Starting phenix.real_space_refine on Sun Dec 29 06:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/12_2024/8yjl_39344.cif" } resolution = 3.51 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 Anisotropic ADP refinement not supported. Converting 253 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 63 5.16 5 C 6023 2.51 5 N 1652 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9853 Number of models: 1 Model: "" Number of chains: 8 Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1968 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 248} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2770 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Time building chain proxies: 6.40, per 1000 atoms: 0.65 Number of scatterers: 9853 At special positions: 0 Unit cell: (102.92, 98.77, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 58 15.00 O 2057 8.00 N 1652 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 882.7 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 28.4% alpha, 27.2% beta 14 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.014A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.173A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 112 removed outlier: 3.860A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.751A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.698A pdb=" N LEU D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 318 through 333 Processing helix chain 'D' and resid 339 through 344 removed outlier: 4.036A pdb=" N PHE D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 62 removed outlier: 4.397A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.591A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 122 through 125 removed outlier: 3.792A pdb=" N GLY D 348 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 203 through 208 removed outlier: 5.344A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.644A pdb=" N THR D 336 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.909A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 172 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 157 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 162 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 203 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 71 removed outlier: 7.228A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71 removed outlier: 7.129A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 29 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.574A pdb=" N ALA D 174 " --> pdb=" O LYS D 30 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2396 1.33 - 1.45: 2045 1.45 - 1.57: 5464 1.57 - 1.70: 113 1.70 - 1.82: 102 Bond restraints: 10120 Sorted by residual: bond pdb=" CB ASP B 243 " pdb=" CG ASP B 243 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.23e+00 bond pdb=" CA ASP B 243 " pdb=" CB ASP B 243 " ideal model delta sigma weight residual 1.530 1.562 -0.032 1.54e-02 4.22e+03 4.34e+00 bond pdb=" C3' DA J 12 " pdb=" O3' DA J 12 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.38e+00 bond pdb=" N GLN D 315 " pdb=" CA GLN D 315 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.42e-02 4.96e+03 3.28e+00 bond pdb=" CB GLU D 221 " pdb=" CG GLU D 221 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.46e+00 ... (remaining 10115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 13604 3.03 - 6.06: 245 6.06 - 9.10: 44 9.10 - 12.13: 8 12.13 - 15.16: 2 Bond angle restraints: 13903 Sorted by residual: angle pdb=" CB MET B 199 " pdb=" CG MET B 199 " pdb=" SD MET B 199 " ideal model delta sigma weight residual 112.70 127.86 -15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C ASN B 187 " pdb=" N VAL B 188 " pdb=" CA VAL B 188 " ideal model delta sigma weight residual 121.97 131.00 -9.03 1.80e+00 3.09e-01 2.51e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 122.08 129.01 -6.93 1.47e+00 4.63e-01 2.22e+01 angle pdb=" N THR C 219 " pdb=" CA THR C 219 " pdb=" C THR C 219 " ideal model delta sigma weight residual 109.81 119.73 -9.92 2.21e+00 2.05e-01 2.02e+01 angle pdb=" CA ASP B 243 " pdb=" CB ASP B 243 " pdb=" CG ASP B 243 " ideal model delta sigma weight residual 112.60 116.91 -4.31 1.00e+00 1.00e+00 1.85e+01 ... (remaining 13898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.05: 5553 28.05 - 56.10: 522 56.10 - 84.16: 46 84.16 - 112.21: 6 112.21 - 140.26: 1 Dihedral angle restraints: 6128 sinusoidal: 2880 harmonic: 3248 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual -86.00 -173.26 87.26 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CA GLU B 198 " pdb=" C GLU B 198 " pdb=" N MET B 199 " pdb=" CA MET B 199 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLU A 198 " pdb=" C GLU A 198 " pdb=" N MET A 199 " pdb=" CA MET A 199 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1335 0.073 - 0.146: 225 0.146 - 0.219: 34 0.219 - 0.292: 6 0.292 - 0.365: 1 Chirality restraints: 1601 Sorted by residual: chirality