Starting phenix.real_space_refine on Thu Jul 2 05:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ss5_25404/07_2026/7ss5_25404.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 48 5.49 5 S 18 5.16 5 C 3844 2.51 5 N 1140 2.21 5 O 1871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6927 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Restraints were copied for chains: B, D Time building chain proxies: 2.12, per 1000 atoms: 0.31 Number of scatterers: 6927 At special positions: 0 Unit cell: (83, 86.32, 106.24, 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) Ca 6 19.99 S 18 16.00 P 48 15.00 O 1871 8.00 N 1140 7.00 C 3844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 305.5 milliseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.8% alpha, 8.3% beta 18 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 90 through 123 Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.050A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 4.029A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 123 Processing helix chain 'B' and resid 161 through 178 removed outlier: 4.049A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.028A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 6.822A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU A 276 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU A 280 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N LYS A 242 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.822A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU B 280 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N LYS B 242 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1665 1.33 - 1.45: 1397 1.45 - 1.57: 3376 1.57 - 1.69: 94 1.69 - 1.81: 32 Bond restraints: 6564 Sorted by residual: bond pdb=" C3' DT D 16 " pdb=" C2' DT D 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT C 16 " pdb=" C2' DT C 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.83e+00 bond pdb=" C3' DA D 11 " pdb=" C2' DA D 11 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.10e+00 bond pdb=" C3' DA C 11 " pdb=" C2' DA C 11 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.94e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.81e+00 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8746 1.56 - 3.11: 304 3.11 - 4.67: 40 4.67 - 6.22: 16 6.22 - 7.78: 4 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N GLU A 292 " pdb=" CA GLU A 292 " pdb=" C GLU A 292 " ideal model delta sigma weight residual 110.68 102.90 7.78 1.39e+00 5.18e-01 3.13e+01 angle pdb=" N GLU B 292 " pdb=" CA GLU B 292 " pdb=" C GLU B 292 " ideal model delta sigma weight residual 110.68 102.94 7.74 1.39e+00 5.18e-01 3.10e+01 angle pdb=" N ARG A 311 " pdb=" CA ARG A 311 " pdb=" C ARG A 311 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N ARG B 311 " pdb=" CA ARG B 311 " pdb=" C ARG B 311 " ideal model delta sigma weight residual 111.28 117.31 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 3547 34.80 - 69.60: 261 69.60 - 104.40: 6 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 3816 sinusoidal: 1858 harmonic: 1958 Sorted by residual: dihedral pdb=" C ALA B 55 " pdb=" N ALA B 55 " pdb=" CA ALA B 55 " pdb=" CB ALA B 55 " ideal model delta harmonic sigma weight residual -122.60 -111.34 -11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C ALA A 55 " pdb=" N ALA A 55 " pdb=" CA ALA A 55 " pdb=" CB ALA A 55 " ideal model delta harmonic sigma weight residual -122.60 -111.36 -11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 896 0.077 - 0.155: 100 0.155 - 0.232: 4 0.232 - 0.309: 0 0.309 - 0.386: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA ALA B 55 " pdb=" N ALA B 55 " pdb=" C ALA B 55 " pdb=" CB ALA B 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA ALA A 55 " pdb=" N ALA A 55 " pdb=" C ALA A 55 " pdb=" CB ALA A 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA GLU B 292 " pdb=" N GLU B 292 " pdb=" C GLU B 292 " pdb=" CB GLU B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 999 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 55 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ALA B 55 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA B 55 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 56 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 55 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ALA A 55 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 55 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ASP A 155 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A 155 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP A 156 " -0.008 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 441 2.72 - 3.27: 6424 3.27 - 3.81: 12394 3.81 - 4.36: 16446 4.36 - 4.90: 24478 Nonbonded interactions: 60183 Sorted by model distance: nonbonded pdb=" CG GLU A 301 " pdb=" CG GLU B 301 " model vdw 2.179 3.840 nonbonded pdb=" CA GLY B 266 " pdb=" OH TYR B 297 " model vdw 2.241 3.440 