Starting phenix.real_space_refine on Wed Mar 12 00:08:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqj_38579/03_2025/8xqj_38579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqj_38579/03_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_38579/03_2025/8xqj_38579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqj_38579/03_2025/8xqj_38579.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqj_38579/03_2025/8xqj_38579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqj_38579/03_2025/8xqj_38579.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.51, per 1000 atoms: 0.65 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: 1.65 Conformation dependent library (CDL) restraints added in 885.9 milliseconds 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: 0.69 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: 1.99 Time building geometry restraints manager: 1.98 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 319 or resid 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: 1.210 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- 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 7090 Z= 0.211 Angle : 0.568 8.661 9660 Z= 0.292 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 : 10.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 51 HIS 0.002 0.000 HIS B 32 PHE 0.014 0.001 PHE D 101 TYR 0.011 0.001 TYR B 94 ARG 0.006 0.000 ARG D 245 *********************** 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 : 0.882 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 162 average time/residue: 0.8741 time to fit residues: 151.6322 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 : 0.662 ------------------------------------------------------------------------------- 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 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.0020 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.153937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129072 restraints weight = 9115.801| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.00 r_work: 0.3516 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7090 Z= 0.266 Angle : 0.566 8.851 9660 Z= 0.291 Chirality : 0.041 0.175 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.900 35.298 1216 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.99 % Allowed : 21.06 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 856 helix: 1.79 (0.23), residues: 476 sheet: -0.37 (0.52), residues: 106 loop : -1.14 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.002 0.001 HIS B 32 PHE 0.020 0.002 PHE C 222 TYR 0.013 0.002 TYR D 264 ARG 0.003 0.000 ARG D 245 *********************** 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 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.8672 (p) cc_final: 0.8238 (t) REVERT: D 245 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7081 (mtt-85) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.8071 time to fit residues: 143.1148 Evaluate side-chains 171 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 15 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129186 restraints weight = 9122.966| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.97 r_work: 0.3501 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7090 Z= 0.339 Angle : 0.584 8.382 9660 Z= 0.298 Chirality : 0.042 0.181 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.961 33.566 1216 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.35 % Allowed : 20.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 856 helix: 1.67 (0.23), residues: 476 sheet: -0.61 (0.50), residues: 114 loop : -1.11 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS A 32 PHE 0.017 0.002 PHE C 214 TYR 0.015 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 *********************** 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 188 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7405 (ptp-170) REVERT: B 4 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (mp) REVERT: D 245 ARG cc_start: 0.7341 (mtt180) cc_final: 0.7079 (mtt-85) outliers start: 32 outliers final: 19 residues processed: 170 average time/residue: 0.8750 time to fit residues: 159.2906 Evaluate side-chains 174 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 55 ARG 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 70 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 170 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 chunk 69 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.156254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130756 restraints weight = 9143.769| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.04 r_work: 0.3521 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7090 Z= 0.212 Angle : 0.552 9.241 9660 Z= 0.279 Chirality : 0.039 0.181 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.657 30.826 1216 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.53 % Allowed : 22.69 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 856 helix: 1.89 (0.23), residues: 474 sheet: -0.32 (0.51), residues: 106 loop : -1.14 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.002 0.001 HIS B 32 PHE 0.023 0.001 PHE C 222 TYR 0.013 0.001 TYR A 94 ARG 0.002 0.000 ARG C 91 *********************** 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 190 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7041 (ptp-170) REVERT: B 4 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (mp) REVERT: C 168 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8185 (ttt90) outliers start: 26 outliers final: 17 residues processed: 175 average time/residue: 0.7885 time to fit residues: 148.4946 Evaluate side-chains 182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 55 ARG 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 68 THR Chi-restraints excluded: chain C residue 81 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.152939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128013 restraints weight = 9079.816| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.99 r_work: 0.3495 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7090 Z= 0.324 Angle : 0.589 9.120 9660 Z= 0.297 Chirality : 0.042 0.186 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.802 30.995 1216 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.53 % Allowed : 22.42 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 856 helix: 1.80 (0.23), residues: 474 sheet: -0.60 (0.50), residues: 114 loop : -1.11 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.004 0.001 HIS A 32 PHE 0.017 0.002 PHE C 101 TYR 0.014 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 *********************** 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 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 102 CYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6850 (t) REVERT: C 168 ARG cc_start: 0.8506 (tpt170) cc_final: 0.8197 (ttt90) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.8433 time to fit residues: 152.9494 Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 59 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.153735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128810 restraints weight = 9152.959| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.01 r_work: 0.3509 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7090 Z= 0.249 Angle : 0.568 9.020 9660 Z= 0.287 Chirality : 0.040 0.184 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.635 29.623 1214 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.80 % Allowed : 22.83 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 