Starting phenix.real_space_refine on Wed Aug 5 13:35:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2026/8yjs_39348.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 331 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 61 5.16 5 C 6031 2.51 5 N 1657 2.21 5 O 2070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9880 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1951 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 246} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 9880 At special positions: 0 Unit cell: (107.07, 98.77, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 61 15.00 O 2070 8.00 N 1657 7.00 C 6031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 301.6 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 30.7% alpha, 24.2% beta 15 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.554A pdb=" N LYS C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 140 through 155 removed outlier: 4.066A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.504A pdb=" N SER D 25 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 26' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 removed outlier: 4.032A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.524A pdb=" N ASN D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 253 removed outlier: 3.552A pdb=" N ALA D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 262 removed outlier: 4.113A pdb=" N ARG D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.533A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 313 removed outlier: 3.669A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 removed outlier: 4.006A pdb=" N GLY D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.146A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.721A pdb=" N PHE C 2 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 205 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 71 removed outlier: 7.163A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 239 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 238 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 127 removed outlier: 6.621A pdb=" N VAL C 123 " --> pdb=" O SER D 349 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER D 349 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN C 125 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 204 through 208 removed outlier: 5.199A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 19 through 21 removed outlier: 3.680A pdb=" N GLU D 206 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP D 34 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.633A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.337A pdb=" N SER A 230 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 229 " --> pdb=" O CYS A 135 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2513 1.33 - 1.45: 1975 1.45 - 1.57: 5443 1.57 - 1.69: 125 1.69 - 1.81: 98 Bond restraints: 10154 Sorted by residual: bond pdb=" C THR C 219 " pdb=" N PRO C 220 " ideal model delta sigma weight residual 1.337 1.388 -0.052 9.80e-03 1.04e+04 2.79e+01 bond pdb=" C1' DT J 16 " pdb=" N1 DT J 16 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C3' DT E 17 " pdb=" C2' DT E 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.73e+00 bond pdb=" C3' DT J 4 " pdb=" C2' DT J 4 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.63e+00 ... (remaining 10149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 13671 3.09 - 6.18: 244 6.18 - 9.26: 40 9.26 - 12.35: 7 12.35 - 15.44: 1 Bond angle restraints: 13963 Sorted by residual: angle pdb=" C ASP D 51 " pdb=" N VAL D 52 " pdb=" CA VAL D 52 " ideal model delta sigma weight residual 121.97 131.68 -9.71 1.80e+00 3.09e-01 2.91e+01 angle pdb=" CA ARG B 64 " pdb=" CB ARG B 64 " pdb=" CG ARG B 64 " ideal model delta sigma weight residual 114.10 124.27 -10.17 2.00e+00 2.50e-01 2.59e+01 angle pdb=" N VAL B 45 " pdb=" CA VAL B 45 " pdb=" C VAL B 45 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.24e+01 angle pdb=" CA VAL D 52 " pdb=" CB VAL D 52 " pdb=" CG1 VAL D 52 " ideal model delta sigma weight residual 110.40 118.35 -7.95 1.70e+00 3.46e-01 2.19e+01 angle pdb=" CB GLN D 112 " pdb=" CG GLN D 112 " pdb=" CD GLN D 112 " ideal model delta sigma weight residual 112.60 120.51 -7.91 1.70e+00 3.46e-01 2.16e+01 ... (remaining 13958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5043 17.89 - 35.79: 731 35.79 - 53.68: 287 