Starting phenix.real_space_refine on Fri Sep 11 06:00:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vo_69846/09_2026/24vo_69846.map" } resolution = 3.64 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= 0.009 sd= 0.083 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5226 2.51 5 N 1276 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7866 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "C" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2006 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 4, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.26 Number of scatterers: 7866 At special positions: 0 Unit cell: (84.786, 106.526, 111.961, 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 39 16.00 P 1 15.00 O 1324 8.00 N 1276 7.00 C 5226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 510.6 milliseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.948A pdb=" N ARG A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.905A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 179 removed outlier: 3.639A pdb=" N ALA A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.606A pdb=" N MET A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.509A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.799A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.606A pdb=" N LEU A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 122 through 143 removed outlier: 3.616A pdb=" N ALA B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 178 Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.528A pdb=" N ALA B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.630A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.604A pdb=" N ALA B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.693A pdb=" N THR B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.723A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 366 removed outlier: 3.650A pdb=" N LEU B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 122 through 142 removed outlier: 3.635A pdb=" N HIS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.545A pdb=" N ALA C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.563A pdb=" N MET C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 244 through 257 removed outlier: 4.145A pdb=" N LEU C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 283 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 327 through 345 removed outlier: 3.649A pdb=" N LEU C 331 " --> pdb=" O TRP C 327 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 366 removed outlier: 3.706A pdb=" N LEU C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.939A pdb=" N ILE D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 145 removed outlier: 3.689A pdb=" N TRP D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 183 Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.783A pdb=" N ILE D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 228 through 253 removed outlier: 3.511A pdb=" N VAL D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.749A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 removed outlier: 4.205A pdb=" N SER D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1572 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: 1.29 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1163 1.31 - 1.44: 2346 1.44 - 1.56: 4503 1.56 - 1.69: 3 1.69 - 1.82: 54 Bond restraints: 8069 Sorted by residual: bond pdb=" C31 9PE C1001 " pdb=" O31 9PE C1001 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C21 9PE C1001 " pdb=" O21 9PE C1001 " ideal model delta sigma weight residual 1.329 1.397 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N ASP D 171 " pdb=" CA ASP D 171 " ideal model delta sigma weight residual 1.459 1.428 0.031 1.23e-02 6.61e+03 6.19e+00 bond pdb=" C ILE D 170 " pdb=" N ASP D 171 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.36e-02 5.41e+03 5.24e+00 bond pdb=" CA ASP D 171 " pdb=" CB ASP D 171 " ideal model delta sigma weight residual 1.528 1.494 0.035 1.59e-02 3.96e+03 4.76e+00 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 10643 2.38 - 4.75: 203 4.75 - 7.13: 59 7.13 - 9.51: 19 9.51 - 11.89: 7 Bond angle restraints: 10931 Sorted by residual: angle pdb=" CA TYR C 112 " pdb=" CB TYR C 112 " pdb=" CG TYR C 112 " ideal model delta sigma weight residual 113.90 122.63 -8.73 1.80e+00 3.09e-01 2.35e+01 angle pdb=" N ARG C 230 " pdb=" CA ARG C 230 " pdb=" C ARG C 230 " ideal model delta sigma weight residual 114.56 108.46 6.10 1.27e+00 6.20e-01 2.31e+01 angle pdb=" N PHE C 171 " pdb=" CA PHE C 171 " pdb=" C PHE C 171 " ideal model delta sigma weight residual 111.14 106.26 4.88 1.08e+00 8.57e-01 2.05e+01 angle pdb=" CA GLU D 116 " pdb=" CB GLU D 116 " pdb=" CG GLU D 116 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.02e+01 angle pdb=" O12 9PE C1001 " pdb=" P 9PE C1001 " pdb=" O14 9PE C1001 " ideal model delta sigma weight residual 120.90 109.01 11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 10926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 4534 35.90 - 71.79: 201 71.79 - 107.68: 26 107.68 - 143.58: 32 143.58 - 179.47: 7 Dihedral angle restraints: 4800 sinusoidal: 2036 harmonic: 2764 Sorted by residual: dihedral pdb=" N 9PE C1001 " pdb=" C11 9PE C1001 " pdb=" C12 9PE C1001 " pdb=" O13 9PE C1001 " ideal model delta sinusoidal sigma weight residual -66.84 112.63 -179.