pdb=" CB VAL B 203 " pdb=" CA VAL B 203 " pdb=" CG1 VAL B 203 " pdb=" CG2 VAL B 203 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1598 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.055 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO B 220 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A 220 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 109 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C LYS D 109 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS D 109 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 110 " -0.015 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3004 2.85 - 3.36: 8360 3.36 - 3.88: 17114 3.88 - 4.39: 19512 4.39 - 4.90: 32634 Nonbonded interactions: 80624 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.339 3.040 nonbonded pdb=" O GLU B 191 " pdb=" OG1 THR B 224 " model vdw 2.354 3.040 nonbonded pdb=" O ALA D 98 " pdb=" OG SER D 101 " model vdw 2.362 3.040 nonbonded pdb=" O VAL D 123 " pdb=" OG1 THR D 127 " model vdw 2.363 3.040 nonbonded pdb=" OE1 GLU D 221 " pdb=" NE2 HIS D 280 " model vdw 2.372 3.120 ... (remaining 80619 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'C' and resid 1 through 254) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.540 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 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: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.057 10120 Z= 0.336 Angle : 0.998 15.161 13903 Z= 0.520 Chirality : 0.058 0.365 1601 Planarity : 0.007 0.081 1589 Dihedral : 19.381 140.260 4011 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -2.81 (0.21), residues: 1107 helix: -2.30 (0.22), residues: 315 sheet: -0.90 (0.26), residues: 357 loop : -2.18 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 28 HIS 0.003 0.001 HIS A 246 PHE 0.021 0.003 PHE D 283 TYR 0.024 0.003 TYR C 133 ARG 0.015 0.001 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.108 Fit side-chains REVERT: A 199 MET cc_start: 0.5430 (tpt) cc_final: 0.5024 (tpp) REVERT: A 244 MET cc_start: 0.7863 (tmm) cc_final: 0.7251 (ttt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2129 time to fit residues: 45.8687 Evaluate side-chains 111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN B 71 ASN B 204 GLN D 137 HIS D 143 HIS D 253 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10120 Z= 0.329 Angle : 0.658 8.260 13903 Z= 0.352 Chirality : 0.046 0.251 1601 Planarity : 0.004 0.053 1589 Dihedral : 20.614 148.735 1871 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 8.99 % Favored : 89.46 % 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: -2.08 (0.23), residues: 1107 helix: -0.89 (0.26), residues: 318 sheet: -1.08 (0.26), residues: 363 loop : -1.86 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 28 HIS 0.004 0.001 HIS D 253 PHE 0.014 0.002 PHE D 316 TYR 0.017 0.002 TYR B 211 ARG 0.005 0.001 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.073 Fit side-chains REVERT: C 25 GLU cc_start: 0.7086 (pm20) cc_final: 0.6706 (pm20) REVERT: B 27 CYS cc_start: 0.7390 (t) cc_final: 0.7094 (p) REVERT: A 244 MET cc_start: 0.8275 (tmm) cc_final: 0.7646 (ttm) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.2150 time to fit residues: 42.5549 Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 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 49 GLN D 48 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10120 Z= 0.265 Angle : 0.605 6.881 13903 Z= 0.324 Chirality : 0.044 0.166 1601 Planarity : 0.004 0.046 1589 Dihedral : 20.396 137.426 1871 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.07 % Allowed : 13.02 % Favored : 84.92 % 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: -1.73 (0.24), residues: 1107 helix: -0.22 (0.28), residues: 317 sheet: -1.14 (0.26), residues: 363 loop : -1.71 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.003 0.001 HIS D 143 PHE 0.011 0.001 PHE D 126 TYR 0.015 0.002 TYR B 211 ARG 0.005 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.012 Fit side-chains REVERT: C 25 GLU cc_start: 0.7135 (pm20) cc_final: 0.6720 (pm20) REVERT: B 27 CYS cc_start: 0.7443 (t) cc_final: 0.7210 (p) REVERT: B 68 MET cc_start: 0.7955 (mmt) cc_final: 0.7122 (mmt) REVERT: B 86 ASP cc_start: 0.6868 (m-30) cc_final: 0.6621 (m-30) REVERT: A 244 MET cc_start: 0.8261 (tmm) cc_final: 0.7731 (ttm) outliers start: 20 outliers final: 12 residues processed: 136 average time/residue: 0.2126 time to fit residues: 41.3984 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 29 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: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10120 Z= 0.214 Angle : 0.576 7.507 13903 Z= 0.308 Chirality : 0.043 0.148 1601 Planarity : 0.003 0.034 1589 Dihedral : 20.421 136.257 1871 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.58 % Allowed : 15.70 % Favored : 81.71 % 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: -1.44 (0.24), residues: 1107 helix: 0.21 (0.29), residues: 