53.68 - 71.57: 62 71.57 - 89.46: 14 Dihedral angle restraints: 6137 sinusoidal: 2903 harmonic: 3234 Sorted by residual: dihedral pdb=" CA GLU B 198 " pdb=" C GLU B 198 " pdb=" N MET B 199 " pdb=" CA MET B 199 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PHE D 126 " pdb=" C PHE D 126 " pdb=" N THR D 127 " pdb=" CA THR D 127 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN C 95 " pdb=" C ASN C 95 " pdb=" N ALA C 96 " pdb=" CA ALA C 96 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 6134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1502 0.111 - 0.223: 95 0.223 - 0.334: 9 0.334 - 0.445: 0 0.445 - 0.556: 1 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CB VAL D 52 " pdb=" CA VAL D 52 " pdb=" CG1 VAL D 52 " pdb=" CG2 VAL D 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" CB ILE C 23 " pdb=" CA ILE C 23 " pdb=" CG1 ILE C 23 " pdb=" CG2 ILE C 23 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A 123 " pdb=" CA VAL A 123 " pdb=" CG1 VAL A 123 " pdb=" CG2 VAL A 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1604 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 201 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO B 202 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 274 " 0.028 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP D 274 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 274 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP D 274 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 274 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 274 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 274 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 274 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 274 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 136 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C VAL B 136 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL B 136 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL B 137 " 0.020 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3071 2.86 - 3.37: 8455 3.37 - 3.88: 17488 3.88 - 4.39: 19562 4.39 - 4.90: 32794 Nonbonded interactions: 81370 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.347 3.040 nonbonded pdb=" O THR B 216 " pdb=" OG1 THR B 219 " model vdw 2.352 3.040 nonbonded pdb=" O THR A 216 " pdb=" OG1 THR A 219 " model vdw 2.373 3.040 nonbonded pdb=" OE2 GLU D 76 " pdb=" NE ARG D 327 " model vdw 2.383 3.120 nonbonded pdb=" OG SER B 222 " pdb=" O THR B 224 " model vdw 2.392 3.040 ... (remaining 81365 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' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'C' and resid 2 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.006 0.071 10157 Z= 0.362 Angle : 1.055 15.440 13969 Z= 0.636 Chirality : 0.061 0.556 1607 Planarity : 0.008 0.119 1587 Dihedral : 19.677 89.464 4030 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.20), residues: 1103 helix: -2.73 (0.20), residues: 311 sheet: -2.07 (0.26), residues: 312 loop : -2.21 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 129 TYR 0.028 0.003 TYR B 249 PHE 0.059 0.003 PHE B 214 TRP 0.073 0.005 TRP D 274 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.36 (10154) covalent geometry : angle 1.05551 / 0.64 (13963) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 0.55622 / 0.29 ( 6) hydrogen bonds : bond 0.20336 / 13.04 ( 460) hydrogen bonds : angle 10.02207 / 6.98 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.362 Fit side-chains REVERT: D 10 ILE cc_start: 0.8766 (mm) cc_final: 0.8529 (mm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0831 time to fit residues: 17.2249 Evaluate side-chains 108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 ASN B 38 GLN B 108 GLN A 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105051 restraints weight = 15331.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108325 restraints weight = 10680.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109256 restraints weight = 6625.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109831 restraints weight = 5830.