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O30 YJ0 D 901 " pdb=" C31 YJ0 D 901 " pdb=" C32 YJ0 D 901 " pdb=" O52 YJ0 D 901 " ideal model delta sinusoidal sigma weight residual 234.92 58.45 176.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O36 YJ0 D 901 " pdb=" C31 YJ0 D 901 " pdb=" C32 YJ0 D 901 " pdb=" O52 YJ0 D 901 " ideal model delta sinusoidal sigma weight residual 124.08 -62.64 -173.28 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.214: 1234 1.214 - 2.429: 0 2.429 - 3.643: 0 3.643 - 4.857: 0 4.857 - 6.072: 10 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C12 YJ0 D 901 " pdb=" C11 YJ0 D 901 " pdb=" C13 YJ0 D 901 " pdb=" C7 YJ0 D 901 " both_signs ideal model delta sigma weight residual False 3.10 -2.98 6.07 2.00e-01 2.50e+01 9.22e+02 chirality pdb=" C16 YJ0 D 901 " pdb=" C11 YJ0 D 901 " pdb=" C15 YJ0 D 901 " pdb=" C17 YJ0 D 901 " both_signs ideal model delta sigma weight residual False -2.82 2.76 -5.58 2.00e-01 2.50e+01 7.77e+02 chirality pdb=" C38 YJ0 D 901 " pdb=" C36 YJ0 D 901 " pdb=" C39 YJ0 D 901 " pdb=" O1 YJ0 D 901 " both_signs ideal model delta sigma weight residual False 2.70 -2.53 5.23 2.00e-01 2.50e+01 6.84e+02 ... (remaining 1241 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 901 " 0.069 2.00e-02 2.50e+03 5.69e-02 4.05e+01 pdb=" C18 YJ0 D 901 " -0.085 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 901 " -0.032 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 901 " -0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 901 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 165 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO D 166 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 130 " 0.020 2.00e-02 2.50e+03 2.00e-02 7.00e+00 pdb=" CG PHE A 130 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 130 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 130 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 130 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 130 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 130 " 0.001 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1537 2.77 - 3.30: 7769 3.30 - 3.84: 12941 3.84 - 4.37: 13523 4.37 - 4.90: 24062 Nonbonded interactions: 59832 Sorted by model distance: nonbonded pdb=" O ARG C 364 " pdb=" NE ARG C 364 " model vdw 2.240 3.120 nonbonded pdb=" OH TYR A 319 " pdb=" OG1 THR D 273 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 313 " pdb=" OH TYR C 319 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR D 94 " pdb=" OE1 GLU D 139 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 140 " pdb=" OG1 THR A 143 " model vdw 2.266 3.040 ... (remaining 59827 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' selection = (chain 'C' and resid 110 through 366) } 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: 1.470 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.270 Find NCS groups from input model: 0.130 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:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.004 0.074 8069 Z= 0.204 Angle : 0.927 11.887 10931 Z= 0.458 Chirality : 0.474 6.072 1244 Planarity : 0.004 0.071 1297 Dihedral : 24.915 179.475 3030 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.02 % Favored : 91.77 % Rotamer: Outliers : 0.38 % Allowed : 34.76 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.29), residues: 948 helix: 1.52 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -3.00 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 119 TYR 0.011 0.001 TYR B 184 PHE 0.047 0.001 PHE A 130 TRP 0.021 0.001 TRP C 176 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 ( 8069) covalent geometry : angle 0.92743 / 0.46 (10931) hydrogen bonds : bond 0.12501 / 8.63 ( 524) hydrogen bonds : angle 5.28243 / 3.84 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.347 Fit side-chains REVERT: A 200 MET cc_start: 0.7467 (ptp) cc_final: 0.7135 (pmm) REVERT: A 236 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7808 (ptp-170) REVERT: C 296 MET cc_start: 0.6406 (mpp) cc_final: 0.5952 (ttt) REVERT: D 207 MET cc_start: 0.7338 (tpp) cc_final: 0.6821 (tpp) outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.0885 time to fit residues: 23.5664 Evaluate side-chains 183 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.159971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119075 restraints weight = 12657.