Starting phenix.real_space_refine on Fri Aug 22 18:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqj_38579/08_2025/8xqj_38579.cif" } resolution = 2.95 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= 0.020 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 58 5.16 5 C 4508 2.51 5 N 1124 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 959 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "B" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 959 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "C" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2437 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain: "D" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2437 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.21 Number of scatterers: 6904 At special positions: 0 Unit cell: (92.56, 81.12, 114.4, 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 58 16.00 O 1214 8.00 N 1124 7.00 C 4508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 281 " distance=2.04 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 281 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 356.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 64.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 86 through 90 removed outlier: 4.162A pdb=" N THR A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.585A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.587A pdb=" N MET B 113 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 56 removed outlier: 3.647A pdb=" N SER C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 62 through 91 removed outlier: 4.232A pdb=" N ILE C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Proline residue: C 83 - end of helix Processing helix chain 'C' and resid 97 through 133 removed outlier: 4.151A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 145 through 167 Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.689A pdb=" N ASN C 175 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 176' Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 193 through 211 Processing helix chain 'C' and resid 211 through 232 removed outlier: 3.691A pdb=" N GLY C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 278 Proline residue: C 263 - end of helix removed outlier: 3.938A pdb=" N SER C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 313 Proline residue: C 292 - end of helix removed outlier: 3.678A pdb=" N ASN C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.709A pdb=" N ARG C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 56 removed outlier: 3.803A pdb=" N SER D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.534A pdb=" N ARG D 61 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 removed outlier: 4.369A pdb=" N ILE D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 98 through 133 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 145 through 167 Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 172 through 176 removed outlier: 4.037A pdb=" N THR D 176 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 210 Processing helix chain 'D' and resid 210 through 232 Processing helix chain 'D' and resid 236 through 278 Proline residue: D 263 - end of helix removed outlier: 3.741A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 313 Proline residue: D 292 - end of helix removed outlier: 4.068A pdb=" N SER D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS D 303 " --> pdb=" O TYR D 299 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 313 through 319 removed outlier: 3.618A pdb=" N ARG D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.514A pdb=" N VAL A 12 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.514A pdb=" N VAL A 12 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.597A pdb=" N GLY B 10 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 12.182A pdb=" N HIS B 32 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR B 52 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.597A pdb=" N GLY B 10 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 22 Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 171 462 hydrogen bonds defined for protein. 1305 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: 0.97 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.46: 1880 1.46 - 1.58: 3028 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 7090 Sorted by residual: bond pdb=" CB ILE D 290 " pdb=" CG2 ILE D 290 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.38e-01 bond pdb=" CB THR D 215 " pdb=" CG2 THR D 215 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.10e-01 bond pdb=" CA ALA B 49 " pdb=" C ALA B 49 " ideal model delta sigma weight residual 1.526 1.518 0.008 1.03e-02 9.43e+03 6.46e-01 bond pdb=" N GLY A 65 " pdb=" CA GLY A 65 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.31e-01 bond pdb=" CA MET A 113 " pdb=" C MET A 113 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.80e-02 3.09e+03 6.29e-01 ... (remaining 7085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9485 