Starting phenix.real_space_refine on Mon Apr 28 03:17:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqj_38579/04_2025/8xqj_38579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqj_38579/04_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_38579/04_2025/8xqj_38579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqj_38579/04_2025/8xqj_38579.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqj_38579/04_2025/8xqj_38579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqj_38579/04_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-5669/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: 4.71, per 1000 atoms: 0.68 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: 1.77 Conformation dependent library (CDL) restraints added in 933.9 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: 0.72 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: 1.97 Time building geometry restraints manager: 2.08 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: 1.490 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.890 Find NCS groups from input model: 0.230 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- 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 : 10.26 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 Details of bonding type rmsd hydrogen bonds : bond 0.11166 ( 454) hydrogen bonds : angle 5.93476 ( 1305) SS BOND : bond 0.00306 ( 8) SS BOND : angle 1.19084 ( 16) covalent geometry : bond 0.00320 ( 7090) covalent geometry : angle 0.56826 ( 9660) *********************** 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 : 0.755 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 162 average time/residue: 0.9669 time to fit residues: 167.1358 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 : 0.715 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.154079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129298 restraints weight = 9112.457| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.99 r_work: 0.3516 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0671 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= 0.173 Angle : 0.569 9.148 9676 Z= 0.292 Chirality : 0.040 0.176 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.961 36.404 1216 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.12 % Allowed : 20.92 % 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 : -1.15 (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 0.019 0.002 PHE C 222 TYR 0.013 0.002 TYR D 264 ARG 0.003 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 454) hydrogen bonds : angle 5.07603 ( 1305) SS BOND : bond 0.00364 ( 8) SS BOND : angle 1.23689 ( 16) covalent geometry : bond 0.00396 ( 7090) covalent geometry : angle 0.56688 ( 9660) *********************** 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 181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.8671 (p) cc_final: 0.8245 (t) REVERT: C 168 ARG cc_start: 0.8487 (tpt170) cc_final: 0.8182 (ttt90) REVERT: D 245 ARG cc_start: 0.7338 (mtt180) cc_final: 0.7083 (mtt-85) outliers start: 23 outliers final: 13 residues processed: 167 average time/residue: 1.0261 time to fit residues: 183.9913 Evaluate side-chains 173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 227 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: 0.8980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 32 optimal weight: 0.2980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.154063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129156 restraints weight = 9128.382| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.00 r_work: 0.3517 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0860 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= 0.162 Angle : 0.549 8.055 9676 Z= 0.281 Chirality : 0.040 0.176 1104 Planarity : 0.004 0.055 1164 Dihedral : 4.741 32.933 1216 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.21 % Allowed : 20.79 % Favored : 75.00 % 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: 0.93 (0.29), residues: 856 helix: 1.81 (0.23), residues: 476 sheet: -0.33 (0.52), residues: 106 loop : -1.14 (0.38), residues: 274 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 0.013 0.001 PHE C 214 TYR 0.012 0.002 TYR D 264 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 454) hydrogen bonds : angle 4.94241 ( 1305) SS BOND : bond 0.00338 ( 8) SS BOND : angle 1.15775 ( 16) covalent geometry : bond 0.00370 ( 7090) covalent geometry : angle 0.54755 ( 9660) *********************** 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 197 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7078 (ptp-170) REVERT: B 4 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (mp) REVERT: C 168 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8178 (ttt90) REVERT: D 245 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7078 (mtt-85) REVERT: D 290 ILE cc_start: 0.8167 (tp) cc_final: 0.7945 (tp) outliers start: 31 outliers final: 19 residues processed: 180 average time/residue: 0.8110 time to fit residues: 157.2609 Evaluate side-chains 177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 THR Chi-restraints excluded: chain B residue 69 ILE 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 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: 0.7980 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.153626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128711 restraints weight = 9185.880| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.01 r_work: 0.3507 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7098 Z= 0.177 Angle : 0.566 9.728 9676 Z= 0.285 Chirality : 0.040 0.176 1104 Planarity : 0.004 0.056 1164 Dihedral : 4.737 31.986 1216 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.53 % Allowed : 22.15 % 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 (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: 1.86 (0.23), residues: 474 sheet: -0.34 (0.51), residues: 106 loop : -1.16 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 PHE 0.021 0.001 PHE C 222 TYR 0.013 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 454) hydrogen bonds : angle 4.91628 ( 1305) SS BOND : bond 0.00355 ( 8) SS BOND : angle 1.17229 ( 16) covalent geometry : bond 0.00407 ( 7090) covalent geometry : angle 0.56493 ( 9660) *********************** 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 191 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (mp) REVERT: C 168 ARG cc_start: 0.8489 (ttt180) cc_final: 0.8179 (ttt90) REVERT: D 290 ILE cc_start: 0.8167 (tp) cc_final: 0.7904 (tp) outliers start: 26 outliers final: 18 residues processed: 175 average time/residue: 0.8055 time to fit residues: 151.7527 Evaluate side-chains 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 276 LEU 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: 6.