Starting phenix.real_space_refine on Thu Jul 2 03:00:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyw_34378/07_2026/8gyw_34378.map" } resolution = 3.9 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= 0.005 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 3994 2.51 5 N 984 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 6076 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: A Time building chain proxies: 1.82, per 1000 atoms: 0.30 Number of scatterers: 6076 At special positions: 0 Unit cell: (97.37, 101.65, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 4 15.00 Mg 4 11.99 O 1042 8.00 N 984 7.00 C 3994 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: 0.85 Conformation dependent library (CDL) restraints added in 455.1 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 80.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 28 through 37 Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR B 177 " --> pdb=" O GLN B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 178 through 204 Processing helix chain 'B' and resid 212 through 237 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 247 through 272 removed outlier: 4.189A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 315 through 341 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 368 through 400 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR A 177 " --> pdb=" O GLN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 178 through 204 Processing helix chain 'A' and resid 212 through 237 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 247 through 272 removed outlier: 4.190A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 368 through 400 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE B 239 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE A 239 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 244 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 441 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1379 1.34 - 1.45: 1411 1.45 - 1.57: 3380 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6248 Sorted by residual: bond pdb=" CB PRO A 115 " pdb=" CG PRO A 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.56e+00 bond pdb=" CB PRO B 115 " pdb=" CG PRO B 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.559 -0.042 1.54e-02 4.22e+03 7.49e+00 bond pdb=" CA PRO B 108 " pdb=" C PRO B 108 " ideal model delta sigma weight residual 1.517 1.558 -0.042 1.54e-02 4.22e+03 7.39e+00 bond pdb=" CB PRO B 108 " pdb=" CG PRO B 108 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.74e+00 ... (remaining 6243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 8287 3.79 - 7.58: 197 7.58 - 11.38: 26 11.38 - 15.17: 12 15.17 - 18.96: 2 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 112.00 99.70 12.30 1.40e+00 5.10e-01 7.72e+01 angle pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.71e+01 angle pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" CD PRO A 108 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.03e+01 angle pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" CD PRO B 108 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 135.26 -18.96 3.50e+00 8.16e-02 2.93e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3164 16.52 - 33.04: 280 33.04 - 49.56: 98 49.56 - 66.08: 30 66.08 - 82.61: 6 Dihedral angle restraints: 3578 sinusoidal: 1370 harmonic: 2208 Sorted by residual: dihedral pdb=" C PRO B 108 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " pdb=" CB PRO B 108 " ideal model delta harmonic sigma weight residual -120.70 -129.60 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PRO A 108 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " pdb=" CB PRO A 108 " ideal model delta harmonic sigma weight residual -120.70 -129.55 8.85 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " pdb=" OD1 ASP A 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 758 0.081 - 0.162: 188 0.162 - 0.244: 30 0.244 - 0.325: 6 0.325 - 0.406: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR A 214 " pdb=" CA THR A 214 " pdb=" OG1 THR A 214 " pdb=" CG2 THR A 214 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 981 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.103 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO A 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO B 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 107 " -0.094 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO A 108 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.071 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 38 2.59 - 3.17: 5029 3.17 - 3.74: 9890 3.74 - 4.32: 12054 4.32 - 4.90: 20504 Nonbonded interactions: 47515 Sorted by model distance: nonbonded pdb=" OD1 ASP B 154 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP A 154 " pdb="MG MG A 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 502 " pdb=" O2B CDC B 503 " model vdw 2.085 2.170 nonbonded pdb="MG MG A 502 " pdb=" O2B CDC A 503 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb=" OH TYR A 304 " model vdw 2.269 3.040 ... (remaining 47510 