond 0.00129 ( 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 137 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7643 (ttt) REVERT: A 62 LEU cc_start: 0.8634 (tp) cc_final: 0.8254 (tt) REVERT: A 193 ARG cc_start: 0.7481 (tpt-90) cc_final: 0.6798 (ttp-110) REVERT: A 202 LEU cc_start: 0.7648 (tp) cc_final: 0.7395 (tp) REVERT: B 515 GLU cc_start: 0.8156 (pm20) cc_final: 0.7635 (pt0) REVERT: C 30 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 164 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7266 (tm-30) REVERT: C 1064 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (p) REVERT: C 1134 CYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6534 (m) outliers start: 26 outliers final: 15 residues processed: 127 average time/residue: 0.0843 time to fit residues: 14.3317 Evaluate side-chains 119 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 197 GLN C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148239 restraints weight = 9046.839| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.66 r_work: 0.3843 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6891 Z= 0.181 Angle : 0.622 7.420 9270 Z= 0.330 Chirality : 0.045 0.161 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.624 97.004 946 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.96 % Allowed : 23.09 % Favored : 72.95 % 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: -1.07 (0.29), residues: 823 helix: 0.42 (0.26), residues: 382 sheet: -0.69 (0.46), residues: 137 loop : -2.16 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.013 0.002 TYR C 2 PHE 0.026 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 covalent geometry : bond 0.00424 ( 6887) covalent geometry : angle 0.62160 ( 9266) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.64026 ( 4) hydrogen bonds : bond 0.03884 ( 348) hydrogen bonds : angle 4.76494 ( 996) Misc. bond : bond 0.00219 ( 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 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7708 (ttt) REVERT: A 62 LEU cc_start: 0.8640 (tp) cc_final: 0.8290 (tt) REVERT: A 140 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7471 (p0) REVERT: A 193 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.6977 (ttp-110) REVERT: A 202 LEU cc_start: 0.7743 (tp) cc_final: 0.7487 (tp) REVERT: B 515 GLU cc_start: 0.8082 (pm20) cc_final: 0.7585 (pt0) REVERT: C 30 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 164 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7371 (tm-30) REVERT: C 1064 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7514 (p) REVERT: C 1134 CYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6666 (m) outliers start: 29 outliers final: 18 residues processed: 121 average time/residue: 0.0968 time to fit residues: 15.4126 Evaluate side-chains 120 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 140 ASN Chi-restraints excluded: chain A residue 161 LEU 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 93 SER 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 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 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: 0.7980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 156 GLN C1130 GLN ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.187278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147634 restraints weight = 9056.715| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.64 r_work: 0.3834 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6891 Z= 0.182 Angle : 0.620 7.458 9270 Z= 0.330 Chirality : 0.045 0.154 1034 Planarity : 0.004 0.045 1191 Dihedral : 7.586 96.820 946 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.64 % Allowed : 23.63 % Favored : 71.72 % 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: -0.96 (0.29), residues: 823 helix: 0.51 (0.26), residues: 382 sheet: -0.69 (0.44), residues: 146 loop : -2.09 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1165 TYR 0.012 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 A 19 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6887) covalent geometry : angle 0.61891 ( 9266) SS BOND : bond 0.00369 ( 2) SS BOND : angle 1.55708 ( 4) hydrogen bonds : bond 0.03842 ( 348) hydrogen bonds : angle 4.77225 ( 996) Misc. bond : bond 0.00219 ( 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 137 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7599 (ttt) REVERT: A 62 LEU cc_start: 0.8640 (tp) cc_final: 0.8291 (tt) REVERT: A 140 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 193 ARG cc_start: 0.7597 (tpt-90) cc_final: 0.7004 (ttp-110) REVERT: B 515 GLU cc_start: 0.8187 (pm20) cc_final: 0.7652 (pt0) REVERT: C 30 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 93 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6284 (p) REVERT: C 164 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7346 (tm-30) REVERT: C 1134 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6663 (m) REVERT: C 1214 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6473 (tpm170) outliers start: 34 outliers final: 21 residues processed: 126 average time/residue: 0.0923 time to fit residues: 15.4499 Evaluate side-chains 126 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 140 ASN 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 