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110129 restraints weight = 5598.828| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10157 Z= 0.172 Angle : 0.664 8.456 13969 Z= 0.364 Chirality : 0.047 0.247 1607 Planarity : 0.005 0.066 1587 Dihedral : 20.986 82.356 1901 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.24 % Allowed : 7.99 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.22), residues: 1103 helix: -1.16 (0.26), residues: 325 sheet: -1.99 (0.27), residues: 296 loop : -1.91 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.010 0.001 TYR C 211 PHE 0.026 0.002 PHE B 214 TRP 0.028 0.002 TRP D 274 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10154) covalent geometry : angle 0.66388 / 0.36 (13963) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 0.58036 / 0.27 ( 6) hydrogen bonds : bond 0.05153 / 3.38 ( 460) hydrogen bonds : angle 7.25508 / 5.08 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.257 Fit side-chains REVERT: D 10 ILE cc_start: 0.8826 (mm) cc_final: 0.8583 (mm) REVERT: B 53 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7799 (mtt-85) REVERT: A 116 MET cc_start: 0.8583 (ttp) cc_final: 0.8372 (ttm) REVERT: A 229 MET cc_start: 0.8020 (pmm) cc_final: 0.7479 (ptp) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.0902 time to fit residues: 16.9694 Evaluate side-chains 115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain A residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN C 49 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN B 84 ASN B 108 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102346 restraints weight = 15329.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105639 restraints weight = 10802.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106522 restraints weight = 6667.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107027 restraints weight = 5945.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107329 restraints weight = 5712.324| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10157 Z= 0.173 Angle : 0.602 6.648 13969 Z= 0.329 Chirality : 0.044 0.242 1607 Planarity : 0.004 0.053 1587 Dihedral : 20.928 86.638 1901 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.76 % Allowed : 11.00 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.23), residues: 1103 helix: -0.40 (0.27), residues: 331 sheet: -2.04 (0.26), residues: 293 loop : -1.74 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.043 0.002 TYR B 211 PHE 0.028 0.002 PHE B 214 TRP 0.022 0.002 TRP D 274 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10154) covalent geometry : angle 0.60218 / 0.33 (13963) SS BOND : bond 0.00274 / 0.14 ( 3) SS BOND : angle 0.47484 / 0.21 ( 6) hydrogen bonds : bond 0.04607 / 3.02 ( 460) hydrogen bonds : angle 6.55614 / 4.60 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.348 Fit side-chains REVERT: C 199 MET cc_start: 0.6973 (tpp) cc_final: 0.5814 (mtm) REVERT: C 244 MET cc_start: 0.8242 (mpp) cc_final: 0.7990 (mpp) REVERT: D 10 ILE cc_start: 0.8886 (mm) cc_final: 0.8645 (mm) REVERT: D 126 PHE cc_start: 0.7481 (m-80) cc_final: 0.7191 (m-10) REVERT: B 53 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7957 (mtt-85) REVERT: B 199 MET cc_start: 0.5586 (tpt) cc_final: 0.3421 (mtm) REVERT: A 229 MET cc_start: 0.8135 (pmm) cc_final: 0.7812 (ptp) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.0802 time to fit residues: 15.9931 Evaluate side-chains 117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.130627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098754 restraints weight = 15498.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101841 restraints weight = 10689.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102257 restraints weight = 6855.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102732 restraints weight = 7089.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103276 restraints weight = 6050.191| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10157 Z= 0.211 Angle : 0.623 8.045 13969 Z= 0.335 Chirality : 0.045 0.253 1607 Planarity : 0.004 0.052 1587 Dihedral : 20.881 87.688 1901 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.28 % Allowed : 14.21 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1103 helix: 0.08 (0.28), residues: 331 sheet: -2.16 (0.27), residues: 290 loop : -1.56 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.017 0.002 TYR B 211 PHE 0.019 0.002 PHE D 27 TRP 0.016 0.001 TRP D 274 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (10154) covalent geometry : angle 0.62311 / 0.34 (13963) SS BOND : bond 0.00075 / 0.04 ( 3) SS BOND : angle 0.56949 / 0.25 ( 6) hydrogen bonds : bond 0.04322 / 2.84 ( 460) hydrogen bonds : angle 6.22921 / 4.38 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.360 Fit side-chains REVERT: D 126 PHE cc_start: 0.7557 (m-80) cc_final: 0.7291 (m-10) REVERT: B 199 MET cc_start: 0.5882 (tpt) cc_final: 0.3770 (mtm) REVERT: B 215 PHE cc_start: 0.8551 (m-80) cc_final: 0.8301 (m-80) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.0817 time to fit residues: 14.9859 Evaluate side-chains 118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100256 restraints weight = 15182.