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 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.008 0.146 6248 Z= 0.354 Angle : 1.459 18.960 8524 Z= 0.833 Chirality : 0.077 0.406 984 Planarity : 0.015 0.199 1036 Dihedral : 15.176 82.606 2154 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.94 % Favored : 79.76 % 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: 1.24 (0.29), residues: 756 helix: 0.99 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 0.67 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 77 TYR 0.047 0.006 TYR A 362 PHE 0.069 0.004 PHE B 234 TRP 0.032 0.004 TRP B 181 HIS 0.007 0.002 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.35 ( 6248) covalent geometry : angle 1.45913 / 0.83 ( 8524) hydrogen bonds : bond 0.22029 / 14.95 ( 441) hydrogen bonds : angle 6.72262 / 4.80 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8526 (mt0) REVERT: B 82 TRP cc_start: 0.8514 (p90) cc_final: 0.8297 (p90) REVERT: B 130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7861 (tp-100) REVERT: B 344 MET cc_start: 0.7872 (mtp) cc_final: 0.7572 (mtt) REVERT: B 361 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8109 (mm-40) REVERT: A 82 TRP cc_start: 0.8500 (p90) cc_final: 0.8279 (p90) REVERT: A 130 GLN cc_start: 0.8264 (tp40) cc_final: 0.7912 (tp-100) REVERT: A 361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8295 (mm-40) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.0820 time to fit residues: 20.2154 Evaluate side-chains 172 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141516 restraints weight = 8049.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146483 restraints weight = 4534.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149914 restraints weight = 3083.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151946 restraints weight = 2390.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153549 restraints weight = 2039.364| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6248 Z= 0.154 Angle : 0.629 8.648 8524 Z= 0.332 Chirality : 0.042 0.131 984 Planarity : 0.005 0.051 1036 Dihedral : 3.919 20.239 818 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.38 % Allowed : 15.86 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 756 helix: 2.14 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 0.99 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.012 0.002 TYR B 387 PHE 0.018 0.002 PHE B 358 TRP 0.013 0.001 TRP B 117 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6248) covalent geometry : angle 0.62876 / 0.33 ( 8524) hydrogen bonds : bond 0.05684 / 3.81 ( 441) hydrogen bonds : angle 4.42522 / 3.17 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8489 (mmm) REVERT: B 142 ARG cc_start: 0.8051 (tpt90) cc_final: 0.7723 (tpt90) REVERT: B 260 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 142 ARG cc_start: 0.8158 (tpt90) cc_final: 0.7792 (tpt90) REVERT: A 260 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8235 (t80) outliers start: 29 outliers final: 18 residues processed: 187 average time/residue: 0.0789 time to fit residues: 19.2687 Evaluate side-chains 174 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 GLN A 69 GLN A 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.182890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142769 restraints weight = 7980.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147737 restraints weight = 4510.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151181 restraints weight = 3085.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153484 restraints weight = 2403.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154791 restraints weight = 2039.849| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6248 Z= 0.128 Angle : 0.562 6.112 8524 Z= 0.294 Chirality : 0.040 0.148 984 Planarity : 0.004 0.036 1036 Dihedral : 3.788 20.972 818 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.23 % Allowed : 19.94 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.30), residues: 756 helix: 2.37 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.02 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.011 0.001 TYR A 387 PHE 0.016 0.001 PHE B 187 TRP 0.007 0.001 TRP A 117 HIS 0.003 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 6248) covalent geometry : angle 0.56209 / 0.29 ( 8524) hydrogen bonds : bond 0.04960 / 3.32 ( 441) hydrogen bonds : angle 4.09833 / 2.93 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 TYR cc_start: 0.8250 (m-80) cc_final: 0.8033 (m-80) REVERT: B 142 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7866 (tpt90) REVERT: B 174 GLN cc_start: 0.9047 (mt0) cc_final: 0.8602 (mt0) REVERT: B 193 PHE cc_start: 0.8194 (t80) cc_final: 0.7992 (t80) REVERT: B 247 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8029 (mtpt) REVERT: B 260 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 45 ARG cc_start: 0.7081 (ttt90) cc_final: 0.6814 (tmm160) REVERT: A 127 PHE cc_start: 0.8688 (t80) cc_final: 0.8351 (t80) REVERT: A 193 PHE cc_start: 0.8265 (t80) cc_final: 0.8056 (t80) REVERT: A 306 LYS cc_start: 0.8036 (tppt) cc_final: 0.7824 (tppt) outliers start: 28 outliers final: 14 residues processed: 181 average time/residue: 0.0798 time to fit residues: 18.7949 Evaluate side-chains 177 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.0020 chunk 58 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141742 restraints weight = 7839.