nonbonded pdb=" CA GLY A 266 " pdb=" OH TYR A 297 " model vdw 2.242 3.440 nonbonded pdb=" O HOH B 553 " pdb=" O HOH B 666 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASN B 92 " pdb=" O HOH B 501 " model vdw 2.287 3.040 ... (remaining 60178 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.004 0.035 6564 Z= 0.315 Angle : 0.687 7.778 9110 Z= 0.489 Chirality : 0.049 0.386 1002 Planarity : 0.004 0.033 1032 Dihedral : 19.806 173.997 2552 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.34), residues: 672 helix: 1.32 (0.34), residues: 280 sheet: -0.62 (0.74), residues: 50 loop : 0.09 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.014 0.001 TYR A 64 PHE 0.021 0.001 PHE A 171 TRP 0.022 0.002 TRP B 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.31 ( 6564) covalent geometry : angle 0.68666 / 0.49 ( 9110) hydrogen bonds : bond 0.17770 / 11.04 ( 268) hydrogen bonds : angle 5.94029 / 3.91 ( 724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.7645 time to fit residues: 122.2727 Evaluate side-chains 88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 129 GLN A 307 HIS B 112 ASN B 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084889 restraints weight = 12252.919| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.53 r_work: 0.2910 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6564 Z= 0.219 Angle : 0.709 7.573 9110 Z= 0.372 Chirality : 0.047 0.247 1002 Planarity : 0.005 0.043 1032 Dihedral : 22.394 176.221 1270 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 14.01 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.35), residues: 672 helix: 1.93 (0.33), residues: 286 sheet: -0.42 (0.76), residues: 50 loop : 0.08 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 311 TYR 0.013 0.002 TYR A 5 PHE 0.009 0.001 PHE B 54 TRP 0.021 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 6564) covalent geometry : angle 0.70925 / 0.37 ( 9110) hydrogen bonds : bond 0.06659 / 4.06 ( 268) hydrogen bonds : angle 4.49482 / 2.95 ( 724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.289 Fit side-chains REVERT: A 202 GLU cc_start: 0.7975 (mp0) cc_final: 0.7774 (mp0) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.7060 time to fit residues: 68.5699 Evaluate side-chains 89 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088894 restraints weight = 11792.601| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.55 r_work: 0.2959 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6564 Z= 0.130 Angle : 0.597 6.655 9110 Z= 0.320 Chirality : 0.043 0.246 1002 Planarity : 0.004 0.034 1032 Dihedral : 22.302 173.945 1270 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.66 % Allowed : 14.36 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.34), residues: 672 helix: 1.92 (0.32), residues: 292 sheet: -0.36 (0.74), residues: 50 loop : 0.15 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 311 TYR 0.013 0.001 TYR B 297 PHE 0.009 0.001 PHE A 54 TRP 0.021 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 6564) covalent geometry : angle 0.59743 / 0.32 ( 9110) hydrogen bonds : bond 0.05908 / 3.54 ( 268) hydrogen bonds : angle 4.18041 / 2.76 ( 724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.259 Fit side-chains REVERT: A 73 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: A 256 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 252 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 256 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8057 (mt-10) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 0.6406 time to fit residues: 63.1297 Evaluate side-chains 88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085531 restraints weight = 12004.326| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.54 r_work: 0.2900 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6564 Z= 0.206 Angle : 0.646 7.878 9110 Z= 0.338 Chirality : 0.045 0.255 1002 Planarity : 0.004 0.029 1032 Dihedral : 22.420 174.602 1270 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.13 % Allowed : 15.25 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.34), residues: 672 helix: 1.99 (0.32), residues: 292 sheet: -0.26 (0.73), residues: 50 loop : 0.13 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 311 TYR 0.021 0.002 TYR B 5 PHE 0.012 0.001 PHE B 171 TRP 0.024 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 ( 6564) covalent geometry : angle 0.64592 / 0.34 ( 9110) hydrogen bonds : bond 0.06305 / 3.90 ( 268) hydrogen bonds : angle 4.15127 / 2.75 ( 724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8056 (mt-10) REVERT: B 252 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: B 256 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7790 (mt-10) outliers start: 12 outliers final: 4 residues processed: 89 average time/residue: 0.6752 time to fit residues: 62.6864 Evaluate side-chains 78 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085645 restraints weight = 