Starting phenix.real_space_refine on Wed Feb 12 01:18:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qpw_4616/02_2025/6qpw_4616.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpw_4616/02_2025/6qpw_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_4616/02_2025/6qpw_4616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpw_4616/02_2025/6qpw_4616.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpw_4616/02_2025/6qpw_4616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpw_4616/02_2025/6qpw_4616.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.71, per 1000 atoms: 0.69 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.69 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: 1.91 Time building geometry restraints manager: 2.00 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: 2.610 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- 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 6887 Z= 0.345 Angle : 0.995 12.782 9266 Z= 0.559 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.003 TRP A 118 HIS 0.007 0.001 HIS C 66 PHE 0.043 0.003 PHE E1235 TYR 0.018 0.002 TYR A 157 ARG 0.005 0.001 ARG A 135 *********************** 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 : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8462 (m) cc_final: 0.8142 (m) REVERT: A 186 GLN cc_start: 0.8482 (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: 0.4297 (ptmt) REVERT: E 1216 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7658 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2577 time to fit residues: 57.8137 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 : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 C1130 GLN E1076 GLN E1248 GLN E1265 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.191380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150440 restraints weight = 8676.125| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.79 r_work: 0.3859 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6887 Z= 0.273 Angle : 0.688 10.450 9266 Z= 0.366 Chirality : 0.046 0.182 1034 Planarity : 0.005 0.053 1191 Dihedral : 8.194 96.637 946 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.32 % Allowed : 18.44 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.27), residues: 823 helix: -0.60 (0.24), residues: 387 sheet: -0.51 (0.45), residues: 123 loop : -2.48 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 133 HIS 0.004 0.001 HIS E1112 PHE 0.028 0.002 PHE E1235 TYR 0.015 0.002 TYR C 2 ARG 0.004 0.001 ARG C1058 *********************** 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7443 (tpt-90) cc_final: 0.6797 (ttp-110) REVERT: C 1064 THR cc_start: 0.7420 (m) cc_final: 0.7168 (p) REVERT: C 1216 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6737 (mp0) outliers start: 17 outliers final: 5 residues processed: 121 average time/residue: 0.2123 time to fit residues: 33.3370 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 : 0.735 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4436 r_free = 0.4436 target = 0.189184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149841 restraints weight = 8817.495| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.59 r_work: 0.3877 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6887 Z= 0.256 Angle : 0.626 7.598 9266 Z= 0.335 Chirality : 0.045 0.139 1034 Planarity : 0.004 0.042 1191 Dihedral : 7.801 97.291 946 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.42 % Allowed : 20.36 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.28), residues: 823 helix: 0.00 (0.25), residues: 385 sheet: -0.87 (0.44), residues: 139 loop : -2.28 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 PHE 0.029 0.002 PHE E1235 TYR 0.015 0.002 TYR C 2 ARG 0.005 0.000 ARG C1058 *********************** 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 130 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.6925 (ttp-110) REVERT: A 202 LEU cc_start: 0.7720 (tp) cc_final: 0.7449 (tp) REVERT: C 30 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 164 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7333 (tm-30) REVERT: C 1064 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 1134 CYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6687 (m) REVERT: C 1187 ARG cc_start: 0.6262 (mmm160) cc_final: 0.5934 (mmp-170) outliers start: 25 outliers final: 15 residues processed: 118 average time/residue: 0.2181 time to fit residues: 33.6135 Evaluate side-chains 112 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 90 ILE 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 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 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 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 156 GLN C1130 GLN 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 = 0.189220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149987 restraints weight = 8903.443| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.60 r_work: 0.3861 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6887 Z= 0.246 Angle : 0.627 10.349 9266 Z= 0.332 Chirality : 0.045 0.156 1034 Planarity : 0.004 0.038 1191 Dihedral : 7.672 97.790 946 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.55 % Allowed : 21.45 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.29), residues: 823 helix: 0.29 (0.26), residues: 383 sheet: -0.73 (0.44), residues: 144 loop : -2.19 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.027 0.002 PHE E1235 TYR 0.016 0.002 TYR C 2 ARG 0.005 0.000 ARG E1126 *********************** 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 131 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7705 (ttt) REVERT: A 193 ARG cc_start: 0.7515 (tpt-90) cc_final: 0.6933 (ttp-110) REVERT: A 202 LEU cc_start: 0.7757 (tp) cc_final: 0.7509 (tp) REVERT: C 30 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 164 