Starting phenix.real_space_refine on Tue Feb 3 20:27:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.map" model { file = "/net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e06_47350/02_2026/9e06_47350.cif" } resolution = 3.1 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4569 2.51 5 N 996 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6660 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 325 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "F" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 325 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "D" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 325 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "E" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Time building chain proxies: 1.32, per 1000 atoms: 0.20 Number of scatterers: 6660 At special positions: 0 Unit cell: (96.512, 100.672, 89.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1062 8.00 N 996 7.00 C 4569 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: 0.54 Conformation dependent library (CDL) restraints added in 213.5 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 89.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 5 through 21 Processing helix chain 'B' and resid 24 through 42 removed outlier: 3.523A pdb=" N THR B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 33 removed outlier: 3.679A pdb=" N GLN A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Proline residue: A 44 - end of helix removed outlier: 3.531A pdb=" N MET A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 196 Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.150A pdb=" N LYS A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'A' and resid 228 through 241 removed outlier: 4.188A pdb=" N PHE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 282 removed outlier: 3.660A pdb=" N GLY A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Proline residue: A 272 - end of helix removed outlier: 3.680A pdb=" N TYR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.991A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 336 Proline residue: A 321 - end of helix Processing helix chain 'F' and resid 5 through 21 removed outlier: 3.533A pdb=" N ILE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 42 Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 24 through 42 Processing helix chain 'E' and resid 5 through 33 removed outlier: 3.727A pdb=" N ILE E 18 " --> pdb=" O GLN E 14 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 60 Proline residue: E 44 - end of helix removed outlier: 3.527A pdb=" N ILE E 55 " --> pdb=" O GLN E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 196 Proline residue: E 185 - end of helix Processing helix chain 'E' and resid 200 through 205 removed outlier: 4.413A pdb=" N LYS E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 228 Processing helix chain 'E' and resid 228 through 241 removed outlier: 4.336A pdb=" N PHE E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 282 removed outlier: 3.900A pdb=" N GLY E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Proline residue: E 272 - end of helix removed outlier: 3.669A pdb=" N TYR E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 292 through 307 removed outlier: 4.186A pdb=" N VAL E 298 " --> pdb=" O LYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 336 Proline residue: E 321 - end of helix removed outlier: 3.640A pdb=" N LEU E 331 " --> pdb=" O GLY E 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 33 removed outlier: 3.725A pdb=" N ILE C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 60 Proline residue: C 44 - end of helix removed outlier: 3.581A pdb=" N ILE C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 196 Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 200 through 228 removed outlier: 4.226A pdb=" N LYS C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N MET C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 207 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.652A pdb=" N GLN C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 282 removed outlier: 3.695A pdb=" N GLY C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Proline residue: C 272 - end of helix removed outlier: 3.792A pdb=" N TYR C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 292 through 307 removed outlier: 3.884A pdb=" N VAL C 298 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 336 Proline residue: C 321 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.146A pdb=" N THR A 246 " --> pdb=" O THR C 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 160 through 161 537 hydrogen bonds defined for protein. 