Starting phenix.real_space_refine on Fri Sep 11 02:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ss5_25404/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ss5_25404/09_2026/7ss5_25404.cif" } 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-2.2.1-6174/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: 2.29, per 1000 atoms: 0.33 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: 0.64 Conformation dependent library (CDL) restraints added in 437.8 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: 0.79 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: 1.18 Time building geometry restraints manager: 0.86 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: 8744 1.56 - 3.11: 306 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.540 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: 0.000 Total: 19.380 ------------------------------------------------------------------------------- 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 : 0.689 7.778 9110 Z= 0.491 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 0.68902 / 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 : 0.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.7139 time to fit residues: 114.2449 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 : 0.163 ------------------------------------------------------------------------------- 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: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 129 GLN A 307 HIS B 39 GLN B 112 ASN B 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085424 restraints weight = 12238.976| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.53 r_work: 0.2916 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6564 Z= 0.217 Angle : 0.694 7.258 9110 Z= 0.364 Chirality : 0.047 0.272 1002 Planarity : 0.004 0.035 1032 Dihedral : 22.260 175.505 1270 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 14.36 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.34), residues: 672 helix: 1.91 (0.33), residues: 286 sheet: -0.41 (0.77), residues: 50 loop : 0.06 (0.35), 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 0.007 0.001 PHE B 54 TRP 0.021 0.002 TRP A 156 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 6564) covalent geometry : angle 0.69415 / 0.36 ( 9110) hydrogen bonds : bond 0.06806 / 4.16 ( 268) hydrogen bonds : angle 4.50676 / 2.96 ( 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 98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.200 Fit side-chains REVERT: A 332 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8552 (pp20) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 0.6672 time to fit residues: 65.5813 Evaluate side-chains 90 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.111158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086166 restraints weight = 11955.682| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.55 r_work: 0.2925 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6564 Z= 0.150 Angle : 0.609 6.564 9110 Z= 0.324 Chirality : 0.044 0.275 1002 Planarity : 0.004 0.035 1032 Dihedral : 22.313 172.755 1270 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.19 % Allowed : 15.25 % Favored : 81.56 % 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: 1.27 (0.34), residues: 672 helix: 1.91 (0.32), residues: 292 sheet: -0.40 (0.74), residues: 50 loop : 0.15 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 311 TYR 0.012 0.002 TYR B 297 PHE 0.008 0.001 PHE A 54 TRP 0.022 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6564) covalent geometry : angle 0.60887 / 0.32 ( 9110) hydrogen bonds : bond 0.06078 / 3.69 ( 268) hydrogen bonds : angle 4.19504 / 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 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.175 Fit side-chains REVERT: A 73 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: A 224 GLN cc_start: 0.9335 (mt0) cc_final: 0.9103 (mp10) REVERT: A 252 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 256 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 39 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8806 (pt0) REVERT: B 129 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8871 (tp40) outliers start: 18 outliers final: 6 residues processed: 98 average time/residue: 0.7349 time to fit residues: 75.2196 Evaluate side-chains 86 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.111561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086938 restraints weight = 11972.552| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.56 r_work: 0.2927 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6564 Z= 0.148 Angle : 0.610 8.055 9110 Z= 0.320 Chirality : 0.044 0.270 1002 Planarity : 0.004 0.054 1032 Dihedral : 22.311 171.695 1270 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.48 % Allowed : 15.25 % Favored : 82.27 % 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: 1.36 (0.34), residues: 672 helix: 1.97 (0.32), residues: 292 sheet: -0.29 (0.74), residues: 50 loop : 0.21 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.016 0.002 TYR A 297 PHE 0.013 0.001 PHE B 171 TRP 0.022 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6564) covalent geometry : angle 0.61040 / 0.32 ( 9110) hydrogen bonds : bond 0.05905 / 3.56 ( 268) hydrogen bonds : angle 4.07968 / 2.70 ( 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 98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: A 36 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.9001 (tt0) REVERT: A 73 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: A 252 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 256 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 252 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8154 (tm130) REVERT: B 314 TYR cc_start: 0.9000 (t80) cc_final: 0.8768 (t80) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 0.7227 time to fit residues: 67.8816 Evaluate side-chains 84 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 321 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.110265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085392 restraints weight = 12075.747| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.55 r_work: 0.2914 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6564 Z= 0.161 Angle : 0.615 8.475 9110 Z= 0.321 Chirality : 0.045 0.273 1002 Planarity : 0.004 0.064 1032 Dihedral : 22.378 172.096 1270 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.60 % Allowed : 17.55 % Favored : 80.85 % 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: -0.26 (0.72), residues: 50 loop : 0.23 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.016 0.002 TYR A 223 PHE 0.008 0.001 PHE B 54 TRP 0.023 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6564) covalent geometry : angle 0.61469 / 0.32 ( 9110) hydrogen bonds : bond 0.05956 / 3.59 ( 268) hydrogen bonds : angle 4.03124 / 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 85 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.253 Fit side-chains REVERT: A 73 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: B 66 ASP cc_start: 0.9232 (m-30) cc_final: 0.9002 (m-30) REVERT: B 121 MET cc_start: 0.9008 (mmp) cc_final: 0.8777 (mmm) REVERT: B 252 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 314 TYR cc_start: 0.9032 (t80) cc_final: 0.8806 (t80) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.6644 time to fit residues: 56.2572 Evaluate side-chains 76 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU 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 321 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085211 restraints weight = 12097.443| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.50 r_work: 0.2899 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2992 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= 0.187 Angle : 0.624 7.840 9110 Z= 0.328 Chirality : 0.045 0.279 1002 Planarity : 0.004 0.055 1032 Dihedral : 22.458 172.393 1270 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 18.09 % Favored : 80.14 % 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: 1.50 (0.34), residues: 672 helix: 2.09 (0.32), residues: 292 sheet: -0.10 (0.70), residues: 48 loop : 0.25 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 311 TYR 0.017 0.002 TYR A 223 PHE 0.009 0.001 PHE A 275 TRP 0.025 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 6564) covalent geometry : angle 0.62433 / 0.33 ( 9110) hydrogen bonds : bond 0.06128 / 3.74 ( 268) hydrogen bonds : angle 4.01684 / 2.68 ( 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 86 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.252 Fit side-chains REVERT: A 256 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 17 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8990 (mp0) REVERT: B 66 ASP cc_start: 0.9254 (m-30) cc_final: 0.9034 (m-30) REVERT: B 252 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 256 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 260 MET cc_start: 0.9153 (mtp) cc_final: 0.8844 (mmt) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.6584 time to fit residues: 57.2907 Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 321 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.109899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084971 restraints weight = 11985.500| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.53 r_work: 0.2956 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6564 Z= 0.142 Angle : 0.605 8.539 9110 Z= 0.317 Chirality : 0.044 0.270 1002 Planarity : 0.004 0.071 1032 Dihedral : 22.413 171.822 1270 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 18.09 % Favored : 80.14 % 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: 1.64 (0.34), residues: 672 helix: 2.20 (0.32), residues: 292 sheet: -0.11 (0.70), residues: 48 loop : 0.35 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 311 TYR 0.012 0.001 TYR A 297 PHE 0.009 0.001 PHE B 54 TRP 0.026 0.002 TRP A 156 HIS 0.001 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6564) covalent geometry : angle 0.60541 / 0.32 ( 9110) hydrogen bonds : bond 0.05836 / 3.48 ( 268) hydrogen bonds : angle 3.96210 / 2.65 ( 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 96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.255 Fit side-chains REVERT: B 63 ASP cc_start: 0.8991 (t0) cc_final: 0.8670 (t0) REVERT: B 252 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 256 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 260 MET cc_start: 0.9177 (mtp) cc_final: 0.8852 (mmt) outliers start: 10 outliers final: 4 residues processed: 93 average time/residue: 0.5746 time to fit residues: 56.1994 Evaluate side-chains 76 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.111144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086490 restraints weight = 12021.032| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.51 r_work: 0.2964 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6564 