12068.397| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.52 r_work: 0.2907 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6564 Z= 0.174 Angle : 0.616 7.184 9110 Z= 0.325 Chirality : 0.045 0.257 1002 Planarity : 0.004 0.043 1032 Dihedral : 22.462 173.585 1270 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.13 % Allowed : 16.84 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.34), residues: 672 helix: 2.08 (0.32), residues: 292 sheet: -0.24 (0.73), residues: 50 loop : 0.23 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 311 TYR 0.023 0.002 TYR B 5 PHE 0.009 0.001 PHE A 54 TRP 0.024 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 6564) covalent geometry : angle 0.61582 / 0.32 ( 9110) hydrogen bonds : bond 0.06074 / 3.70 ( 268) hydrogen bonds : angle 4.03665 / 2.69 ( 724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.241 Fit side-chains REVERT: A 252 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 252 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: B 256 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7817 (mt-10) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.6332 time to fit residues: 55.1076 Evaluate side-chains 77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083765 restraints weight = 12145.934| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.51 r_work: 0.2877 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6564 Z= 0.232 Angle : 0.652 8.468 9110 Z= 0.342 Chirality : 0.046 0.262 1002 Planarity : 0.004 0.039 1032 Dihedral : 22.565 175.209 1270 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 18.26 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.34), residues: 672 helix: 2.07 (0.32), residues: 292 sheet: -0.12 (0.70), residues: 48 loop : 0.20 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 205 TYR 0.026 0.002 TYR B 5 PHE 0.008 0.001 PHE B 87 TRP 0.025 0.002 TRP A 156 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 6564) covalent geometry : angle 0.65234 / 0.34 ( 9110) hydrogen bonds : bond 0.06487 / 4.04 ( 268) hydrogen bonds : angle 4.09983 / 2.74 ( 724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.240 Fit side-chains REVERT: B 66 ASP cc_start: 0.9256 (m-30) cc_final: 0.9018 (m-30) REVERT: B 252 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: B 256 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7836 (mt-10) outliers start: 10 outliers final: 4 residues processed: 79 average time/residue: 0.6429 time to fit residues: 53.2942 Evaluate side-chains 73 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 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 = 0.3505 r_free = 0.3505 target = 0.110486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086110 restraints weight = 12173.300| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.52 r_work: 0.2946 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6564 Z= 0.130 Angle : 0.598 8.124 9110 Z= 0.314 Chirality : 0.044 0.243 1002 Planarity : 0.004 0.043 1032 Dihedral : 22.433 173.674 1270 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.60 % Allowed : 17.73 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 672 helix: 2.22 (0.32), residues: 290 sheet: -0.03 (0.72), residues: 48 loop : 0.38 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 311 TYR 0.015 0.002 TYR B 5 PHE 0.011 0.001 PHE B 54 TRP 0.027 0.002 TRP A 156 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 6564) covalent geometry : angle 0.59806 / 0.31 ( 9110) hydrogen bonds : bond 0.05784 / 3.40 ( 268) hydrogen bonds : angle 3.93511 / 2.63 ( 724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.177 Fit side-chains REVERT: A 85 ASP cc_start: 0.8598 (m-30) cc_final: 0.8360 (m-30) REVERT: A 203 MET cc_start: 0.9403 (ppp) cc_final: 0.9000 (ppp) REVERT: B 36 GLN cc_start: 0.8839 (tt0) cc_final: 0.8276 (tt0) REVERT: B 66 ASP cc_start: 0.9223 (m-30) cc_final: 0.9015 (m-30) REVERT: B 121 MET cc_start: 0.9052 (mmp) cc_final: 0.8805 (mmm) REVERT: B 252 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: B 256 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 260 MET cc_start: 0.9150 (mtp) cc_final: 0.8874 (mmt) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.6661 time to fit residues: 57.9160 Evaluate side-chains 77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086290 restraints weight = 12261.868| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.49 r_work: 0.2951 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6564 Z= 0.123 Angle : 0.583 7.330 9110 Z= 0.306 Chirality : 0.043 0.239 1002 Planarity : 0.003 0.027 1032 Dihedral : 22.428 174.072 1270 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.89 % Allowed : 18.44 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.34), residues: 672 helix: 2.33 (0.32), residues: 292 sheet: -0.11 (0.70), residues: 48 loop : 0.43 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 311 TYR 0.013 0.001 TYR A 223 PHE 0.008 0.001 PHE B 54 TRP 0.027 0.002 TRP A 156 HIS 0.001 0.000 