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121649 restraints weight = 8102.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123262 restraints weight = 6201.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124068 restraints weight = 5327.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124773 restraints weight = 4907.192| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8069 Z= 0.200 Angle : 0.990 36.048 10931 Z= 0.421 Chirality : 0.087 2.151 1244 Planarity : 0.004 0.046 1297 Dihedral : 18.254 173.649 1292 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 4.28 % Allowed : 31.11 % Favored : 64.61 % 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: 0.67 (0.29), residues: 948 helix: 1.56 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.99 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 152 TYR 0.012 0.001 TYR B 184 PHE 0.023 0.002 PHE A 269 TRP 0.023 0.001 TRP D 145 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 8069) covalent geometry : angle 0.98965 / 0.42 (10931) hydrogen bonds : bond 0.05512 / 3.68 ( 524) hydrogen bonds : angle 4.63925 / 3.36 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.306 Fit side-chains REVERT: C 124 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7627 (tt) REVERT: D 171 ASP cc_start: 0.7918 (m-30) cc_final: 0.7680 (m-30) outliers start: 34 outliers final: 20 residues processed: 209 average time/residue: 0.0810 time to fit residues: 23.6782 Evaluate side-chains 196 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.161016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119656 restraints weight = 12663.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122318 restraints weight = 8094.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123954 restraints weight = 6192.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125026 restraints weight = 5319.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125488 restraints weight = 4862.673| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8069 Z= 0.151 Angle : 0.924 34.160 10931 Z= 0.389 Chirality : 0.086 2.068 1244 Planarity : 0.004 0.043 1297 Dihedral : 17.666 174.243 1292 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 5.04 % Allowed : 29.72 % Favored : 65.24 % 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: 0.75 (0.29), residues: 948 helix: 1.65 (0.20), residues: 705 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.028 0.001 TYR C 112 PHE 0.017 0.001 PHE A 269 TRP 0.017 0.001 TRP D 145 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8069) covalent geometry : angle 0.92423 / 0.39 (10931) hydrogen bonds : bond 0.04970 / 3.32 ( 524) hydrogen bonds : angle 4.45032 / 3.22 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 125 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: B 237 MET cc_start: 0.8259 (mmm) cc_final: 0.8037 (mmm) outliers start: 40 outliers final: 24 residues processed: 216 average time/residue: 0.0846 time to fit residues: 25.4026 Evaluate side-chains 202 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 365 GLN 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 = 0.161944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120950 restraints weight = 12875.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123528 restraints weight = 8244.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125248 restraints weight = 6311.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126340 restraints weight = 5395.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126788 restraints weight = 4915.724| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8069 Z= 0.143 Angle : 0.914 34.783 10931 Z= 0.382 Chirality : 0.084 2.041 1244 Planarity : 0.003 0.042 1297 Dihedral : 17.199 173.858 1292 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.59 % Favored : 92.19 % Rotamer: Outliers : 5.16 % Allowed : 30.60 % Favored : 64.23 % 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: 0.87 (0.29), residues: 948 helix: 1.69 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -2.99 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 152 TYR 0.013 0.001 TYR D 73 PHE 0.018 0.001 PHE A 269 TRP 0.015 0.001 TRP D 145 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8069) covalent geometry : angle 0.91379 / 0.38 (10931) hydrogen bonds : bond 0.04773 / 3.18 ( 524) hydrogen bonds : angle 4.30802 / 3.12 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: C 130 PHE cc_start: 0.7012 (t80) cc_final: 0.6637 (t80) REVERT: C 190 ARG cc_start: 0.7875 (mtm180) cc_final: 0.6894 (mtt180) outliers start: 41 outliers final: 21 residues processed: 220 average time/residue: 0.0910 time to fit residues: 27.1675 Evaluate side-chains 202 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN C 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122383 restraints weight = 12729.