Z= 0.139 Angle : 0.614 7.711 9110 Z= 0.322 Chirality : 0.044 0.269 1002 Planarity : 0.004 0.045 1032 Dihedral : 22.409 171.919 1270 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.60 % Allowed : 17.91 % Favored : 80.50 % 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: 1.68 (0.34), residues: 672 helix: 2.26 (0.32), residues: 292 sheet: -0.22 (0.69), residues: 48 loop : 0.37 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 65 TYR 0.015 0.002 TYR A 223 PHE 0.008 0.001 PHE B 54 TRP 0.027 0.002 TRP A 156 HIS 0.001 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6564) covalent geometry : angle 0.61423 / 0.32 ( 9110) hydrogen bonds : bond 0.05731 / 3.38 ( 268) hydrogen bonds : angle 3.92773 / 2.63 ( 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 86 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.302 Fit side-chains REVERT: A 203 MET cc_start: 0.9266 (ppp) cc_final: 0.8948 (ppp) REVERT: A 256 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8023 (mt-10) REVERT: B 121 MET cc_start: 0.9051 (mmp) cc_final: 0.8791 (mmm) REVERT: B 252 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 256 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 260 MET cc_start: 0.9170 (mtp) cc_final: 0.8838 (mmt) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 0.6126 time to fit residues: 54.5809 Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL 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: 0.0570 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.111478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.087220 restraints weight = 12044.124| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.49 r_work: 0.2940 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6564 Z= 0.134 Angle : 0.604 7.364 9110 Z= 0.316 Chirality : 0.044 0.267 1002 Planarity : 0.004 0.084 1032 Dihedral : 22.436 174.386 1270 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.06 % Allowed : 18.62 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.34), residues: 672 helix: 2.27 (0.31), residues: 294 sheet: -0.16 (0.69), residues: 48 loop : 0.41 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 65 TYR 0.017 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 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6564) covalent geometry : angle 0.60426 / 0.32 ( 9110) hydrogen bonds : bond 0.05643 / 3.31 ( 268) hydrogen bonds : angle 3.91415 / 2.63 ( 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 87 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.182 Fit side-chains REVERT: A 203 MET cc_start: 0.9259 (ppp) cc_final: 0.8943 (ppp) REVERT: B 121 MET cc_start: 0.9042 (mmp) cc_final: 0.8790 (mmm) REVERT: B 129 GLN cc_start: 0.9007 (tp40) cc_final: 0.8740 (tp40) REVERT: B 252 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 256 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.6488 time to fit residues: 58.5916 Evaluate side-chains 81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.110851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085685 restraints weight = 11993.707| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.54 r_work: 0.2915 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6564 Z= 0.174 Angle : 0.634 7.337 9110 Z= 0.330 Chirality : 0.045 0.275 1002 Planarity : 0.004 0.050 1032 Dihedral : 22.527 175.257 1270 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.24 % Allowed : 18.62 % Favored : 80.14 % 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: 2.22 (0.32), residues: 294 sheet: -0.06 (0.66), residues: 48 loop : 0.39 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 65 TYR 0.017 0.002 TYR A 223 PHE 0.007 0.001 PHE A 241 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 0.00397 / 0.17 ( 6564) covalent geometry : angle 0.63374 / 0.33 ( 9110) hydrogen bonds : bond 0.05913 / 3.56 ( 268) hydrogen bonds : angle 3.97486 / 2.69 ( 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 84 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.270 Fit side-chains REVERT: B 121 MET cc_start: 0.9060 (mmp) cc_final: 0.8822 (mmm) REVERT: B 129 GLN cc_start: 0.9033 (tp40) cc_final: 0.8758 (tp40) REVERT: B 252 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 256 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7849 (mt-10) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.6470 time to fit residues: 56.3409 Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.111031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085828 restraints weight = 12041.027| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.54 r_work: 0.2918 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6564 Z= 0.167 Angle : 0.633 7.344 9110 Z= 0.331 Chirality : 0.045 0.277 1002 Planarity : 0.003 0.030 1032 Dihedral : 22.569 175.883 1270 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.06 % Allowed : 18.44 % Favored : 80.50 % 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: 1.75 (0.34), residues: 672 helix: 2.27 (0.31), residues: 292 sheet: -0.06 (0.65), residues: 48 loop : 0.43 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 65 TYR 0.017 0.002 TYR A 223 PHE 0.008 0.001 PHE B 54 TRP 0.028 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 6564) covalent geometry : angle 0.63307 / 0.33 ( 9110) hydrogen bonds : bond 0.05861 / 3.52 ( 268) hydrogen bonds : angle 3.98171 / 2.69 ( 724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.79 seconds wall clock time: 42 minutes 56.44 seconds (2576.44 seconds total)