1611 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: 0.68 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1901 1.34 - 1.46: 1400 1.46 - 1.58: 3473 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6840 Sorted by residual: bond pdb=" CB VAL E 312 " pdb=" CG2 VAL E 312 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.51e-01 bond pdb=" CA PRO A 247 " pdb=" C PRO A 247 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 6.91e-01 bond pdb=" N PRO E 247 " pdb=" CA PRO E 247 " ideal model delta sigma weight residual 1.479 1.468 0.012 1.71e-02 3.42e+03 4.80e-01 bond pdb=" C LEU D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.66e-01 bond pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 1.479 1.468 0.012 1.71e-02 3.42e+03 4.61e-01 ... (remaining 6835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9066 1.37 - 2.74: 159 2.74 - 4.11: 34 4.11 - 5.49: 31 5.49 - 6.86: 1 Bond angle restraints: 9291 Sorted by residual: angle pdb=" N GLY F 3 " pdb=" CA GLY F 3 " pdb=" C GLY F 3 " ideal model delta sigma weight residual 114.95 110.02 4.93 1.41e+00 5.03e-01 1.22e+01 angle pdb=" N GLY D 3 " pdb=" CA GLY D 3 " pdb=" C GLY D 3 " ideal model delta sigma weight residual 115.63 110.50 5.13 1.49e+00 4.50e-01 1.19e+01 angle pdb=" N SER F 7 " pdb=" CA SER F 7 " pdb=" C SER F 7 " ideal model delta sigma weight residual 112.38 109.00 3.38 1.22e+00 6.72e-01 7.69e+00 angle pdb=" N GLU C 57 " pdb=" CA GLU C 57 " pdb=" C GLU C 57 " ideal model delta sigma weight residual 112.93 110.25 2.68 1.12e+00 7.97e-01 5.74e+00 angle pdb=" CA GLY D 3 " pdb=" C GLY D 3 " pdb=" N MET D 4 " ideal model delta sigma weight residual 118.64 115.77 2.87 1.24e+00 6.50e-01 5.36e+00 ... (remaining 9286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3350 17.88 - 35.75: 436 35.75 - 53.62: 126 53.62 - 71.50: 18 71.50 - 89.37: 3 Dihedral angle restraints: 3933 sinusoidal: 1509 harmonic: 2424 Sorted by residual: dihedral pdb=" CB GLU E 270 " pdb=" CG GLU E 270 " pdb=" CD GLU E 270 " pdb=" OE1 GLU E 270 " ideal model delta sinusoidal sigma weight residual 0.00 -89.37 89.37 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 -89.34 89.34 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 270 " pdb=" CG GLU C 270 " pdb=" CD GLU C 270 " pdb=" OE1 GLU C 270 " ideal model delta sinusoidal sigma weight residual 0.00 -89.27 89.27 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 617 0.024 - 0.048: 254 0.048 - 0.072: 152 0.072 - 0.097: 66 0.097 - 0.121: 24 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA THR C 230 " pdb=" N THR C 230 " pdb=" C THR C 230 " pdb=" CB THR C 230 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA THR E 230 " pdb=" N THR E 230 " pdb=" C THR E 230 " pdb=" CB THR E 230 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA THR A 230 " pdb=" N THR A 230 " pdb=" C THR A 230 " pdb=" CB THR A 230 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 1110 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 309 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 310 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 309 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.67e+00 pdb=" N PRO C 310 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 310 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 310 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 309 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO E 310 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 310 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 310 " -0.017 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 89 2.68 - 3.23: 6574 3.23 - 3.79: 10515 3.79 - 4.34: 13377 4.34 - 4.90: 22204 Nonbonded interactions: 52759 Sorted by model distance: nonbonded pdb=" O ALA E 304 " pdb=" OG1 THR E 308 " model vdw 2.122 3.040 nonbonded pdb=" O ALA A 304 " pdb=" OG1 THR A 308 " model vdw 2.140 3.040 nonbonded pdb=" O ALA C 304 " pdb=" OG1 THR C 308 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLU B 8 " pdb=" NE2 GLN A 315 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR C 161 " pdb=" OE2 GLU C 252 " model vdw 2.215 3.040 ... (remaining 52754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.690 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.003 0.032 6840 Z= 0.137 Angle : 0.545 6.858 9291 Z= 0.287 Chirality : 0.039 0.121 1113 Planarity : 0.004 0.033 1110 Dihedral : 17.027 89.374 2373 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.55 % Allowed : 29.66 % Favored : 68.79 % 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 (0.30), residues: 825 helix: 1.60 (0.20), residues: 693 sheet: -3.14 (0.97), residues: 30 loop : -2.59 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.013 0.001 TYR E 295 PHE 0.011 0.001 PHE A 243 TRP 0.007 0.001 TRP A 40 HIS 0.008 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6840) covalent geometry : angle 0.54481 ( 9291) hydrogen