856 helix: 1.87 (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 TRP 0.007 0.001 TRP C 51 HIS 0.003 0.001 HIS A 32 PHE 0.026 0.001 PHE C 222 TYR 0.013 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 *********************** 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 189 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 168 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8192 (ttt90) REVERT: D 55 ARG cc_start: 0.7034 (ptt90) cc_final: 0.6791 (ptt180) REVERT: D 245 ARG cc_start: 0.7349 (mtt180) cc_final: 0.7094 (mtt-85) outliers start: 28 outliers final: 21 residues processed: 173 average time/residue: 0.8023 time to fit residues: 149.4356 Evaluate side-chains 185 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 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 227 THR Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.153026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128192 restraints weight = 9128.563| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.01 r_work: 0.3498 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7090 Z= 0.291 Angle : 0.583 9.346 9660 Z= 0.295 Chirality : 0.041 0.187 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.697 29.495 1214 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.99 % Allowed : 24.05 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 856 helix: 1.83 (0.23), residues: 474 sheet: -0.63 (0.50), residues: 114 loop : -1.11 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS A 32 PHE 0.016 0.001 PHE C 214 TYR 0.014 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 *********************** 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 : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8178 (mp) REVERT: C 168 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8203 (ttt90) REVERT: D 55 ARG cc_start: 0.7060 (ptt90) cc_final: 0.6827 (ptt180) REVERT: D 245 ARG cc_start: 0.7354 (mtt180) cc_final: 0.7087 (mtt-85) outliers start: 22 outliers final: 19 residues processed: 169 average time/residue: 0.8336 time to fit residues: 150.9388 Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.152822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127388 restraints weight = 9087.765| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.03 r_work: 0.3493 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7090 Z= 0.328 Angle : 0.602 9.600 9660 Z= 0.304 Chirality : 0.042 0.188 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.750 28.954 1214 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.26 % Allowed : 23.78 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.29), residues: 856 helix: 1.79 (0.23), residues: 474 sheet: -0.65 (0.49), residues: 114 loop : -1.15 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 197 HIS 0.004 0.001 HIS A 32 PHE 0.027 0.002 PHE C 222 TYR 0.014 0.002 TYR D 264 ARG 0.002 0.000 ARG B 45 *********************** 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 177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: B 4 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 82 MET cc_start: 0.4252 (mmp) cc_final: 0.2950 (pp-130) REVERT: C 168 ARG cc_start: 0.8519 (ttt180) cc_final: 0.8206 (ttt90) REVERT: D 55 ARG cc_start: 0.7063 (ptt90) cc_final: 0.6827 (ptt180) REVERT: D 107 TYR cc_start: 0.8301 (t80) cc_final: 0.7994 (t80) REVERT: D 245 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7078 (mtt-85) outliers start: 24 outliers final: 21 residues processed: 164 average time/residue: 0.8803 time to fit residues: 154.8809 Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 69 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128584 restraints weight = 9293.804| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.03 r_work: 0.3504 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7090 Z= 0.261 Angle : 0.595 10.005 9660 Z= 0.301 Chirality : 0.041 0.206 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.671 28.138 1214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.99 % Allowed : 24.32 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 856 helix: 1.83 (0.23), residues: 474 sheet: -0.62 (0.50), residues: 114 loop : -1.10 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE D 101 TYR 0.013 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 *********************** 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: 22 poor density : 151 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6196 (tm-30) REVERT: B 4 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8195 (mp) REVERT: B 82 MET cc_start: 0.4115 (mmp) cc_final: 0.2878 (pp-130) REVERT: C 168 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8203 (ttt90) REVERT: D 55 ARG cc_start: 0.7060 (ptt90) cc_final: 0.6824 (ptt180) REVERT: D 245 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7118 (mtt-85) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.8891 time to fit residues: 153.1101 Evaluate side-chains 169 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 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 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 173 LEU 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 55 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.0050 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.155272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130424 restraints weight = 9291.693| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.03 r_work: 0.3525 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7090 Z= 0.190 Angle : 0.581 9.780 9660 Z= 0.293 Chirality : 0.039 0.184 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.550 28.836 1214 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.99 % Allowed : 25.14 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 856 helix: 1.96 (0.23), residues: 474 sheet: -0.30 (0.52), residues: 102 loop : -1.18 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 119 HIS 0.002 0.000 HIS B 32 PHE 0.026 0.001 PHE C 222 TYR 0.011 0.001 TYR A 94 ARG 0.008 0.000 ARG C 61 ********************** 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 173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: B 4 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 82 MET cc_start: 0.4071 (mmp) cc_final: 0.2900 (pp-130) REVERT: C 168 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8209 (ttt90) REVERT: D 55 ARG cc_start: 0.7051 (ptt90) cc_final: 0.6808 (ptt180) REVERT: D 245 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7125 (mtt-85) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 0.8680 time to fit residues: 150.7300 Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET 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 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.154154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129110 restraints weight = 9214.630| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.02 r_work: 0.3507 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7090 Z= 0.258 Angle : 0.606 9.715 9660 Z= 0.305 Chirality : 0.041 0.193 1104 Planarity : 0.005 0.057 1164 Dihedral : 4.638 29.083 1214 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 25.00 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 856 helix: 1.89 (0.23), residues: 474 sheet: -0.60 (0.49), residues: 114 loop : -1.01 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 24 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE C 101 TYR 0.013 0.001 TYR D 264 ARG 0.009 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.79 seconds wall clock time: 84 minutes 50.03 seconds (5090.03 seconds total)