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 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 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 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 = 0.4432 r_free = 0.4432 target = 0.188430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147817 restraints weight = 8880.660| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.78 r_work: 0.3831 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3289 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= 0.158 Angle : 0.599 7.408 9270 Z= 0.320 Chirality : 0.044 0.150 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.452 97.470 946 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.78 % Allowed : 24.59 % 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: -0.87 (0.29), residues: 823 helix: 0.61 (0.26), residues: 382 sheet: -0.68 (0.44), residues: 146 loop : -2.09 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1126 TYR 0.011 0.002 TYR C 116 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 covalent geometry : bond 0.00367 ( 6887) covalent geometry : angle 0.59803 ( 9266) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.46458 ( 4) hydrogen bonds : bond 0.03742 ( 348) hydrogen bonds : angle 4.70983 ( 996) Misc. bond : bond 0.00188 ( 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 135 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7601 (ttt) REVERT: A 62 LEU cc_start: 0.8663 (tp) cc_final: 0.8278 (tt) REVERT: A 140 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 193 ARG cc_start: 0.7549 (tpt-90) cc_final: 0.6775 (ttm-80) REVERT: A 212 GLU cc_start: 0.8089 (tt0) cc_final: 0.7193 (tp30) REVERT: A 214 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7913 (mp0) REVERT: B 515 GLU cc_start: 0.8221 (pm20) cc_final: 0.7663 (pt0) REVERT: C 30 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 89 MET cc_start: 0.7013 (tpp) cc_final: 0.6775 (tpt) REVERT: C 164 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7331 (tm-30) REVERT: C 197 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6550 (p0) REVERT: C 200 MET cc_start: -0.1515 (ptp) cc_final: -0.1784 (ttp) REVERT: C 1130 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: C 1134 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6568 (m) REVERT: C 1214 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6301 (tpm170) outliers start: 35 outliers final: 22 residues processed: 124 average time/residue: 0.0883 time to fit residues: 14.6552 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 : 0.281 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 140 ASN 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 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ASN 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 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 1140 ILE 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: 5.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN C1039 ASN ** 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 = 0.4437 r_free = 0.4437 target = 0.188812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148666 restraints weight = 9030.801| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.78 r_work: 0.3836 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3390 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= 0.148 Angle : 0.604 7.063 9270 Z= 0.322 Chirality : 0.044 0.153 1034 Planarity : 0.003 0.035 1191 Dihedral : 7.355 97.705 946 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: -0.76 (0.29), residues: 823 helix: 0.68 (0.26), residues: 382 sheet: -0.54 (0.44), residues: 142 loop : -2.02 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.011 0.002 TYR C 116 PHE 0.025 0.002 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6887) covalent geometry : angle 0.60373 ( 9266) SS BOND : bond 0.00388 ( 2) SS BOND : angle 1.41956 ( 4) hydrogen bonds : bond 0.03664 ( 348) hydrogen bonds : angle 4.66129 ( 996) Misc. bond : bond 0.00172 ( 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 134 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7634 (ttt) REVERT: A 62 LEU cc_start: 0.8645 (tp) cc_final: 0.8263 (tt) REVERT: A 140 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7393 (p0) REVERT: A 193 ARG cc_start: 0.7499 (tpt-90) cc_final: 0.6841 (ttp-110) REVERT: B 515 GLU cc_start: 0.8212 (pm20) cc_final: 0.7674 (pt0) REVERT: C 30 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 164 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7325 (tm-30) REVERT: C 1134 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6529 (m) outliers start: 29 outliers final: 21 residues processed: 123 average time/residue: 0.0844 time to fit residues: 14.1759 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 : 0.475 ------------------------------------------------------------------------------- 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 140 ASN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** 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 = 0.4438 r_free = 0.4438 target = 0.189141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.148651 restraints weight = 9011.883| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.80 r_work: 0.3844 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6891 Z= 0.148 Angle : 0.630 12.707 9270 