bonds : bond 0.20493 ( 537) hydrogen bonds : angle 6.80885 ( 1611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.248 Fit side-chains REVERT: A 184 MET cc_start: 0.7733 (tpp) cc_final: 0.7444 (tpp) REVERT: A 324 LEU cc_start: 0.8003 (mm) cc_final: 0.7716 (mm) REVERT: F 1 MET cc_start: 0.6591 (ppp) cc_final: 0.6249 (ppp) REVERT: E 206 MET cc_start: 0.7719 (ppp) cc_final: 0.7322 (ppp) REVERT: E 318 MET cc_start: 0.8015 (tpp) cc_final: 0.7425 (tpp) REVERT: C 206 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7402 (ppp) REVERT: C 331 LEU cc_start: 0.8065 (mm) cc_final: 0.7705 (mp) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.0452 time to fit residues: 8.9207 Evaluate side-chains 130 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.141024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119316 restraints weight = 9170.563| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.88 r_work: 0.3262 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6840 Z= 0.139 Angle : 0.547 6.376 9291 Z= 0.270 Chirality : 0.040 0.127 1113 Planarity : 0.004 0.036 1110 Dihedral : 5.608 55.389 897 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.37 % Allowed : 22.32 % Favored : 72.32 % 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: 2.07 (0.29), residues: 825 helix: 2.00 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -2.33 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 59 TYR 0.013 0.001 TYR E 295 PHE 0.008 0.001 PHE C 306 TRP 0.012 0.002 TRP C 192 HIS 0.008 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6840) covalent geometry : angle 0.54667 ( 9291) hydrogen bonds : bond 0.03978 ( 537) hydrogen bonds : angle 4.27763 ( 1611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.249 Fit side-chains REVERT: F 1 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5845 (ppp) REVERT: F 10 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7705 (mm) REVERT: D 10 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7761 (mm) REVERT: E 191 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (tt) REVERT: E 206 MET cc_start: 0.7942 (ppp) cc_final: 0.7585 (ppp) REVERT: E 318 MET cc_start: 0.8047 (tpp) cc_final: 0.7518 (tpp) REVERT: C 206 MET cc_start: 0.7692 (ppp) cc_final: 0.7388 (ppp) REVERT: C 331 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7696 (mm) outliers start: 38 outliers final: 17 residues processed: 137 average time/residue: 0.0431 time to fit residues: 9.3546 Evaluate side-chains 134 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.139990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118492 restraints weight = 9022.358| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.86 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6840 Z= 0.178 Angle : 0.547 6.812 9291 Z= 0.270 Chirality : 0.042 0.151 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.769 47.402 884 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 6.21 % Allowed : 19.35 % Favored : 74.44 % 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: 2.17 (0.29), residues: 825 helix: 2.08 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.34 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.012 0.001 TYR C 295 PHE 0.009 0.001 PHE A 224 TRP 0.011 0.002 TRP C 192 HIS 0.008 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6840) covalent geometry : angle 0.54696 ( 9291) hydrogen bonds : bond 0.03946 ( 537) hydrogen bonds : angle 4.14844 ( 1611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.245 Fit side-chains REVERT: A 206 MET cc_start: 0.7549 (ppp) cc_final: 0.7273 (ppp) REVERT: F 1 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6091 (ppp) REVERT: F 10 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7838 (mm) REVERT: E 191 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8018 (tt) REVERT: E 206 MET cc_start: 0.7967 (ppp) cc_final: 0.7605 (ppp) REVERT: C 206 MET cc_start: 0.7682 (ppp) cc_final: 0.7429 (ppp) REVERT: C 331 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7685 (mm) outliers start: 44 outliers final: 22 residues processed: 143 average time/residue: 0.0476 time to fit residues: 10.7076 Evaluate side-chains 140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.138782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117567 restraints weight = 9007.865| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.86 r_work: 0.3267 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6840 Z= 0.137 Angle : 0.517 6.444 9291 Z= 0.253 Chirality : 0.041 0.179 1113 Planarity : 0.004 0.038 1110 Dihedral : 4.658 47.418 884 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.65 % Allowed : 20.90 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.45 (0.29), residues: 825 helix: 2.26 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -2.24 