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7331 (tm-30) REVERT: C 1064 THR cc_start: 0.7687 (m) cc_final: 0.7451 (p) REVERT: C 1134 CYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6655 (m) REVERT: C 1187 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5873 (mmp-170) outliers start: 26 outliers final: 17 residues processed: 123 average time/residue: 0.3314 time to fit residues: 52.4989 Evaluate side-chains 119 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 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 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4439 r_free = 0.4439 target = 0.189322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150170 restraints weight = 8809.515| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.58 r_work: 0.3860 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6887 Z= 0.218 Angle : 0.587 7.498 9266 Z= 0.314 Chirality : 0.044 0.156 1034 Planarity : 0.004 0.049 1191 Dihedral : 7.484 98.472 946 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.96 % Allowed : 22.13 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 823 helix: 0.52 (0.26), residues: 382 sheet: -0.59 (0.45), residues: 142 loop : -2.14 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.027 0.002 PHE E1235 TYR 0.012 0.002 TYR C 2 ARG 0.007 0.000 ARG C1214 *********************** 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 137 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7624 (ttt) REVERT: A 193 ARG cc_start: 0.7535 (tpt-90) cc_final: 0.6954 (ttp-110) REVERT: C 30 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8438 (mp) REVERT: C 164 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7334 (tm-30) REVERT: C 1134 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6686 (m) outliers start: 29 outliers final: 19 residues processed: 128 average time/residue: 0.2169 time to fit residues: 36.3515 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 1212 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4436 r_free = 0.4436 target = 0.189006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149889 restraints weight = 8897.271| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.57 r_work: 0.3866 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6887 Z= 0.220 Angle : 0.588 7.040 9266 Z= 0.314 Chirality : 0.043 0.152 1034 Planarity : 0.004 0.043 1191 Dihedral : 7.366 98.510 946 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.10 % Allowed : 23.77 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.29), residues: 823 helix: 0.68 (0.26), residues: 381 sheet: -0.53 (0.45), residues: 144 loop : -2.15 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.026 0.002 PHE E1235 TYR 0.010 0.002 TYR C 2 ARG 0.007 0.000 ARG C1165 *********************** 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 128 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7635 (ttt) REVERT: A 193 ARG cc_start: 0.7486 (tpt-90) cc_final: 0.6941 (ttp-110) REVERT: A 212 GLU cc_start: 0.8027 (tt0) cc_final: 0.7189 (tp30) REVERT: C 30 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8422 (mp) REVERT: C 164 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7328 (tm-30) REVERT: C 200 MET cc_start: -0.1368 (ptp) cc_final: -0.1601 (ttp) outliers start: 30 outliers final: 23 residues processed: 118 average time/residue: 0.1924 time to fit residues: 30.3668 Evaluate side-chains 118 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1212 VAL 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 1160 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 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 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 = 0.4427 r_free = 0.4427 target = 0.188077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149269 restraints weight = 8826.461| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.54 r_work: 0.3863 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6887 Z= 0.235 Angle : 0.595 7.328 9266 Z= 0.317 Chirality : 0.043 0.151 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.320 97.839 946 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.23 % Allowed : 24.32 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.29), residues: 823 helix: 0.74 (0.26), residues: 381 sheet: -0.57 (0.46), residues: 137 loop : -2.15 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.026 0.002 PHE E1235 TYR 0.011 0.002 TYR C 2 ARG 0.005 0.000 ARG E1126 *********************** 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 131 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: A 193 ARG cc_start: 0.7517 (tpt-90) cc_final: 0.6956 (ttp-110) REVERT: A 212 GLU cc_start: 0.8013 (tt0) cc_final: 0.7185 (tp30) REVERT: A 214 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7857 (mp0) REVERT: C 30 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 164 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7374 (tm-30) REVERT: C 168 ASP cc_start: 0.8406 (m-30) cc_final: 0.7633 (m-30) REVERT: C 197 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6364 (p0) REVERT: C 200 MET cc_start: -0.1332 (ptp) cc_final: -0.1595 (ttp) REVERT: E 1251 ASN cc_start: 0.8181 (t0) cc_final: 0.7968 (t0) outliers start: 31 outliers final: 22 residues processed: 120 average time/residue: 0.1921 time to fit residues: 31.3489 Evaluate side-chains 121 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 ASN 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 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1212 VAL 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 40 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4427 r_free = 0.4427 target = 0.187908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149037 restraints weight = 8943.497| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.56 r_work: 0.3855 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6887 Z= 0.232 Angle : 0.611 7.058 9266 Z= 