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104220 restraints weight = 10698.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104788 restraints weight = 6346.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105300 restraints weight = 5845.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105578 restraints weight = 5545.222| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10157 Z= 0.155 Angle : 0.568 7.271 13969 Z= 0.308 Chirality : 0.044 0.290 1607 Planarity : 0.004 0.050 1587 Dihedral : 20.786 86.327 1901 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.39 % Allowed : 14.52 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1103 helix: 0.39 (0.28), residues: 331 sheet: -2.15 (0.26), residues: 295 loop : -1.43 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.020 0.002 TYR B 211 PHE 0.016 0.001 PHE D 27 TRP 0.014 0.001 TRP D 274 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10154) covalent geometry : angle 0.56829 / 0.31 (13963) SS BOND : bond 0.00059 / 0.03 ( 3) SS BOND : angle 0.43618 / 0.19 ( 6) hydrogen bonds : bond 0.04047 / 2.67 ( 460) hydrogen bonds : angle 6.08840 / 4.28 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.354 Fit side-chains REVERT: C 244 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: D 10 ILE cc_start: 0.8912 (mm) cc_final: 0.8683 (mm) REVERT: D 126 PHE cc_start: 0.7591 (m-80) cc_final: 0.7315 (m-10) REVERT: D 259 ILE cc_start: 0.7985 (mm) cc_final: 0.7548 (mt) REVERT: B 86 ASP cc_start: 0.7814 (m-30) cc_final: 0.7587 (m-30) REVERT: B 199 MET cc_start: 0.5786 (tpt) cc_final: 0.3737 (mtm) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.0746 time to fit residues: 14.8215 Evaluate side-chains 123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100141 restraints weight = 15125.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103505 restraints weight = 11087.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104507 restraints weight = 6813.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105014 restraints weight = 6017.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105322 restraints weight = 5760.568| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10157 Z= 0.148 Angle : 0.564 7.820 13969 Z= 0.304 Chirality : 0.043 0.310 1607 Planarity : 0.003 0.049 1587 Dihedral : 20.717 85.699 1901 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.90 % Allowed : 14.52 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 1103 helix: 0.71 (0.29), residues: 326 sheet: -2.15 (0.25), residues: 305 loop : -1.25 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.017 0.001 TYR B 211 PHE 0.025 0.001 PHE B 215 TRP 0.013 0.001 TRP D 274 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (10154) covalent geometry : angle 0.56365 / 0.30 (13963) SS BOND : bond 0.00061 / 0.03 ( 3) SS BOND : angle 0.39470 / 0.18 ( 6) hydrogen bonds : bond 0.03885 / 2.58 ( 460) hydrogen bonds : angle 5.94464 / 4.19 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.354 Fit side-chains REVERT: C 244 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: D 10 ILE cc_start: 0.8880 (mm) cc_final: 0.8634 (mm) REVERT: D 126 PHE cc_start: 0.7569 (m-80) cc_final: 0.7325 (m-10) REVERT: D 214 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7103 (tm-30) REVERT: D 259 ILE cc_start: 0.8081 (mm) cc_final: 0.7653 (mt) REVERT: B 75 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8169 (tmm) REVERT: B 86 ASP cc_start: 0.7848 (m-30) cc_final: 0.7632 (m-30) REVERT: B 199 MET cc_start: 0.5757 (tpt) cc_final: 0.3759 (mtm) REVERT: B 215 PHE cc_start: 0.8623 (m-80) cc_final: 0.8371 (m-80) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.0784 time to fit residues: 15.8237 Evaluate side-chains 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099014 restraints weight = 15097.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102363 restraints weight = 10580.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103084 restraints weight = 6474.