Z= 0.332 Chirality : 0.045 0.189 1034 Planarity : 0.004 0.035 1191 Dihedral : 7.273 97.604 946 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.10 % Allowed : 25.55 % Favored : 70.36 % 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: -0.72 (0.29), residues: 823 helix: 0.74 (0.26), residues: 382 sheet: -0.52 (0.44), residues: 142 loop : -2.04 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.011 0.001 TYR C 116 PHE 0.025 0.002 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6887) covalent geometry : angle 0.62994 ( 9266) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.38992 ( 4) hydrogen bonds : bond 0.03665 ( 348) hydrogen bonds : angle 4.65000 ( 996) Misc. bond : bond 0.00166 ( 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 133 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7627 (ttt) REVERT: A 62 LEU cc_start: 0.8648 (tp) cc_final: 0.8274 (tt) REVERT: A 140 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7435 (p0) REVERT: A 193 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.6845 (ttp-110) REVERT: B 515 GLU cc_start: 0.8165 (pm20) cc_final: 0.7661 (pt0) REVERT: C 30 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 57 LYS cc_start: 0.6339 (pttp) cc_final: 0.6080 (mptt) REVERT: C 164 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7381 (tm-30) REVERT: C 200 MET cc_start: -0.1591 (ptp) cc_final: -0.1826 (ttp) REVERT: C 1134 CYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6550 (m) outliers start: 30 outliers final: 22 residues processed: 124 average time/residue: 0.0901 time to fit residues: 14.7862 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 : 0.267 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 140 ASN 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 543 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** 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 = 0.4431 r_free = 0.4431 target = 0.188218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148591 restraints weight = 8909.776| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.73 r_work: 0.3841 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3619 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= 0.164 Angle : 0.658 13.891 9270 Z= 0.342 Chirality : 0.046 0.188 1034 Planarity : 0.004 0.034 1191 Dihedral : 7.280 96.961 946 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.69 % Allowed : 26.50 % Favored : 69.81 % 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: -0.69 (0.29), residues: 823 helix: 0.77 (0.26), residues: 382 sheet: -0.53 (0.44), residues: 142 loop : -2.03 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.028 0.002 TYR C 143 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 covalent geometry : bond 0.00386 ( 6887) covalent geometry : angle 0.65720 ( 9266) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.43586 ( 4) hydrogen bonds : bond 0.03669 ( 348) hydrogen bonds : angle 4.66651 ( 996) Misc. bond : bond 0.00184 ( 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: A 62 LEU cc_start: 0.8638 (tp) cc_final: 0.8268 (tt) REVERT: A 140 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7385 (p0) REVERT: A 193 ARG cc_start: 0.7507 (tpt-90) cc_final: 0.6797 (ttm-80) REVERT: B 515 GLU cc_start: 0.8113 (pm20) cc_final: 0.7648 (pt0) REVERT: C 30 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 57 LYS cc_start: 0.6345 (pttp) cc_final: 0.6120 (mptt) REVERT: C 164 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7417 (tm-30) REVERT: C 200 MET cc_start: -0.1500 (ptp) cc_final: -0.1718 (ttp) REVERT: C 1114 ASN cc_start: 0.7906 (p0) cc_final: 0.7476 (p0) REVERT: C 1134 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6593 (m) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.0714 time to fit residues: 11.5648 Evaluate side-chains 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 140 ASN 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 543 SER 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 77 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 60 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** 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 = 0.4441 r_free = 0.4441 target = 0.189170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149382 restraints weight = 8955.280| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.75 r_work: 0.3846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6891 Z= 0.145 Angle : 0.640 13.998 9270 Z= 0.334 Chirality : 0.045 0.187 1034 Planarity : 0.004 0.033 1191 Dihedral : 7.209 97.792 946 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.83 % Allowed : 26.78 % Favored : 69.40 % 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: -0.61 (0.29), residues: 823 helix: 0.86 (0.26), residues: 381 sheet: -0.49 (0.45), residues: 137 loop : -2.01 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1126 TYR 0.038 0.002 TYR C 143 PHE 0.025 0.002 PHE E1235 TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6887) covalent geometry : angle 0.63967 ( 9266) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.38952 ( 4) hydrogen bonds : bond 0.03591 ( 348) hydrogen bonds : angle 4.62409 ( 996) Misc. bond : bond 0.00153 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.16 seconds wall clock time: 31 minutes 48.25 seconds (1908.25 seconds total)