0.325 Chirality : 0.044 0.155 1034 Planarity : 0.004 0.065 1191 Dihedral : 7.268 97.995 946 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.23 % Allowed : 25.00 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.29), residues: 823 helix: 0.80 (0.26), residues: 382 sheet: -0.59 (0.46), residues: 137 loop : -2.14 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.026 0.002 PHE E1235 TYR 0.010 0.002 TYR C 2 ARG 0.007 0.000 ARG C1187 *********************** 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 135 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7642 (ttt) REVERT: A 193 ARG cc_start: 0.7526 (tpt-90) cc_final: 0.6968 (ttp-110) REVERT: A 212 GLU cc_start: 0.8038 (tt0) cc_final: 0.7141 (tp30) REVERT: C 30 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8410 (mp) REVERT: C 93 SER cc_start: 0.7038 (OUTLIER) cc_final: 0.6449 (p) REVERT: C 164 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7374 (tm-30) REVERT: C 1114 ASN cc_start: 0.7813 (p0) cc_final: 0.7457 (p0) REVERT: C 1130 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: E 1251 ASN cc_start: 0.8157 (t0) cc_final: 0.7945 (t0) outliers start: 31 outliers final: 21 residues processed: 124 average time/residue: 0.1914 time to fit residues: 32.2154 Evaluate side-chains 119 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 520 THR 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 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 1130 GLN Chi-restraints excluded: chain C residue 1132 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 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 = 0.4435 r_free = 0.4435 target = 0.188762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.150011 restraints weight = 8893.810| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.56 r_work: 0.3871 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6887 Z= 0.223 Angle : 0.624 9.264 9266 Z= 0.330 Chirality : 0.044 0.182 1034 Planarity : 0.004 0.058 1191 Dihedral : 7.217 98.116 946 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.87 % Allowed : 25.96 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.29), residues: 823 helix: 0.82 (0.26), residues: 382 sheet: -0.57 (0.46), residues: 137 loop : -2.10 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.025 0.001 PHE E1235 TYR 0.024 0.002 TYR C 143 ARG 0.006 0.000 ARG E1126 *********************** 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 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7666 (ttt) REVERT: A 193 ARG cc_start: 0.7494 (tpt-90) cc_final: 0.6957 (ttp-110) REVERT: C 30 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 164 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7383 (tm-30) REVERT: C 200 MET cc_start: -0.1547 (ptp) cc_final: -0.1772 (ttp) REVERT: C 1114 ASN cc_start: 0.7752 (p0) cc_final: 0.7440 (p0) REVERT: E 1251 ASN cc_start: 0.8165 (t0) cc_final: 0.7961 (t0) outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.1963 time to fit residues: 28.8227 Evaluate side-chains 109 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 520 THR 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 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR 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 1157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 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 = 0.4422 r_free = 0.4422 target = 0.187605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148670 restraints weight = 9054.936| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.59 r_work: 0.3848 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6887 Z= 0.247 Angle : 0.655 9.742 9266 Z= 0.345 Chirality : 0.045 0.184 1034 Planarity : 0.004 0.052 1191 Dihedral : 7.246 97.436 946 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.73 % Allowed : 27.05 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.29), residues: 823 helix: 0.81 (0.26), residues: 381 sheet: -0.64 (0.45), residues: 138 loop : -2.12 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.026 0.002 PHE E1235 TYR 0.037 0.002 TYR C 143 ARG 0.006 0.000 ARG E1126 ********************** 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 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7646 (ttt) REVERT: A 193 ARG cc_start: 0.7545 (tpt-90) cc_final: 0.6973 (ttp-110) REVERT: C 30 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 164 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7414 (tm-30) REVERT: C 1114 ASN cc_start: 0.7692 (p0) cc_final: 0.7350 (p0) outliers start: 20 outliers final: 18 residues processed: 106 average time/residue: 0.2000 time to fit residues: 28.4202 Evaluate side-chains 111 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 520 THR 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 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR 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 1157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 ASN ** 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 = 0.4451 r_free = 0.4451 target = 0.190538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151616 restraints weight = 8942.498| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.58 r_work: 0.3885 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6887 Z= 0.186 Angle : 0.619 10.098 9266 Z= 0.328 Chirality : 0.044 0.184 1034 Planarity : 0.003 0.049 1191 Dihedral : 7.058 99.435 946 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.60 % Allowed : 27.73 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 823 helix: 0.93 (0.26), residues: 382 sheet: -0.47 (0.46), residues: 138 loop : -2.04 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.003 0.001 HIS E1112 PHE 0.024 0.001 PHE E1235 TYR 0.030 0.001 TYR C 143 ARG 0.007 0.000 ARG E1126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.93 seconds wall clock time: 64 minutes 41.04 seconds (3881.04 seconds total)