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125015 restraints weight = 8075.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126785 restraints weight = 6127.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127619 restraints weight = 5217.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128402 restraints weight = 4803.567| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8069 Z= 0.137 Angle : 0.917 34.547 10931 Z= 0.383 Chirality : 0.084 2.022 1244 Planarity : 0.004 0.041 1297 Dihedral : 16.889 173.746 1292 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.17 % Favored : 92.62 % Rotamer: Outliers : 4.41 % Allowed : 31.49 % Favored : 64.11 % 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: 0.95 (0.29), residues: 948 helix: 1.76 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.013 0.001 TYR D 73 PHE 0.020 0.001 PHE A 269 TRP 0.014 0.001 TRP D 145 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 8069) covalent geometry : angle 0.91661 / 0.38 (10931) hydrogen bonds : bond 0.04557 / 3.03 ( 524) hydrogen bonds : angle 4.22830 / 3.06 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8669 (mp0) cc_final: 0.8338 (mt-10) REVERT: B 125 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: B 192 LYS cc_start: 0.8678 (mttt) cc_final: 0.8298 (pttm) REVERT: B 237 MET cc_start: 0.8241 (mmm) cc_final: 0.8007 (mmm) REVERT: C 190 ARG cc_start: 0.7771 (mtm180) cc_final: 0.6866 (mtt180) REVERT: D 85 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6779 (tm-30) outliers start: 35 outliers final: 20 residues processed: 213 average time/residue: 0.0868 time to fit residues: 25.3151 Evaluate side-chains 201 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN C 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124905 restraints weight = 12595.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127613 restraints weight = 7951.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129440 restraints weight = 6026.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130315 restraints weight = 5122.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130449 restraints weight = 4695.394| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8069 Z= 0.129 Angle : 0.926 34.355 10931 Z= 0.383 Chirality : 0.083 2.009 1244 Planarity : 0.003 0.040 1297 Dihedral : 16.529 173.431 1289 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.96 % Favored : 92.72 % Rotamer: Outliers : 4.03 % Allowed : 32.75 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 948 helix: 1.80 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.013 0.001 TYR D 73 PHE 0.017 0.001 PHE A 269 TRP 0.018 0.001 TRP C 176 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 8069) covalent geometry : angle 0.92583 / 0.38 (10931) hydrogen bonds : bond 0.04372 / 2.92 ( 524) hydrogen bonds : angle 4.18446 / 3.01 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.293 Fit side-chains REVERT: A 174 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7529 (ttm170) REVERT: A 236 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7902 (ptp-170) REVERT: A 260 GLU cc_start: 0.8631 (mp0) cc_final: 0.8328 (mt-10) REVERT: B 125 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: B 192 LYS cc_start: 0.8674 (mttt) cc_final: 0.8368 (pttm) REVERT: B 198 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6246 (mp) REVERT: B 237 MET cc_start: 0.8342 (mmm) cc_final: 0.8003 (mmm) REVERT: B 360 GLN cc_start: 0.8377 (tt0) cc_final: 0.8086 (tm-30) REVERT: C 190 ARG cc_start: 0.7778 (mtm180) cc_final: 0.6897 (mtt180) REVERT: C 296 MET cc_start: 0.5946 (mpp) cc_final: 0.5625 (ttt) REVERT: D 209 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7245 (tmm-80) outliers start: 32 outliers final: 19 residues processed: 216 average time/residue: 0.0851 time to fit residues: 25.4259 Evaluate side-chains 207 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120574 restraints weight = 12805.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123021 restraints weight = 8487.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124634 restraints weight = 6619.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125395 restraints weight = 5717.