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.012 0.001 TYR C 295 PHE 0.008 0.001 PHE A 224 TRP 0.009 0.001 TRP E 192 HIS 0.008 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6840) covalent geometry : angle 0.51667 ( 9291) hydrogen bonds : bond 0.03452 ( 537) hydrogen bonds : angle 4.01652 ( 1611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.241 Fit side-chains REVERT: A 184 MET cc_start: 0.7823 (tpp) cc_final: 0.7452 (tpp) REVERT: A 205 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7756 (mtmm) REVERT: A 206 MET cc_start: 0.7476 (ppp) cc_final: 0.7114 (ppp) REVERT: A 324 LEU cc_start: 0.7976 (mm) cc_final: 0.7698 (mm) REVERT: F 1 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6037 (ppp) REVERT: F 10 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7829 (mm) REVERT: E 191 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7994 (tt) REVERT: E 206 MET cc_start: 0.7992 (ppp) cc_final: 0.7641 (ppp) REVERT: E 306 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: C 206 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7424 (ppp) outliers start: 40 outliers final: 24 residues processed: 129 average time/residue: 0.0486 time to fit residues: 9.6470 Evaluate side-chains 139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118305 restraints weight = 9149.519| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.85 r_work: 0.3239 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6840 Z= 0.168 Angle : 0.529 6.201 9291 Z= 0.261 Chirality : 0.043 0.211 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.693 48.420 884 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.93 % Allowed : 20.20 % Favored : 73.87 % 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: 2.40 (0.29), residues: 825 helix: 2.21 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -2.10 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 59 TYR 0.010 0.001 TYR C 295 PHE 0.009 0.001 PHE A 224 TRP 0.008 0.001 TRP E 192 HIS 0.008 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6840) covalent geometry : angle 0.52870 ( 9291) hydrogen bonds : bond 0.03671 ( 537) hydrogen bonds : angle 4.05568 ( 1611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.242 Fit side-chains REVERT: A 205 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7735 (mtmm) REVERT: A 206 MET cc_start: 0.7506 (ppp) cc_final: 0.7133 (ppp) REVERT: A 324 LEU cc_start: 0.7980 (mm) cc_final: 0.7690 (mm) REVERT: F 1 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6064 (ppp) REVERT: D 25 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6178 (tp) REVERT: E 191 LEU cc_start: 0.8207 (tt) cc_final: 0.7974 (tt) REVERT: E 206 MET cc_start: 0.7981 (ppp) cc_final: 0.7633 (ppp) REVERT: E 219 LEU cc_start: 0.7959 (tp) cc_final: 0.7675 (mp) REVERT: C 206 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7403 (ppp) outliers start: 42 outliers final: 26 residues processed: 135 average time/residue: 0.0481 time to fit residues: 10.0033 Evaluate side-chains 146 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3654 r_free = 0.3654 target = 0.139627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118141 restraints weight = 9015.653| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.86 r_work: 0.3245 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6840 Z= 0.169 Angle : 0.524 6.218 9291 Z= 0.258 Chirality : 0.042 0.210 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.618 49.828 882 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.93 % Allowed : 20.34 % Favored : 73.73 % 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: 2.47 (0.29), residues: 825 helix: 2.27 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 59 TYR 0.008 0.001 TYR C 295 PHE 0.009 0.001 PHE A 224 TRP 0.008 0.001 TRP E 192 HIS 0.006 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6840) covalent geometry : angle 0.52394 ( 9291) hydrogen bonds : bond 0.03601 ( 537) hydrogen bonds : angle 4.06458 ( 1611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.242 Fit side-chains REVERT: A 184 MET cc_start: 0.7837 (tpp) cc_final: 0.7462 (tpp) REVERT: A 205 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7732 (mtmm) REVERT: A 206 MET cc_start: 0.7482 (ppp) cc_final: 0.7117 (ppp) REVERT: A 324 LEU cc_start: 0.8025 (mm) cc_final: 0.7731 (mm) REVERT: F 1 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6082 (ppp) REVERT: D 4 MET cc_start: 0.7811 (ttm) cc_final: 0.7466 (mtp) REVERT: D 10 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7831 (mt) REVERT: D 25 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6288 (tp) REVERT: E 191 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (tt) REVERT: E 206 MET cc_start: 0.8023 (ppp) cc_final: 0.7680 (ppp) REVERT: C 206 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (ppp) outliers