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 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 = 0.3964 r_free = 0.3964 target = 0.153353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128468 restraints weight = 9059.324| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.98 r_work: 0.3505 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7098 Z= 0.188 Angle : 0.571 8.940 9676 Z= 0.289 Chirality : 0.041 0.181 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.733 30.707 1216 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.08 % Allowed : 21.88 % 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: 0.92 (0.29), residues: 856 helix: 1.84 (0.23), residues: 474 sheet: -0.53 (0.50), residues: 114 loop : -1.09 (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 0.015 0.001 PHE C 214 TYR 0.013 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 454) hydrogen bonds : angle 4.92053 ( 1305) SS BOND : bond 0.00383 ( 8) SS BOND : angle 1.20599 ( 16) covalent geometry : bond 0.00435 ( 7090) covalent geometry : angle 0.56930 ( 9660) *********************** 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 195 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.7026 (ptp-170) REVERT: B 4 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 168 ARG cc_start: 0.8488 (ttt180) cc_final: 0.8176 (ttt90) REVERT: D 290 ILE cc_start: 0.8167 (tp) cc_final: 0.7878 (tp) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.8441 time to fit residues: 161.7560 Evaluate side-chains 186 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 VAL 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 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 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 276 LEU 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: 0.5980 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.154311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129513 restraints weight = 9162.775| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.00 r_work: 0.3521 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7098 Z= 0.147 Angle : 0.564 8.975 9676 Z= 0.284 Chirality : 0.039 0.181 1104 Planarity : 0.004 0.055 1164 Dihedral : 4.615 29.879 1216 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.40 % Allowed : 22.83 % 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: 1.04 (0.29), residues: 856 helix: 1.96 (0.23), residues: 474 sheet: -0.32 (0.51), residues: 106 loop : -1.15 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.003 0.001 HIS B 32 PHE 0.025 0.001 PHE C 222 TYR 0.012 0.001 TYR A 94 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 454) hydrogen bonds : angle 4.84493 ( 1305) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.11540 ( 16) covalent geometry : bond 0.00331 ( 7090) covalent geometry : angle 0.56284 ( 9660) *********************** 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 191 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (mp) REVERT: C 168 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8169 (ttt90) REVERT: D 55 ARG cc_start: 0.7037 (ptt90) cc_final: 0.6801 (ptt180) REVERT: D 245 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7084 (mtt-85) REVERT: D 290 ILE cc_start: 0.8164 (tp) cc_final: 0.7866 (tp) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.8753 time to fit residues: 167.7027 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 : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 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: 0.8980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128110 restraints weight = 9108.284| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.99 r_work: 0.3500 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7098 Z= 0.211 Angle : 0.594 9.152 9676 Z= 0.300 Chirality : 0.042 0.187 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.727 29.878 1214 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.80 % Allowed : 22.69 % Favored : 73.51 % 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: 0.90 (0.29), residues: 856 helix: 1.85 (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 TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS A 32 PHE 0.018 0.002 PHE C 101 TYR 0.014 0.002 TYR D 264 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 454) hydrogen bonds : angle 4.92760 ( 1305) SS BOND : bond 0.00425 ( 8) SS BOND : angle 1.17182 ( 16) covalent geometry : bond 0.00491 ( 7090) covalent geometry : angle 0.59293 ( 9660) *********************** 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 181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7985 (mtt) REVERT: B 4 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 168 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8184 (ttt90) REVERT: D 55 ARG cc_start: 0.7059 (ptt90) cc_final: 0.6842 (ptt180) REVERT: D 107 TYR cc_start: 0.8309 (t80) cc_final: 0.7958 (t80) REVERT: D 162 MET cc_start: 0.7926 (tpp) cc_final: 0.7714 (tpp) REVERT: D 245 ARG cc_start: 0.7334 (mtt180) cc_final: 0.7077 (mtt-85) REVERT: D 290 ILE cc_start: 0.8173 (tp) cc_final: 0.7886 (tp) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.8252 time to fit residues: 146.1544 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 : 0.638 ------------------------------------------------------------------------------- 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 3 GLN 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 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: 0.0070 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 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: 0.3598 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.154526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129926 restraints weight = 