318 sheet: -1.06 (0.27), residues: 352 loop : -1.61 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.003 0.001 HIS D 143 PHE 0.009 0.001 PHE D 126 TYR 0.013 0.002 TYR B 211 ARG 0.004 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7104 (pm20) cc_final: 0.6695 (pm20) REVERT: B 27 CYS cc_start: 0.7436 (t) cc_final: 0.7148 (p) REVERT: B 68 MET cc_start: 0.7910 (mmt) cc_final: 0.7115 (mmt) REVERT: B 86 ASP cc_start: 0.6887 (m-30) cc_final: 0.6638 (m-30) REVERT: A 17 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 199 MET cc_start: 0.6979 (tpp) cc_final: 0.6720 (mmm) REVERT: A 244 MET cc_start: 0.8186 (tmm) cc_final: 0.7737 (ttm) outliers start: 25 outliers final: 15 residues processed: 148 average time/residue: 0.2055 time to fit residues: 44.0796 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN B 184 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10120 Z= 0.228 Angle : 0.584 8.257 13903 Z= 0.311 Chirality : 0.043 0.163 1601 Planarity : 0.003 0.034 1589 Dihedral : 20.397 132.490 1871 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.79 % Allowed : 16.84 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.25), residues: 1107 helix: 0.41 (0.30), residues: 315 sheet: -0.98 (0.27), residues: 372 loop : -1.44 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 PHE 0.010 0.001 PHE D 316 TYR 0.014 0.001 TYR B 211 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7151 (pm20) cc_final: 0.6729 (pm20) REVERT: C 135 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7528 (t) REVERT: B 3 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: B 27 CYS cc_start: 0.7453 (t) cc_final: 0.7161 (p) REVERT: B 86 ASP cc_start: 0.6893 (m-30) cc_final: 0.6677 (m-30) REVERT: A 17 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 244 MET cc_start: 0.8193 (tmm) cc_final: 0.7782 (ttm) REVERT: D 40 TYR cc_start: 0.8920 (m-80) cc_final: 0.8592 (m-10) REVERT: D 67 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6682 (mtm) outliers start: 27 outliers final: 17 residues processed: 139 average time/residue: 0.2071 time to fit residues: 41.4663 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0020 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN A 49 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10120 Z= 0.210 Angle : 0.578 8.228 13903 Z= 0.306 Chirality : 0.043 0.192 1601 Planarity : 0.003 0.033 1589 Dihedral : 20.386 130.154 1871 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.79 % Allowed : 17.98 % Favored : 79.24 % 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: -1.11 (0.25), residues: 1107 helix: 0.53 (0.30), residues: 315 sheet: -0.92 (0.27), residues: 372 loop : -1.39 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 PHE 0.008 0.001 PHE C 169 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7192 (pm20) cc_final: 0.6763 (pm20) REVERT: C 135 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7507 (t) REVERT: B 27 CYS cc_start: 0.7419 (t) cc_final: 0.7166 (p) REVERT: B 86 ASP cc_start: 0.6881 (m-30) cc_final: 0.6659 (m-30) REVERT: A 8 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: A 17 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: D 40 TYR cc_start: 0.8915 (m-80) cc_final: 0.8610 (m-10) outliers start: 27 outliers final: 16 residues processed: 137 average time/residue: 0.2106 time to fit residues: 41.3613 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN A 49 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10120 Z= 0.210 Angle : 0.587 8.326 13903 Z= 0.308 Chirality : 0.043 0.326 1601 Planarity : 0.003 0.034 1589 Dihedral : 20.371 127.686 1871 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.31 % Allowed : 17.36 % Favored : 79.34 % 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: -1.06 (0.25), residues: 1107 helix: 0.63 (0.30), residues: 316 sheet: -0.94 (0.27), residues: 372 loop : -1.36 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 PHE 0.008 0.001 PHE C 169 TYR 0.013 0.001 TYR B 211 ARG 0.005 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7217 (pm20) cc_final: 0.6733 (pm20) REVERT: C 135 CYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (t) REVERT: B 3 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: B 27 CYS cc_start: 0.7455 (t) cc_final: 0.7161 (p) REVERT: B 86 ASP cc_start: 0.6888 (m-30) cc_final: 0.6657 (m-30) REVERT: B 139 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: A 8 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: A 17 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: D 40 TYR cc_start: 0.8921 (m-80) cc_final: 0.8545 (m-10) REVERT: D 75 MET cc_start: 0.8340 (mmm) cc_final: 0.8094 (mmm) outliers start: 32 outliers final: 16 residues processed: 143 average time/residue: 0.2062 time to fit residues: 42.5319 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN A 38 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10120 Z= 0.253 Angle : 0.616 8.290 13903 Z= 0.322 Chirality : 0.044 0.315 1601 Planarity : 0.003 