start: 42 outliers final: 28 residues processed: 128 average time/residue: 0.0494 time to fit residues: 9.8544 Evaluate side-chains 141 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.136375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115620 restraints weight = 9017.073| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.84 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6840 Z= 0.142 Angle : 0.506 6.152 9291 Z= 0.248 Chirality : 0.041 0.194 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.537 48.541 882 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.51 % Allowed : 20.90 % Favored : 73.59 % 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: 2.69 (0.29), residues: 825 helix: 2.39 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -1.97 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 59 TYR 0.006 0.001 TYR A 254 PHE 0.009 0.001 PHE A 224 TRP 0.008 0.001 TRP E 192 HIS 0.006 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6840) covalent geometry : angle 0.50563 ( 9291) hydrogen bonds : bond 0.03370 ( 537) hydrogen bonds : angle 3.96965 ( 1611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.242 Fit side-chains REVERT: A 205 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7694 (mtmm) REVERT: A 206 MET cc_start: 0.7446 (ppp) cc_final: 0.7069 (ppp) REVERT: A 324 LEU cc_start: 0.7998 (mm) cc_final: 0.7711 (mm) REVERT: F 1 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6051 (ppp) REVERT: D 1 MET cc_start: 0.6161 (ppp) cc_final: 0.5432 (ppp) REVERT: D 10 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7833 (mt) REVERT: D 25 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6218 (tp) REVERT: E 191 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7928 (tt) REVERT: E 206 MET cc_start: 0.8039 (ppp) cc_final: 0.7708 (ppp) REVERT: E 219 LEU cc_start: 0.7953 (tp) cc_final: 0.7658 (mp) REVERT: E 306 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: C 206 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7395 (ppp) outliers start: 39 outliers final: 28 residues processed: 126 average time/residue: 0.0504 time to fit residues: 9.8981 Evaluate side-chains 145 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 49 optimal weight: 0.0070 chunk 54 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.132287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111689 restraints weight = 9041.761| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.79 r_work: 0.3279 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6840 Z= 0.126 Angle : 0.492 6.159 9291 Z= 0.240 Chirality : 0.040 0.196 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.463 48.808 882 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.94 % Allowed : 21.47 % Favored : 73.59 % 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: 2.89 (0.28), residues: 825 helix: 2.53 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -1.93 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.008 0.001 TYR E 254 PHE 0.008 0.001 PHE A 224 TRP 0.007 0.001 TRP E 192 HIS 0.006 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6840) covalent geometry : angle 0.49209 ( 9291) hydrogen bonds : bond 0.03223 ( 537) hydrogen bonds : angle 3.88305 ( 1611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.257 Fit side-chains REVERT: A 184 MET cc_start: 0.7797 (tpp) cc_final: 0.7445 (tpp) REVERT: A 205 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7667 (mtmm) REVERT: A 206 MET cc_start: 0.7447 (ppp) cc_final: 0.7045 (ppp) REVERT: F 1 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5960 (ppp) REVERT: D 10 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7771 (mt) REVERT: D 25 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6083 (tp) REVERT: E 191 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (tt) REVERT: E 206 MET cc_start: 0.8060 (ppp) cc_final: 0.7720 (ppp) REVERT: E 219 LEU cc_start: 0.7927 (tp) cc_final: 0.7638 (mp) REVERT: E 259 THR cc_start: 0.8288 (p) cc_final: 0.8067 (p) REVERT: E 306 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: C 206 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7382 (ppp) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 0.0546 time to fit residues: 10.6761 Evaluate side-chains 139 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115072 restraints weight = 9159.368| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.85 r_work: 0.3250 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6840 Z= 0.164 Angle : 0.516 6.015 9291 Z= 0.254 Chirality : 0.042 0.186 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.544 48.713 882 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.94 % Allowed : 21.75 % Favored : 73.31 % 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: 2.76 (0.28), residues: 