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146744 restraints weight = 4412.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150232 restraints weight = 2982.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152584 restraints weight = 2284.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153940 restraints weight = 1933.398| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6248 Z= 0.121 Angle : 0.554 9.850 8524 Z= 0.284 Chirality : 0.041 0.150 984 Planarity : 0.004 0.038 1036 Dihedral : 3.705 19.575 818 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.08 % Allowed : 20.69 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.30), residues: 756 helix: 2.39 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.07 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.010 0.001 TYR B 387 PHE 0.021 0.001 PHE A 234 TRP 0.006 0.001 TRP B 235 HIS 0.003 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 6248) covalent geometry : angle 0.55420 / 0.28 ( 8524) hydrogen bonds : bond 0.04602 / 3.08 ( 441) hydrogen bonds : angle 3.99794 / 2.87 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 ARG cc_start: 0.8135 (tpt90) cc_final: 0.7842 (tpt90) REVERT: B 174 GLN cc_start: 0.9084 (mt0) cc_final: 0.8746 (mt0) REVERT: B 193 PHE cc_start: 0.8214 (t80) cc_final: 0.7970 (t80) REVERT: B 260 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7913 (t80) REVERT: A 50 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8321 (mtp85) REVERT: A 119 TYR cc_start: 0.8280 (m-80) cc_final: 0.8066 (m-80) REVERT: A 127 PHE cc_start: 0.8704 (t80) cc_final: 0.8421 (t80) REVERT: A 174 GLN cc_start: 0.9082 (mt0) cc_final: 0.8717 (mt0) REVERT: A 193 PHE cc_start: 0.8235 (t80) cc_final: 0.8025 (t80) REVERT: A 260 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 302 MET cc_start: 0.8317 (mmt) cc_final: 0.7995 (mtp) REVERT: A 367 ILE cc_start: 0.8290 (mm) cc_final: 0.8066 (tt) outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 0.0847 time to fit residues: 20.2922 Evaluate side-chains 187 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131749 restraints weight = 8537.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136834 restraints weight = 4735.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140221 restraints weight = 3193.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142332 restraints weight = 2468.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143918 restraints weight = 2104.407| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6248 Z= 0.209 Angle : 0.654 8.599 8524 Z= 0.334 Chirality : 0.044 0.157 984 Planarity : 0.005 0.039 1036 Dihedral : 3.932 21.129 818 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 6.19 % Allowed : 20.39 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.30), residues: 756 helix: 2.17 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 1.29 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.009 0.002 TYR B 201 PHE 0.013 0.002 PHE B 351 TRP 0.012 0.001 TRP A 374 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 6248) covalent geometry : angle 0.65397 / 0.33 ( 8524) hydrogen bonds : bond 0.05475 / 3.67 ( 441) hydrogen bonds : angle 4.24589 / 3.06 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7581 (mmt-90) REVERT: B 127 PHE cc_start: 0.8790 (t80) cc_final: 0.8550 (t80) REVERT: B 260 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 306 LYS cc_start: 0.8079 (tppt) cc_final: 0.7806 (tppt) REVERT: B 307 SER cc_start: 0.9029 (t) cc_final: 0.8816 (t) REVERT: A 50 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8406 (mtp85) REVERT: A 55 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7628 (mmt-90) REVERT: A 127 PHE cc_start: 0.8799 (t80) cc_final: 0.8570 (t80) REVERT: A 260 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 306 LYS cc_start: 0.8052 (tppt) cc_final: 0.7798 (tppt) REVERT: A 307 SER cc_start: 0.8984 (t) cc_final: 0.8749 (t) outliers start: 41 outliers final: 30 residues processed: 195 average time/residue: 0.0856 time to fit residues: 21.2186 Evaluate side-chains 193 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 HIS A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.174893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136011 restraints weight = 8274.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141254 restraints weight = 4533.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144771 restraints weight = 3030.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147108 restraints weight = 2325.