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6564) covalent geometry : angle 0.58282 / 0.31 ( 9110) hydrogen bonds : bond 0.05584 / 3.24 ( 268) hydrogen bonds : angle 3.87432 / 2.59 ( 724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.214 Fit side-chains REVERT: A 203 MET cc_start: 0.9345 (ppp) cc_final: 0.8968 (ppp) REVERT: B 36 GLN cc_start: 0.8890 (tt0) cc_final: 0.8497 (tt0) REVERT: B 121 MET cc_start: 0.9045 (mmp) cc_final: 0.8815 (mmm) REVERT: B 252 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: B 256 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 260 MET cc_start: 0.9127 (mtp) cc_final: 0.8852 (mmt) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.5997 time to fit residues: 48.3909 Evaluate side-chains 73 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 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 = 0.3511 r_free = 0.3511 target = 0.111098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086506 restraints weight = 12177.352| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.54 r_work: 0.2953 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6564 Z= 0.133 Angle : 0.598 7.183 9110 Z= 0.313 Chirality : 0.044 0.247 1002 Planarity : 0.003 0.028 1032 Dihedral : 22.465 175.346 1270 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.60 % Allowed : 17.20 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.34), residues: 672 helix: 2.31 (0.32), residues: 294 sheet: -0.13 (0.69), residues: 48 loop : 0.44 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 311 TYR 0.018 0.002 TYR A 297 PHE 0.008 0.001 PHE B 54 TRP 0.029 0.002 TRP A 156 HIS 0.001 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6564) covalent geometry : angle 0.59811 / 0.31 ( 9110) hydrogen bonds : bond 0.05612 / 3.28 ( 268) hydrogen bonds : angle 3.83372 / 2.57 ( 724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.199 Fit side-chains REVERT: A 203 MET cc_start: 0.9340 (ppp) cc_final: 0.8989 (ppp) REVERT: B 36 GLN cc_start: 0.8933 (tt0) cc_final: 0.8527 (tt0) REVERT: B 121 MET cc_start: 0.9050 (mmp) cc_final: 0.8832 (mmm) REVERT: B 252 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: B 256 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 260 MET cc_start: 0.9137 (mtp) cc_final: 0.8805 (mmt) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.5454 time to fit residues: 43.9639 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 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 = 0.3464 r_free = 0.3464 target = 0.108403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083983 restraints weight = 12099.259| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.50 r_work: 0.2876 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6564 Z= 0.256 Angle : 0.680 6.975 9110 Z= 0.355 Chirality : 0.048 0.258 1002 Planarity : 0.004 0.047 1032 Dihedral : 22.759 179.695 1270 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.06 % Allowed : 17.55 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.34), residues: 672 helix: 2.17 (0.32), residues: 294 sheet: -0.06 (0.67), residues: 48 loop : 0.30 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 311 TYR 0.028 0.003 TYR B 5 PHE 0.015 0.001 PHE A 275 TRP 0.029 0.003 TRP A 156 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 ( 6564) covalent geometry : angle 0.68033 / 0.35 ( 9110) hydrogen bonds : bond 0.06814 / 4.31 ( 268) hydrogen bonds : angle 4.08349 / 2.75 ( 724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.236 Fit side-chains REVERT: B 121 MET cc_start: 0.9089 (mmp) cc_final: 0.8882 (mmm) REVERT: B 129 GLN cc_start: 0.9128 (tp40) cc_final: 0.8804 (tp40) REVERT: B 252 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: B 256 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 314 TYR cc_start: 0.9053 (t80) cc_final: 0.8853 (t80) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.5879 time to fit residues: 43.1732 Evaluate side-chains 67 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084702 restraints weight = 12203.668| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.50 r_work: 0.2923 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6564 Z= 0.178 Angle : 0.628 8.334 9110 Z= 0.330 Chirality : 0.045 0.256 1002 Planarity : 0.004 0.031 1032 Dihedral : 22.678 177.902 1270 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.89 % Allowed : 17.91 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.34), residues: 672 helix: 2.26 (0.32), residues: 292 sheet: -0.04 (0.67), residues: 48 loop : 0.37 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 311 TYR 0.022 0.002 TYR B 5 PHE 0.013 0.001 PHE A 275 TRP 0.029 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 6564) covalent geometry : angle 0.62842 / 0.33 ( 9110) hydrogen bonds : bond 0.06068 / 3.67 ( 268) hydrogen bonds : angle 3.98346 / 2.68 ( 724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.27 seconds wall clock time: 41 minutes 14.12 seconds (2474.12 seconds total)