1.73 - 3.46: 136 3.46 - 5.20: 31 5.20 - 6.93: 6 6.93 - 8.66: 2 Bond angle restraints: 9660 Sorted by residual: angle pdb=" CA MET A 113 " pdb=" CB MET A 113 " pdb=" CG MET A 113 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.12e+00 angle pdb=" CA LEU A 20 " pdb=" CB LEU A 20 " pdb=" CG LEU A 20 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.12e+00 angle pdb=" CB ARG D 127 " pdb=" CG ARG D 127 " pdb=" CD ARG D 127 " ideal model delta sigma weight residual 111.30 116.71 -5.41 2.30e+00 1.89e-01 5.54e+00 angle pdb=" C PHE D 214 " pdb=" N THR D 215 " pdb=" CA THR D 215 " ideal model delta sigma weight residual 120.29 117.01 3.28 1.42e+00 4.96e-01 5.34e+00 angle pdb=" N VAL A 48 " pdb=" CA VAL A 48 " pdb=" C VAL A 48 " ideal model delta sigma weight residual 111.48 109.43 2.05 9.40e-01 1.13e+00 4.77e+00 ... (remaining 9655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3821 17.64 - 35.28: 386 35.28 - 52.92: 101 52.92 - 70.56: 17 70.56 - 88.20: 1 Dihedral angle restraints: 4326 sinusoidal: 1814 harmonic: 2512 Sorted by residual: dihedral pdb=" CB CYS B 33 " pdb=" SG CYS B 33 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual 93.00 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 95 " pdb=" CB CYS A 95 " ideal model delta sinusoidal sigma weight residual 93.00 45.99 47.01 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS A 33 " pdb=" SG CYS A 33 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual -86.00 -41.41 -44.59 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 4323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 805 0.038 - 0.075: 222 0.075 - 0.113: 68 0.113 - 0.150: 7 0.150 - 0.188: 2 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CG LEU A 20 " pdb=" CB LEU A 20 " pdb=" CD1 LEU A 20 " pdb=" CD2 LEU A 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB VAL B 63 " pdb=" CA VAL B 63 " pdb=" CG1 VAL B 63 " pdb=" CG2 VAL B 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA PHE C 291 " pdb=" N PHE C 291 " pdb=" C PHE C 291 " pdb=" CB PHE C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1101 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 262 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO D 263 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 263 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 263 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 313 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 314 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 314 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 314 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 66 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE D 66 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE D 66 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE D 67 " -0.009 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1519 2.78 - 3.31: 6706 3.31 - 3.84: 11942 3.84 - 4.37: 14010 4.37 - 4.90: 24167 Nonbonded interactions: 58344 Sorted by model distance: nonbonded pdb=" OE1 GLN B 3 " pdb=" OG SER B 25 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR A 90 " pdb=" O VAL A 127 " model vdw 2.247 3.040 nonbonded pdb=" O TYR C 299 " pdb=" OG SER C 302 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG B 66 " pdb=" O SER B 84 " model vdw 2.289 3.120 nonbonded pdb=" OE2 GLU D 18 " pdb=" OH TYR D 21 " model vdw 2.298 3.040 ... (remaining 58339 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 'B' } ncs_group { reference = (chain 'C' and resid 17 through 401) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.250 Find NCS groups from input model: 0.070 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 0.037 7098 Z= 0.146 Angle : 0.570 8.661 9676 Z= 0.293 Chirality : 0.039 0.188 1104 Planarity : 0.005 0.055 1164 Dihedral : 14.507 88.198 2694 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 23.78 % Favored : 76.22 % 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 aren not related in a simple way. whole: 0.73 (0.28), residues: 856 helix: 1.59 (0.23), residues: 478 sheet: -0.42 (0.56), residues: 94 loop : -1.09 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 245 TYR 0.011 0.001 TYR B 94 PHE 0.014 0.001 PHE D 101 TRP 0.009 0.001 TRP C 51 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7090) covalent geometry : angle 0.56826 ( 9660) SS BOND : bond 0.00306 ( 8) SS BOND : angle 1.19084 ( 16) hydrogen bonds : bond 0.11166 ( 454) hydrogen bonds : angle 5.93476 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.198 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 162 average time/residue: 0.3507 time to fit residues: 60.7625 Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 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 32 HIS C 137 ASN D 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130514 restraints weight = 9180.046| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.00 r_work: 0.3526 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7098 Z= 0.170 Angle : 0.566 