9123.096| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.99 r_work: 0.3526 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7098 Z= 0.133 Angle : 0.562 9.643 9676 Z= 0.284 Chirality : 0.039 0.186 1104 Planarity : 0.004 0.055 1164 Dihedral : 4.544 29.051 1214 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.58 % Allowed : 24.32 % 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 (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: 1.06 (0.29), residues: 856 helix: 1.92 (0.23), residues: 482 sheet: -0.34 (0.51), residues: 106 loop : -1.11 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 119 HIS 0.002 0.000 HIS B 32 PHE 0.028 0.001 PHE C 222 TYR 0.012 0.001 TYR A 94 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 454) hydrogen bonds : angle 4.83860 ( 1305) SS BOND : bond 0.00311 ( 8) SS BOND : angle 1.02155 ( 16) covalent geometry : bond 0.00292 ( 7090) covalent geometry : angle 0.56064 ( 9660) *********************** 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 179 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8154 (mp) REVERT: B 82 MET cc_start: 0.4175 (mmp) cc_final: 0.2929 (pp-130) REVERT: C 168 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8189 (ttt90) REVERT: D 55 ARG cc_start: 0.7026 (ptt90) cc_final: 0.6797 (ptt180) REVERT: D 228 ILE cc_start: 0.7525 (mp) cc_final: 0.7303 (mp) REVERT: D 245 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7042 (mtt-85) REVERT: D 290 ILE cc_start: 0.8153 (tp) cc_final: 0.7871 (tp) outliers start: 19 outliers final: 13 residues processed: 169 average time/residue: 0.9078 time to fit residues: 165.1396 Evaluate side-chains 173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.154140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129137 restraints weight = 9261.149| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.03 r_work: 0.3511 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7098 Z= 0.160 Angle : 0.582 9.808 9676 Z= 0.294 Chirality : 0.040 0.173 1104 Planarity : 0.005 0.055 1164 Dihedral : 4.596 29.407 1214 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.45 % Allowed : 24.86 % 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: 1.03 (0.29), residues: 856 helix: 1.88 (0.23), residues: 482 sheet: -0.55 (0.49), residues: 114 loop : -1.01 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.003 0.000 HIS B 32 PHE 0.014 0.001 PHE D 101 TYR 0.012 0.001 TYR D 264 ARG 0.007 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 454) hydrogen bonds : angle 4.84942 ( 1305) SS BOND : bond 0.00346 ( 8) SS BOND : angle 1.11052 ( 16) covalent geometry : bond 0.00364 ( 7090) covalent geometry : angle 0.58082 ( 9660) *********************** 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 179 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 168 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8199 (ttt90) REVERT: D 55 ARG cc_start: 0.7064 (ptt90) cc_final: 0.6827 (ptt180) REVERT: D 290 ILE cc_start: 0.8182 (tp) cc_final: 0.7899 (tp) outliers start: 18 outliers final: 15 residues processed: 172 average time/residue: 1.2001 time to fit residues: 220.4647 Evaluate side-chains 175 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 181 CYS Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 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 = 0.3970 r_free = 0.3970 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128269 restraints weight = 9256.833| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.06 r_work: 0.3503 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7098 Z= 0.170 Angle : 0.598 9.946 9676 Z= 0.303 Chirality : 0.040 0.177 1104 Planarity : 0.005 0.056 1164 Dihedral : 4.641 29.162 1214 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.72 % Allowed : 24.73 % 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 (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: 1.06 (0.29), residues: 856 helix: 1.96 (0.23), residues: 474 sheet: -0.53 (0.50), residues: 114 loop : -1.02 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 36 HIS 0.003 0.001 HIS B 32 PHE 0.028 0.001 PHE C 222 TYR 0.013 0.002 TYR D 264 ARG 0.009 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 454) hydrogen bonds : angle 4.85391 ( 1305) SS BOND : bond 0.00363 ( 8) SS BOND : angle 1.13910 ( 16) covalent geometry : bond 0.00391 ( 7090) covalent geometry : angle 0.59678 ( 9660) ********************** 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 183 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 82 MET cc_start: 0.4338 (mmp) cc_final: 0.2618 (ppp) REVERT: C 168 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8208 (ttt90) REVERT: D 55 ARG cc_start: 0.7087 (ptt90) cc_final: 0.6861 (ptt180) REVERT: D 290 ILE cc_start: 0.8198 (tp) cc_final: 0.7916 (tp) outliers start: 20 outliers final: 15 residues processed: 174 average time/residue: 1.0051 time to fit residues: 189.2389 Evaluate side-chains 179 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 chunk 81 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.0040 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 overall best weight: 0.2230 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.157202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131735 restraints weight = 9246.504| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.08 r_work: 0.3536 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7098 Z= 0.120 Angle : 0.574 9.999 9676 Z= 0.290 Chirality : 0.039 0.190 1104 Planarity : 0.005 0.054 1164 Dihedral : 4.502 29.740 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.17 % Allowed : 25.54 % Favored : 72.28 % 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: 1.22 (0.29), residues: 856 helix: 2.09 (0.23), residues: 474 sheet: -0.29 (0.51), residues: 106 loop : -1.04 (0.38), residues: 276 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 0.013 0.001 PHE D 78 TYR 0.011 0.001 TYR D 182 ARG 0.009 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 454) hydrogen bonds : angle 4.74025 ( 1305) SS BOND : bond 0.00282 ( 8) SS BOND : angle 0.96332 ( 16) covalent geometry : bond 0.00252 ( 7090) covalent geometry : angle 0.57352 ( 9660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.42 seconds wall clock time: 105 minutes 25.29 seconds (6325.29 seconds total)