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126094 restraints weight = 5293.103| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8069 Z= 0.162 Angle : 0.949 34.656 10931 Z= 0.399 Chirality : 0.084 2.004 1244 Planarity : 0.003 0.040 1297 Dihedral : 16.490 173.488 1289 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 4.03 % Allowed : 32.87 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.29), residues: 948 helix: 1.69 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 119 TYR 0.014 0.001 TYR D 73 PHE 0.022 0.002 PHE A 269 TRP 0.019 0.001 TRP C 176 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 8069) covalent geometry : angle 0.94884 / 0.40 (10931) hydrogen bonds : bond 0.04833 / 3.21 ( 524) hydrogen bonds : angle 4.24866 / 3.06 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.264 Fit side-chains REVERT: A 184 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: A 260 GLU cc_start: 0.8654 (mp0) cc_final: 0.8356 (mt-10) REVERT: B 125 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: B 192 LYS cc_start: 0.8725 (mttt) cc_final: 0.8412 (pttm) REVERT: B 198 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6458 (mp) REVERT: B 237 MET cc_start: 0.8462 (mmm) cc_final: 0.8144 (mmm) REVERT: C 190 ARG cc_start: 0.7858 (mtm180) cc_final: 0.6944 (mtt180) REVERT: C 201 LEU cc_start: 0.8666 (mm) cc_final: 0.7885 (tp) REVERT: D 321 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8044 (mm-30) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 0.0882 time to fit residues: 24.3625 Evaluate side-chains 198 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 62 optimal weight: 0.0030 chunk 56 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123727 restraints weight = 12737.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126117 restraints weight = 8462.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127622 restraints weight = 6614.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128331 restraints weight = 5742.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128884 restraints weight = 5316.466| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8069 Z= 0.142 Angle : 0.948 34.352 10931 Z= 0.398 Chirality : 0.084 1.999 1244 Planarity : 0.004 0.043 1297 Dihedral : 16.383 173.197 1289 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.28 % Favored : 92.51 % Rotamer: Outliers : 3.27 % Allowed : 34.26 % Favored : 62.47 % 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: 1.03 (0.29), residues: 948 helix: 1.81 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.77 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 209 TYR 0.014 0.001 TYR D 73 PHE 0.020 0.001 PHE A 269 TRP 0.021 0.001 TRP C 176 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8069) covalent geometry : angle 0.94828 / 0.40 (10931) hydrogen bonds : bond 0.04535 / 3.04 ( 524) hydrogen bonds : angle 4.18356 / 3.01 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.346 Fit side-chains REVERT: A 184 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7239 (m-10) REVERT: A 236 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7896 (ptp-170) REVERT: A 260 GLU cc_start: 0.8603 (mp0) cc_final: 0.8325 (mt-10) REVERT: A 341 VAL cc_start: 0.9060 (m) cc_final: 0.8853 (m) REVERT: B 125 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: B 192 LYS cc_start: 0.8684 (mttt) cc_final: 0.8393 (pttm) REVERT: B 198 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6380 (mp) REVERT: B 237 MET cc_start: 0.8448 (mmm) cc_final: 0.8153 (mmm) REVERT: C 190 ARG cc_start: 0.7794 (mtm180) cc_final: 0.6899 (mtt180) REVERT: C 200 MET cc_start: 0.8035 (tpt) cc_final: 0.7723 (tpp) REVERT: D 321 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7972 (mm-30) outliers start: 26 outliers final: 19 residues processed: 202 average time/residue: 0.0868 time to fit residues: 24.2982 Evaluate side-chains 198 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 GLN 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 = 0.161646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121946 restraints weight = 12698.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124414 restraints weight = 8316.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125698 restraints weight = 6438.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126838 restraints weight = 5610.