0.033 1589 Dihedral : 20.396 122.978 1871 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.89 % Allowed : 18.70 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.12 (0.25), residues: 1107 helix: 0.54 (0.30), residues: 316 sheet: -0.97 (0.27), residues: 372 loop : -1.37 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 PHE 0.008 0.001 PHE B 169 TYR 0.014 0.002 TYR B 211 ARG 0.003 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7308 (pm20) cc_final: 0.6790 (pm20) REVERT: C 135 CYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7509 (t) REVERT: B 3 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: B 27 CYS cc_start: 0.7480 (t) cc_final: 0.7201 (p) REVERT: B 86 ASP cc_start: 0.6919 (m-30) cc_final: 0.6678 (m-30) REVERT: B 139 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.6990 (ppp) REVERT: A 8 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: A 17 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: D 40 TYR cc_start: 0.8954 (m-80) cc_final: 0.8579 (m-10) REVERT: D 148 MET cc_start: 0.7488 (mtt) cc_final: 0.7201 (mtt) outliers start: 28 outliers final: 17 residues processed: 138 average time/residue: 0.2189 time to fit residues: 43.2746 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10120 Z= 0.218 Angle : 0.600 8.532 13903 Z= 0.316 Chirality : 0.044 0.222 1601 Planarity : 0.003 0.033 1589 Dihedral : 20.337 119.178 1871 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.79 % Allowed : 19.52 % Favored : 77.69 % 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: -1.07 (0.25), residues: 1107 helix: 0.60 (0.30), residues: 316 sheet: -0.97 (0.27), residues: 372 loop : -1.34 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 PHE 0.009 0.001 PHE C 169 TYR 0.014 0.001 TYR B 211 ARG 0.003 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7340 (pm20) cc_final: 0.6791 (pm20) REVERT: C 135 CYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7523 (t) REVERT: B 3 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: B 27 CYS cc_start: 0.7460 (t) cc_final: 0.7148 (p) REVERT: B 86 ASP cc_start: 0.6876 (m-30) cc_final: 0.6646 (m-30) REVERT: B 139 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6957 (ppp) REVERT: A 8 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: A 17 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: D 40 TYR cc_start: 0.8928 (m-80) cc_final: 0.8503 (m-10) REVERT: D 148 MET cc_start: 0.7508 (mtt) cc_final: 0.7229 (mtt) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.2034 time to fit residues: 40.1636 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 90 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10120 Z= 0.189 Angle : 0.593 8.508 13903 Z= 0.312 Chirality : 0.043 0.247 1601 Planarity : 0.003 0.033 1589 Dihedral : 20.266 116.130 1871 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 19.52 % Favored : 77.89 % 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: -0.94 (0.25), residues: 1107 helix: 0.73 (0.30), residues: 315 sheet: -0.91 (0.27), residues: 372 loop : -1.26 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 PHE 0.009 0.001 PHE C 169 TYR 0.014 0.001 TYR C 211 ARG 0.004 0.000 ARG D 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: C 25 GLU cc_start: 0.7361 (pm20) cc_final: 0.6812 (pm20) REVERT: C 135 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7472 (t) REVERT: B 3 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: B 27 CYS cc_start: 0.7434 (t) cc_final: 0.7127 (p) REVERT: B 86 ASP cc_start: 0.6819 (m-30) cc_final: 0.6575 (m-30) REVERT: B 139 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6907 (ppp) REVERT: A 8 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: A 17 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: D 40 TYR cc_start: 0.8961 (m-80) cc_final: 0.8555 (m-10) REVERT: D 276 HIS cc_start: 0.7894 (p-80) cc_final: 0.6810 (m90) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 0.1981 time to fit residues: 41.7108 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.149786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114320 restraints weight = 12545.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117743 restraints weight = 8885.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118850 restraints weight = 5821.375| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10120 Z= 0.252 Angle : 0.629 9.236 13903 Z= 0.327 Chirality : 0.045 0.286 1601 Planarity : 0.003 0.033 1589 Dihedral : 20.310 113.369 1871 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.48 % Allowed : 19.94 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.25), residues: 1107 helix: 0.66 (0.30), residues: 316 sheet: -0.89 (0.27), residues: 368 loop : -1.32 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.005 0.001 HIS D 280 PHE 0.025 0.001 PHE A 2 TYR 0.015 0.002 TYR B 211 ARG 0.004 0.000 ARG D 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.72 seconds wall clock time: 39 minutes 0.93 seconds (2340.93 seconds total)