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148138 restraints weight = 1956.929| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6248 Z= 0.135 Angle : 0.611 11.639 8524 Z= 0.308 Chirality : 0.041 0.131 984 Planarity : 0.004 0.037 1036 Dihedral : 3.845 20.653 818 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.83 % Allowed : 23.56 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.30), residues: 756 helix: 2.20 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.14 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.017 0.001 TYR B 362 PHE 0.019 0.001 PHE A 234 TRP 0.005 0.001 TRP B 235 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 6248) covalent geometry : angle 0.61050 / 0.31 ( 8524) hydrogen bonds : bond 0.04852 / 3.24 ( 441) hydrogen bonds : angle 4.06833 / 2.93 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.8792 (t80) cc_final: 0.8573 (t80) REVERT: B 260 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7924 (t80) REVERT: B 302 MET cc_start: 0.8565 (mmt) cc_final: 0.8231 (mmm) REVERT: B 306 LYS cc_start: 0.8057 (tppt) cc_final: 0.7813 (tppt) REVERT: A 260 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 306 LYS cc_start: 0.8070 (tppt) cc_final: 0.7838 (tppt) outliers start: 32 outliers final: 26 residues processed: 179 average time/residue: 0.0920 time to fit residues: 20.8638 Evaluate side-chains 188 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 GLN A 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.174607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135887 restraints weight = 8275.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141107 restraints weight = 4546.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144623 restraints weight = 3047.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146941 restraints weight = 2340.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148253 restraints weight = 1976.775| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6248 Z= 0.136 Angle : 0.629 12.337 8524 Z= 0.310 Chirality : 0.041 0.128 984 Planarity : 0.004 0.039 1036 Dihedral : 3.770 20.020 818 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.23 % Allowed : 26.13 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.30), residues: 756 helix: 2.20 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.17 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 61 TYR 0.018 0.001 TYR B 362 PHE 0.013 0.001 PHE B 187 TRP 0.005 0.001 TRP A 117 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 6248) covalent geometry : angle 0.62902 / 0.31 ( 8524) hydrogen bonds : bond 0.04744 / 3.17 ( 441) hydrogen bonds : angle 4.05361 / 2.92 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7866 (t80) REVERT: B 302 MET cc_start: 0.8517 (mmt) cc_final: 0.8184 (mmm) REVERT: B 306 LYS cc_start: 0.8016 (tppt) cc_final: 0.7768 (tppt) REVERT: B 307 SER cc_start: 0.8956 (t) cc_final: 0.8691 (t) REVERT: A 246 MET cc_start: 0.8058 (tpp) cc_final: 0.7748 (tpp) REVERT: A 260 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7978 (t80) REVERT: A 306 LYS cc_start: 0.8040 (tppt) cc_final: 0.7810 (tppt) REVERT: A 307 SER cc_start: 0.8975 (t) cc_final: 0.8700 (t) outliers start: 28 outliers final: 25 residues processed: 174 average time/residue: 0.0799 time to fit residues: 17.9962 Evaluate side-chains 189 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.173168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134348 restraints weight = 8328.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139499 restraints weight = 4603.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143047 restraints weight = 3097.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145347 restraints weight = 2387.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146931 restraints weight = 2011.065| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6248 Z= 0.154 Angle : 0.666 12.666 8524 Z= 0.325 Chirality : 0.042 0.129 984 Planarity : 0.004 0.040 1036 Dihedral : 3.817 20.163 818 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.59 % Allowed : 25.23 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.30), residues: 756 helix: 2.12 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.02 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 50 TYR 0.018 0.002 TYR B 362 PHE 0.012 0.001 PHE B 187 TRP 0.005 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6248) covalent geometry : angle 0.66582 / 0.33 ( 8524) hydrogen bonds : bond 0.04936 / 3.30 ( 441) hydrogen bonds : angle 4.10547 / 2.95 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.8817 (t80) cc_final: 0.8578 (t80) REVERT: B 260 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 302 MET cc_start: 0.8576 (mmt) cc_final: 0.8184 (mmm) REVERT: B 306 LYS cc_start: 0.7922 (tppt) cc_final: 0.7031 (mmtt) REVERT: B 307 SER cc_start: 0.9019 (t) cc_final: 0.8780 (t) REVERT: A 98 CYS cc_start: 0.7681 (m) cc_final: 0.7384 (p) REVERT: A 246 MET cc_start: 0.8060 (tpp) cc_final: 0.7746 (tpp) REVERT: A 260 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 306 LYS cc_start: 0.7877 (tppt) cc_final: 0.7061 (mmtt) REVERT: A 307 SER cc_start: 0.9041 (t) cc_final: 0.8788 (t) outliers start: 37 outliers final: 31 residues processed: 184 average time/residue: 0.0911 time to fit residues: 21.2097 Evaluate side-chains 200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 62 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135929 restraints weight = 8341.