9.024 9676 Z= 0.291 Chirality : 0.040 0.175 1104 Planarity : 0.005 0.055 1164 Dihedral : 4.913 35.768 1216 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 20.79 % Favored : 76.22 % 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 aren not related in a simple way. whole: 0.90 (0.29), residues: 856 helix: 1.80 (0.23), residues: 476 sheet: -0.37 (0.52), residues: 106 loop : -1.15 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 245 TYR 0.013 0.002 TYR D 264 PHE 0.020 0.002 PHE C 222 TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7090) covalent geometry : angle 0.56438 ( 9660) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.23817 ( 16) hydrogen bonds : bond 0.04685 ( 454) hydrogen bonds : angle 5.05070 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.8661 (p) cc_final: 0.8236 (t) REVERT: C 168 ARG cc_start: 0.8481 (tpt170) cc_final: 0.8177 (ttt90) REVERT: D 245 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7060 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 0.3662 time to fit residues: 66.3099 Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129852 restraints weight = 9124.048| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.99 r_work: 0.3526 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7098 Z= 0.139 Angle : 0.538 8.416 9676 Z= 0.275 Chirality : 0.039 0.171 1104 Planarity : 0.004 0.055 1164 Dihedral : 4.697 33.437 1216 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.80 % Allowed : 20.92 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.29), residues: 856 helix: 1.89 (0.23), residues: 476 sheet: -0.03 (0.57), residues: 86 loop : -1.10 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.012 0.001 TYR A 94 PHE 0.013 0.001 PHE D 101 TRP 0.007 0.001 TRP C 51 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7090) covalent geometry : angle 0.53660 ( 9660) SS BOND : bond 0.00303 ( 8) SS BOND : angle 1.10170 ( 16) hydrogen bonds : bond 0.04442 ( 454) hydrogen bonds : angle 4.90813 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6812 (ptp-170) REVERT: B 4 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8152 (mp) REVERT: C 168 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8166 (ttt90) REVERT: D 245 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7053 (mtt-85) REVERT: D 290 ILE cc_start: 0.8156 (tp) cc_final: 0.7939 (tp) outliers start: 28 outliers final: 16 residues processed: 187 average time/residue: 0.3203 time to fit residues: 64.6241 Evaluate side-chains 190 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127610 restraints weight = 9225.733| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.99 r_work: 0.3493 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7098 Z= 0.235 Angle : 0.594 10.311 9676 Z= 0.300 Chirality : 0.042 0.182 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.874 32.690 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.94 % Allowed : 21.20 % Favored : 74.86 % 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 aren not related in a simple way. whole: 0.80 (0.29), residues: 856 helix: 1.73 (0.23), residues: 476 sheet: -0.61 (0.50), residues: 114 loop : -1.12 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.015 0.002 TYR D 264 PHE 0.021 0.002 PHE C 222 TRP 0.009 0.001 TRP C 51 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 7090) covalent geometry : angle 0.59232 ( 9660) SS BOND : bond 0.00430 ( 8) SS BOND : angle 1.29078 ( 16) hydrogen bonds : bond 0.04822 ( 454) hydrogen bonds : angle 4.98838 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8196 (mp) REVERT: C 168 ARG cc_start: 0.8516 (tpt170) cc_final: 0.8197 (ttt90) REVERT: D 245 ARG cc_start: 0.7335 (mtt180) cc_final: 0.7059 (mtt-85) REVERT: D 290 ILE cc_start: 0.8187 (tp) cc_final: 0.7925 (tp) outliers start: 29 outliers final: 16 residues processed: 170 average time/residue: 0.3713 time to fit residues: 67.5555 Evaluate side-chains 175 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129074 restraints weight = 9233.223| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.05 r_work: 0.3496 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7098 Z= 0.187 Angle : 0.573 8.941 9676 Z= 0.290 Chirality : 0.041 0.178 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.759 30.379 1216 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.40 % Allowed : 22.28 % Favored : 74.32 % 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 aren not related in a simple way. whole: 0.84 (0.29), residues: 856 helix: 1.80 (0.23), residues: 474 sheet: -0.58 (0.50), residues: 114 loop : -1.16 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.013 0.002 TYR D 264 PHE 0.015 0.001 PHE D 101 TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7090) covalent geometry : angle 0.57115 ( 9660) SS BOND : bond 0.00377 ( 8) SS BOND : angle 1.23713 ( 16) hydrogen bonds : bond 0.04617 ( 454) hydrogen bonds : angle 4.93775 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8201 (mp) REVERT: C 102 CYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6817 (t) REVERT: C 168 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8200 (ttt90) REVERT: D 290 ILE cc_start: 0.8168 (tp) cc_final: 0.7885 (tp) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.3684 time to fit residues: 66.5114 Evaluate side-chains 175 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127399 restraints weight = 9223.508| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.00 r_work: 0.3490 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7098 Z= 0.222 Angle : 0.598 9.129 9676 Z= 0.303 Chirality : 0.042 0.190 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.834 29.881 1216 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.67 % Allowed : 22.42 % Favored : 73.91 % 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 aren not related in a simple way. whole: 0.77 (0.29), residues: 856 helix: 1.73 (0.23), residues: 474 sheet: -0.64 (0.50), residues: 114 loop : -1.16 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.014 0.002 TYR D 264 PHE 0.025 0.002 PHE C 222 TRP 0.009 0.001 TRP C 197 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 7090) covalent geometry : angle 0.59619 ( 9660) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.30509 ( 16) hydrogen bonds : bond 0.04777 ( 454) hydrogen bonds : angle 4.97469 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 THR cc_start: 0.8157 (m) cc_final: 0.7934 (m) REVERT: B 4 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 102 CYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6889 (t) REVERT: C 168 ARG cc_start: 0.8522 (tpt170) cc_final: 0.8208 (ttt90) REVERT: D 55 ARG cc_start: 0.7066 (ptt90) cc_final: 0.6832 (ptt180) REVERT: D 245 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7084 (mtt-85) REVERT: D 290 ILE cc_start: 0.8189 (tp) cc_final: 0.7886 (tp) outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.3212 time to fit residues: 57.4995 Evaluate side-chains 177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.153260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128379 restraints weight = 9146.799| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.02 r_work: 0.3501 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7098 Z= 0.180 Angle : 0.587 9.404 9676 Z= 0.295 Chirality : 0.040 0.188 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.667 28.477 1214 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 23.91 % Favored : 73.10 % 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 aren not related in a simple way. whole: 0.85 (0.29), residues: 856 helix: 1.81 (0.23), residues: 474 sheet: -0.59 (0.50), residues: 114 loop : -1.15 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.013 0.002 TYR D 264 PHE 0.014 0.001 PHE D 101 TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7090) covalent geometry : angle 0.58531 ( 9660) SS BOND : bond 0.00374 ( 8) SS BOND : angle 1.24316 ( 16) hydrogen bonds : bond 0.04571 ( 454) hydrogen bonds : angle 4.92054 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.8001 (mtt) REVERT: B 4 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8189 (mp) REVERT: C 102 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6820 (t) REVERT: C 168 ARG cc_start: 0.8473 (tpt170) cc_final: 0.8175 (ttt90) REVERT: D 55 ARG cc_start: 0.7051 (ptt90) cc_final: 0.6823 (ptt180) REVERT: D 245 ARG cc_start: 0.7347 (mtt180) cc_final: 0.7082 (mtt-85) REVERT: D 290 ILE cc_start: 0.8204 (tp) cc_final: 0.7914 (tp) outliers start: 22 outliers final: 16 residues processed: 170 average time/residue: 0.3776 time to fit residues: 68.9087 Evaluate side-chains 175 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129566 restraints weight = 9279.933| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.03 r_work: 0.3513 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7098 Z= 0.144 Angle : 0.573 9.836 9676 Z= 0.289 Chirality : 0.039 0.182 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.590 28.731 1214 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.12 % Allowed : 23.78 % Favored : 73.10 % 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 aren not related in a simple way. whole: 1.01 (0.29), residues: 856 helix: 1.94 (0.23), residues: 474 sheet: -0.56 (0.50), residues: 114 loop : -1.09 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.012 0.001 TYR A 94 PHE 0.028 0.001 PHE C 222 TRP 0.007 0.001 TRP C 51 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7090) covalent geometry : angle 0.57176 ( 9660) SS BOND : bond 0.00310 ( 8) SS BOND : angle 1.14931 ( 16) hydrogen bonds : bond 0.04343 ( 454) hydrogen bonds : angle 4.87175 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (mtt) REVERT: A 124 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: B 4 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 82 MET cc_start: 0.4222 (mmp) cc_final: 0.2685 (ppp) REVERT: C 168 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8167 (ttt90) REVERT: D 55 ARG cc_start: 0.7027 (ptt90) cc_final: 0.6797 (ptt180) REVERT: D 228 ILE cc_start: 0.7538 (mp) cc_final: 0.7314 (mp) REVERT: D 245 ARG cc_start: 0.7341 (mtt180) cc_final: 0.7081 (mtt-85) REVERT: D 290 ILE cc_start: 0.8180 (tp) cc_final: 0.7894 (tp) outliers start: 23 outliers final: 14 residues processed: 165 average time/residue: 0.4147 time to fit residues: 73.0665 Evaluate side-chains 171 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN D 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129015 restraints weight = 9228.963| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.03 r_work: 0.3508 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7098 Z= 0.166 Angle : 0.590 9.943 9676 Z= 0.297 Chirality : 0.040 0.179 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.630 29.068 1214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.85 % Allowed : 24.73 % Favored : 72.42 % 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 aren not related in a simple way. whole: 0.97 (0.29), residues: 856 helix: 1.91 (0.23), residues: 474 sheet: -0.59 (0.50), residues: 114 loop : -1.08 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 61 TYR 0.012 0.001 TYR D 264 PHE 0.014 0.001 PHE D 101 TRP 0.007 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7090) covalent geometry : angle 0.58854 ( 9660) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.16845 ( 16) hydrogen bonds : bond 0.04432 ( 454) hydrogen bonds : angle 4.87904 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: A 124 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: B 4 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8169 (mp) REVERT: B 82 MET cc_start: 0.4329 (mmp) cc_final: 0.2736 (pp-130) REVERT: C 168 ARG cc_start: 0.8498 (ttt180) cc_final: 0.8192 (ttt90) REVERT: D 55 ARG cc_start: 0.7045 (ptt90) cc_final: 0.6808 (ptt180) REVERT: D 245 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7086 (mtt-85) REVERT: D 290 ILE cc_start: 0.8190 (tp) cc_final: 0.7900 (tp) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 0.3535 time to fit residues: 62.1299 Evaluate side-chains 169 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.153237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127808 restraints weight = 9135.231| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.03 r_work: 0.3501 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7098 Z= 0.191 Angle : 0.604 10.054 9676 Z= 0.306 Chirality : 0.041 0.180 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.718 28.870 1214 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.12 % Allowed : 24.32 % Favored : 72.55 % 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 aren not related in a simple way. whole: 0.92 (0.29), residues: 856 helix: 1.87 (0.23), residues: 474 sheet: -0.60 (0.50), residues: 114 loop : -1.12 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 61 TYR 0.014 0.002 TYR D 264 PHE 0.028 0.002 PHE C 222 TRP 0.007 0.001 TRP C 197 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7090) covalent geometry : angle 0.60246 ( 9660) SS BOND : bond 0.00433 ( 8) SS BOND : angle 1.19061 ( 16) hydrogen bonds : bond 0.04557 ( 454) hydrogen bonds : angle 4.91204 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6266 (tm-30) REVERT: B 4 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 82 MET cc_start: 0.4366 (mmp) cc_final: 0.2585 (ppp) REVERT: C 168 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8198 (ttt90) REVERT: D 55 ARG cc_start: 0.7077 (ptt90) cc_final: 0.6828 (ptt180) REVERT: D 245 ARG cc_start: 0.7324 (mtt180) cc_final: 0.7111 (mtt-85) REVERT: D 290 ILE cc_start: 0.8183 (tp) cc_final: 0.7911 (tp) outliers start: 23 outliers final: 16 residues processed: 165 average time/residue: 0.4035 time to fit residues: 71.3078 Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 0.2980 chunk 37 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN D 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.155281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130437 restraints weight = 9172.513| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.03 r_work: 0.3528 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7098 Z= 0.128 Angle : 0.579 9.970 9676 Z= 0.293 Chirality : 0.039 0.195 1104 Planarity : 0.005 0.055 1164 Dihedral : 4.557 29.170 1214 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.17 % Allowed : 25.68 % Favored : 72.15 % 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 aren not related in a simple way. whole: 1.11 (0.29), residues: 856 helix: 2.01 (0.23), residues: 474 sheet: -0.34 (0.51), residues: 106 loop : -1.09 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 61 TYR 0.011 0.001 TYR A 94 PHE 0.013 0.001 PHE D 101 TRP 0.007 0.001 TRP A 36 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7090) covalent geometry : angle 0.57805 ( 9660) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.03256 ( 16) hydrogen bonds : bond 0.04212 ( 454) hydrogen bonds : angle 4.79281 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.04 seconds wall clock time: 41 minutes 19.07 seconds (2479.07 seconds total)