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103317 restraints weight = 6420.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105305 restraints weight = 5795.832| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10157 Z= 0.182 Angle : 0.581 7.569 13969 Z= 0.311 Chirality : 0.044 0.348 1607 Planarity : 0.003 0.049 1587 Dihedral : 20.693 87.132 1901 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.11 % Allowed : 15.04 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.24), residues: 1103 helix: 0.79 (0.29), residues: 327 sheet: -2.12 (0.26), residues: 303 loop : -1.18 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 262 TYR 0.023 0.002 TYR B 211 PHE 0.023 0.002 PHE B 215 TRP 0.012 0.001 TRP D 274 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (10154) covalent geometry : angle 0.58079 / 0.31 (13963) SS BOND : bond 0.00099 / 0.05 ( 3) SS BOND : angle 0.49618 / 0.23 ( 6) hydrogen bonds : bond 0.03939 / 2.61 ( 460) hydrogen bonds : angle 5.86553 / 4.12 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 244 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: D 10 ILE cc_start: 0.8923 (mm) cc_final: 0.8695 (mm) REVERT: D 126 PHE cc_start: 0.7655 (m-80) cc_final: 0.7336 (m-10) REVERT: D 259 ILE cc_start: 0.8185 (mm) cc_final: 0.7758 (mt) REVERT: B 75 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8213 (tmm) REVERT: B 199 MET cc_start: 0.5797 (tpt) cc_final: 0.3759 (mtm) REVERT: B 215 PHE cc_start: 0.8737 (m-80) cc_final: 0.8479 (m-80) outliers start: 30 outliers final: 23 residues processed: 128 average time/residue: 0.0837 time to fit residues: 16.2341 Evaluate side-chains 133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099778 restraints weight = 15006.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103298 restraints weight = 10793.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104035 restraints weight = 6552.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104727 restraints weight = 5919.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104961 restraints weight = 5624.755| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10157 Z= 0.145 Angle : 0.560 6.579 13969 Z= 0.302 Chirality : 0.044 0.343 1607 Planarity : 0.003 0.049 1587 Dihedral : 20.648 86.731 1901 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 15.66 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.24), residues: 1103 helix: 0.87 (0.29), residues: 328 sheet: -2.04 (0.26), residues: 304 loop : -1.13 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 262 TYR 0.020 0.002 TYR B 211 PHE 0.024 0.001 PHE B 215 TRP 0.013 0.001 TRP D 274 HIS 0.002 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (10154) covalent geometry : angle 0.55956 / 0.30 (13963) SS BOND : bond 0.00080 / 0.04 ( 3) SS BOND : angle 0.44270 / 0.21 ( 6) hydrogen bonds : bond 0.03758 / 2.49 ( 460) hydrogen bonds : angle 5.81036 / 4.08 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: C 244 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8308 (mtp) REVERT: D 10 ILE cc_start: 0.8910 (mm) cc_final: 0.8682 (mm) REVERT: D 126 PHE cc_start: 0.7646 (m-80) cc_final: 0.7353 (m-10) REVERT: D 259 ILE cc_start: 0.8179 (mm) cc_final: 0.7748 (mt) REVERT: D 274 TRP cc_start: 0.8061 (t60) cc_final: 0.7671 (t60) REVERT: B 75 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8139 (tmm) REVERT: B 199 MET cc_start: 0.5788 (tpt) cc_final: 0.3737 (mtm) REVERT: B 215 PHE cc_start: 0.8781 (m-80) cc_final: 0.8504 (m-80) REVERT: A 199 MET cc_start: 0.5544 (tpt) cc_final: 0.5231 (tpt) outliers start: 28 outliers final: 21 residues processed: 126 average time/residue: 0.0843 time to fit residues: 16.0947 Evaluate side-chains 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099108 restraints weight = 14963.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102458 restraints weight = 11019.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103299 restraints weight = 6766.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104062 restraints weight = 6007.