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141328 restraints weight = 4525.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144956 restraints weight = 3008.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147196 restraints weight = 2296.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148879 restraints weight = 1936.620| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6248 Z= 0.137 Angle : 0.676 12.970 8524 Z= 0.326 Chirality : 0.041 0.134 984 Planarity : 0.004 0.038 1036 Dihedral : 3.795 20.362 818 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.83 % Allowed : 26.28 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.30), residues: 756 helix: 2.14 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.04 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.019 0.001 TYR B 362 PHE 0.020 0.001 PHE A 234 TRP 0.006 0.001 TRP B 82 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6248) covalent geometry : angle 0.67588 / 0.33 ( 8524) hydrogen bonds : bond 0.04721 / 3.15 ( 441) hydrogen bonds : angle 4.04385 / 2.91 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7867 (t80) REVERT: B 306 LYS cc_start: 0.7836 (tppt) cc_final: 0.7168 (mmtt) REVERT: B 307 SER cc_start: 0.8994 (t) cc_final: 0.8574 (t) REVERT: B 405 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6785 (mtt90) REVERT: A 130 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7721 (tp-100) REVERT: A 260 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 306 LYS cc_start: 0.7899 (tppt) cc_final: 0.7110 (mmtt) REVERT: A 307 SER cc_start: 0.9006 (t) cc_final: 0.8748 (t) outliers start: 32 outliers final: 25 residues processed: 187 average time/residue: 0.0912 time to fit residues: 21.5679 Evaluate side-chains 195 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.175127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136239 restraints weight = 8374.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141626 restraints weight = 4575.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145285 restraints weight = 3037.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147554 restraints weight = 2317.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149175 restraints weight = 1952.797| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6248 Z= 0.148 Angle : 0.714 12.989 8524 Z= 0.340 Chirality : 0.042 0.136 984 Planarity : 0.004 0.041 1036 Dihedral : 3.850 19.961 818 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.23 % Allowed : 27.34 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.30), residues: 756 helix: 2.04 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 0.77 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 141 TYR 0.021 0.002 TYR A 362 PHE 0.012 0.001 PHE B 187 TRP 0.004 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 6248) covalent geometry : angle 0.71379 / 0.34 ( 8524) hydrogen bonds : bond 0.04773 / 3.18 ( 441) hydrogen bonds : angle 4.08275 / 2.94 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7808 (t80) REVERT: B 306 LYS cc_start: 0.8014 (tppt) cc_final: 0.7227 (mmtt) REVERT: B 307 SER cc_start: 0.8975 (t) cc_final: 0.8712 (t) REVERT: B 405 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6886 (mtt90) REVERT: A 260 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7902 (t80) REVERT: A 306 LYS cc_start: 0.7962 (tppt) cc_final: 0.7257 (mmtt) REVERT: A 307 SER cc_start: 0.9028 (t) cc_final: 0.8732 (t) REVERT: A 361 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7967 (mm110) outliers start: 28 outliers final: 26 residues processed: 179 average time/residue: 0.0833 time to fit residues: 19.0157 Evaluate side-chains 193 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 0.0170 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137262 restraints weight = 8202.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142610 restraints weight = 4425.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146179 restraints weight = 2925.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148412 restraints weight = 2219.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149994 restraints weight = 1864.019| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6248 Z= 0.143 Angle : 0.700 13.246 8524 Z= 0.334 Chirality : 0.042 0.136 984 Planarity : 0.004 0.042 1036 Dihedral : 3.860 19.957 818 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.14 % Allowed : 26.28 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.30), residues: 756 helix: 2.04 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 0.70 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.021 0.002 TYR A 362 PHE 0.024 0.001 PHE A 234 TRP 0.006 0.001 TRP A 117 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6248) covalent geometry : angle 0.70025 / 0.33 ( 8524) hydrogen bonds : bond 0.04709 / 3.14 ( 441) hydrogen bonds : angle 4.07544 / 2.93 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.04 seconds wall clock time: 19 minutes 52.50 seconds (1192.50 seconds total)