825 helix: 2.43 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -1.89 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 59 TYR 0.008 0.001 TYR E 254 PHE 0.009 0.001 PHE B 19 TRP 0.007 0.001 TRP E 192 HIS 0.007 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6840) covalent geometry : angle 0.51634 ( 9291) hydrogen bonds : bond 0.03521 ( 537) hydrogen bonds : angle 4.03749 ( 1611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.153 Fit side-chains REVERT: A 205 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7710 (mtmm) REVERT: A 206 MET cc_start: 0.7601 (ppp) cc_final: 0.7261 (ppp) REVERT: A 324 LEU cc_start: 0.8068 (mm) cc_final: 0.7770 (mm) REVERT: F 1 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6081 (ppp) REVERT: F 29 MET cc_start: 0.4903 (tmm) cc_final: 0.4606 (tmm) REVERT: D 25 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6077 (tp) REVERT: E 184 MET cc_start: 0.8069 (tpp) cc_final: 0.7858 (mmt) REVERT: E 206 MET cc_start: 0.8000 (ppp) cc_final: 0.7693 (ppp) REVERT: E 219 LEU cc_start: 0.8006 (tp) cc_final: 0.7712 (mp) REVERT: E 259 THR cc_start: 0.8380 (p) cc_final: 0.8174 (p) REVERT: C 182 MET cc_start: 0.8649 (mtp) cc_final: 0.8373 (mtp) REVERT: C 206 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7499 (ppp) outliers start: 35 outliers final: 30 residues processed: 129 average time/residue: 0.0505 time to fit residues: 10.0605 Evaluate side-chains 144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 67 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.130554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109962 restraints weight = 9062.797| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.79 r_work: 0.3251 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6840 Z= 0.172 Angle : 0.522 6.139 9291 Z= 0.258 Chirality : 0.042 0.224 1113 Planarity : 0.004 0.039 1110 Dihedral : 4.599 49.782 882 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.23 % Allowed : 21.61 % Favored : 73.16 % 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: 2.69 (0.29), residues: 825 helix: 2.46 (0.19), residues: 693 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.009 0.001 TYR E 295 PHE 0.009 0.001 PHE A 224 TRP 0.008 0.001 TRP E 192 HIS 0.007 0.002 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6840) covalent geometry : angle 0.52240 ( 9291) hydrogen bonds : bond 0.03583 ( 537) hydrogen bonds : angle 4.08625 ( 1611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.206 Fit side-chains REVERT: A 184 MET cc_start: 0.7821 (tpp) cc_final: 0.7465 (tpp) REVERT: A 205 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7697 (mtmm) REVERT: A 206 MET cc_start: 0.7596 (ppp) cc_final: 0.7256 (ppp) REVERT: A 324 LEU cc_start: 0.8043 (mm) cc_final: 0.7748 (mm) REVERT: F 1 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6067 (ppp) REVERT: F 29 MET cc_start: 0.4884 (tmm) cc_final: 0.4595 (tmm) REVERT: D 10 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7723 (mt) REVERT: D 25 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6091 (tp) REVERT: E 184 MET cc_start: 0.8065 (tpp) cc_final: 0.7858 (mmt) REVERT: E 191 LEU cc_start: 0.8122 (tp) cc_final: 0.7827 (tt) REVERT: E 206 MET cc_start: 0.8029 (ppp) cc_final: 0.7709 (ppp) REVERT: E 259 THR cc_start: 0.8347 (p) cc_final: 0.8137 (p) REVERT: C 182 MET cc_start: 0.8615 (mtp) cc_final: 0.8397 (mtp) REVERT: C 206 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7449 (ppp) outliers start: 37 outliers final: 25 residues processed: 124 average time/residue: 0.0437 time to fit residues: 8.4251 Evaluate side-chains 134 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 31 optimal weight: 0.0570 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.137295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116698 restraints weight = 9052.915| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.83 r_work: 0.3282 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6840 Z= 0.113 Angle : 0.495 7.104 9291 Z= 0.239 Chirality : 0.040 0.172 1113 Planarity : 0.004 0.038 1110 Dihedral : 4.461 49.857 882 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.53 % Allowed : 23.16 % Favored : 73.31 % 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: 3.14 (0.29), residues: 825 helix: 2.71 (0.19), residues: 699 sheet: None (None), residues: 0 loop : -1.89 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.005 0.001 TYR E 254 PHE 0.008 0.001 PHE E 224 TRP 0.008 0.001 TRP E 192 HIS 0.006 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6840) covalent geometry : angle 0.49498 ( 9291) hydrogen bonds : bond 0.03067 ( 537) hydrogen bonds : angle 3.89443 ( 1611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.23 seconds wall clock time: 29 minutes 25.61 seconds (1765.61 seconds total)