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126838 restraints weight = 5125.854| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8069 Z= 0.158 Angle : 0.958 34.463 10931 Z= 0.405 Chirality : 0.084 2.000 1244 Planarity : 0.004 0.040 1297 Dihedral : 16.259 173.037 1289 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 3.65 % Allowed : 34.26 % Favored : 62.09 % 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: 1.01 (0.29), residues: 948 helix: 1.77 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -2.72 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 209 TYR 0.013 0.001 TYR D 73 PHE 0.027 0.001 PHE D 141 TRP 0.023 0.001 TRP C 176 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8069) covalent geometry : angle 0.95779 / 0.40 (10931) hydrogen bonds : bond 0.04730 / 3.15 ( 524) hydrogen bonds : angle 4.20821 / 3.03 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.336 Fit side-chains REVERT: A 184 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: A 260 GLU cc_start: 0.8641 (mp0) cc_final: 0.8355 (mt-10) REVERT: B 125 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: B 192 LYS cc_start: 0.8703 (mttt) cc_final: 0.8479 (pttm) REVERT: C 190 ARG cc_start: 0.7891 (mtm180) cc_final: 0.6965 (mtt180) REVERT: C 200 MET cc_start: 0.8072 (tpt) cc_final: 0.7760 (tpp) REVERT: D 321 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8016 (mm-30) outliers start: 29 outliers final: 23 residues processed: 191 average time/residue: 0.0803 time to fit residues: 21.6894 Evaluate side-chains 198 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.161709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121153 restraints weight = 12594.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123593 restraints weight = 8393.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125131 restraints weight = 6554.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126034 restraints weight = 5682.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126309 restraints weight = 5247.978| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8069 Z= 0.158 Angle : 0.961 34.394 10931 Z= 0.405 Chirality : 0.084 1.999 1244 Planarity : 0.004 0.042 1297 Dihedral : 16.205 172.989 1289 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.28 % Favored : 92.51 % Rotamer: Outliers : 3.02 % Allowed : 35.01 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.29), residues: 948 helix: 1.78 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.68 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 209 TYR 0.012 0.001 TYR D 73 PHE 0.021 0.001 PHE A 269 TRP 0.024 0.001 TRP C 176 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8069) covalent geometry : angle 0.96052 / 0.41 (10931) hydrogen bonds : bond 0.04694 / 3.12 ( 524) hydrogen bonds : angle 4.20878 / 3.03 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.325 Fit side-chains REVERT: A 184 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: A 236 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7870 (ptp-170) REVERT: A 260 GLU cc_start: 0.8663 (mp0) cc_final: 0.8373 (mt-10) REVERT: B 125 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: B 192 LYS cc_start: 0.8711 (mttt) cc_final: 0.8449 (ptpt) REVERT: B 237 MET cc_start: 0.8491 (mmm) cc_final: 0.8266 (mmm) REVERT: C 190 ARG cc_start: 0.7904 (mtm180) cc_final: 0.6967 (mtt180) REVERT: C 200 MET cc_start: 0.8049 (tpt) cc_final: 0.7830 (tpt) REVERT: C 296 MET cc_start: 0.6161 (mpp) cc_final: 0.5655 (ttt) REVERT: D 321 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8018 (mm-30) outliers start: 24 outliers final: 21 residues processed: 189 average time/residue: 0.0823 time to fit residues: 21.8605 Evaluate side-chains 196 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 overall best weight: 0.1620 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.166551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126325 restraints weight = 12719.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129135 restraints weight = 8011.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130940 restraints weight = 6058.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131793 restraints weight = 5145.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132654 restraints weight = 4713.211| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8069 Z= 0.133 Angle : 0.951 33.851 10931 Z= 0.399 Chirality : 0.084 1.993 1244 Planarity : 0.003 0.041 1297 Dihedral : 16.047 172.366 1289 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.96 % Favored : 92.83 % Rotamer: Outliers : 1.64 % Allowed : 36.78 % Favored : 61.59 % 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: 1.07 (0.29), residues: 948 helix: 1.81 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.64 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 209 TYR 0.012 0.001 TYR D 73 PHE 0.026 0.001 PHE C 171 TRP 0.024 0.001 TRP C 176 HIS 0.003 0.000 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8069) covalent geometry : angle 0.95064 / 0.40 (10931) hydrogen bonds : bond 0.04025 / 2.69 ( 524) hydrogen bonds : angle 4.07068 / 2.93 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.59 seconds wall clock time: 26 minutes 44.05 seconds (1604.05 seconds total)