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104277 restraints weight = 5720.840| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10157 Z= 0.160 Angle : 0.572 6.388 13969 Z= 0.306 Chirality : 0.044 0.343 1607 Planarity : 0.003 0.049 1587 Dihedral : 20.633 87.241 1901 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.90 % Allowed : 15.56 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1103 helix: 0.87 (0.29), residues: 328 sheet: -2.04 (0.25), residues: 320 loop : -1.07 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 262 TYR 0.021 0.002 TYR B 211 PHE 0.022 0.002 PHE B 215 TRP 0.013 0.001 TRP D 274 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10154) covalent geometry : angle 0.57252 / 0.31 (13963) SS BOND : bond 0.00102 / 0.05 ( 3) SS BOND : angle 0.46155 / 0.22 ( 6) hydrogen bonds : bond 0.03770 / 2.51 ( 460) hydrogen bonds : angle 5.77326 / 4.06 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.361 Fit side-chains REVERT: C 244 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: D 10 ILE cc_start: 0.8951 (mm) cc_final: 0.8736 (mm) REVERT: D 126 PHE cc_start: 0.7665 (m-80) cc_final: 0.7370 (m-10) REVERT: D 259 ILE cc_start: 0.8216 (mm) cc_final: 0.7786 (mt) REVERT: D 274 TRP cc_start: 0.8060 (t60) cc_final: 0.7735 (t60) REVERT: B 75 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8192 (tmm) REVERT: B 215 PHE cc_start: 0.8786 (m-80) cc_final: 0.8502 (m-80) outliers start: 28 outliers final: 22 residues processed: 125 average time/residue: 0.0883 time to fit residues: 16.3497 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098887 restraints weight = 15212.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102298 restraints weight = 10379.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103079 restraints weight = 6314.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103635 restraints weight = 5677.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103915 restraints weight = 5408.694| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10157 Z= 0.140 Angle : 0.561 6.653 13969 Z= 0.304 Chirality : 0.044 0.371 1607 Planarity : 0.003 0.050 1587 Dihedral : 20.568 87.061 1901 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 16.29 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.24), residues: 1103 helix: 0.92 (0.29), residues: 328 sheet: -1.98 (0.25), residues: 320 loop : -1.03 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.018 0.001 TYR B 211 PHE 0.023 0.001 PHE B 215 TRP 0.016 0.001 TRP D 274 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10154) covalent geometry : angle 0.56144 / 0.30 (13963) SS BOND : bond 0.00085 / 0.04 ( 3) SS BOND : angle 0.43777 / 0.21 ( 6) hydrogen bonds : bond 0.03662 / 2.44 ( 460) hydrogen bonds : angle 5.73986 / 4.04 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.331 Fit side-chains REVERT: C 244 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: D 10 ILE cc_start: 0.8939 (mm) cc_final: 0.8724 (mm) REVERT: D 126 PHE cc_start: 0.7645 (m-80) cc_final: 0.7347 (m-10) REVERT: D 259 ILE cc_start: 0.8160 (mm) cc_final: 0.7736 (mt) REVERT: D 274 TRP cc_start: 0.8131 (t60) cc_final: 0.7761 (t60) REVERT: B 75 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8161 (tmm) REVERT: B 215 PHE cc_start: 0.8780 (m-80) cc_final: 0.8521 (m-80) REVERT: A 199 MET cc_start: 0.5588 (tpt) cc_final: 0.5203 (tpt) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.0807 time to fit residues: 15.1778 Evaluate side-chains 121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100998 restraints weight = 15386.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104353 restraints weight = 10781.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105267 restraints weight = 6545.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105741 restraints weight = 5848.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106032 restraints weight = 5619.535| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10157 Z= 0.120 Angle : 0.544 6.951 13969 Z= 0.295 Chirality : 0.043 0.357 1607 Planarity : 0.003 0.051 1587 Dihedral : 20.458 86.168 1901 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.24), residues: 1103 helix: 1.04 (0.29), residues: 328 sheet: -1.80 (0.26), residues: 320 loop : -1.02 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 129 TYR 0.017 0.001 TYR B 211 PHE 0.024 0.001 PHE B 215 TRP 0.018 0.001 TRP D 274 HIS 0.003 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10154) covalent geometry : angle 0.54392 / 0.29 (13963) SS BOND : bond 0.00044 / 0.02 ( 3) SS BOND : angle 0.37519 / 0.17 ( 6) hydrogen bonds : bond 0.03500 / 2.33 ( 460) hydrogen bonds : angle 5.58428 / 3.94 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.55 seconds wall clock time: 26 minutes 52.98 seconds (1612.98 seconds total)