Starting phenix.real_space_refine on Wed Feb 4 00:21:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfk_61433/02_2026/9jfk_61433.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5025 2.51 5 N 1372 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7892 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2505 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1800 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 364 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2122 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LE1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'CHO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.39, per 1000 atoms: 0.18 Number of scatterers: 7892 At special positions: 0 Unit cell: (99.704, 95.584, 131.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1445 8.00 N 1372 7.00 C 5025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 199 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 288.5 milliseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 4 through 25 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.676A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 4.337A pdb=" N ASN A 132 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.179A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.850A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 205 removed outlier: 3.526A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'R' and resid 46 through 79 removed outlier: 4.428A pdb=" N ALA R 50 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR R 51 " --> pdb=" O ASP R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 102 removed outlier: 3.627A pdb=" N LEU R 98 " --> pdb=" O ALA R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 109 removed outlier: 4.108A pdb=" N PHE R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 154 removed outlier: 3.614A pdb=" N GLY R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 160 Processing helix chain 'R' and resid 164 through 188 removed outlier: 4.664A pdb=" N LEU R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Proline residue: R 183 - end of helix removed outlier: 3.682A pdb=" N MET R 188 " --> pdb=" O VAL R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 220 Processing helix chain 'R' and resid 220 through 242 Processing helix chain 'R' and resid 258 through 271 Processing helix chain 'R' and resid 272 through 275 Processing helix chain 'R' and resid 276 through 281 Processing helix chain 'R' and resid 282 through 284 No H-bonds generated for 'chain 'R' and resid 282 through 284' Processing helix chain 'R' and resid 289 through 316 removed outlier: 3.688A pdb=" N CYS R 302 " --> pdb=" O TYR R 298 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 319 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 50 removed outlier: 3.590A pdb=" N ARG A 46 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR A 50 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 336 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 328 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 318 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 330 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 6.775A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 4.027A pdb=" N ARG A 137 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 151 removed outlier: 6.788A pdb=" N SER A 160 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS A 149 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 158 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE A 151 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN A 156 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 166 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR A 179 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 168 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.597A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 202 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 208 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.608A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 254 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 259 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.996A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 306 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 76 removed outlier: 6.118A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 36 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 86 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU B 38 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.658A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.93 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: 1271 1.31 - 1.44: 2199 1.44 - 1.57: 4519 1.57 - 1.70: 0 1.70 - 1.83: 69 Bond restraints: 8058 Sorted by residual: bond pdb=" C PHE C 3 " pdb=" N TRP C 4 " ideal model delta sigma weight residual 1.327 1.515 -0.187 1.11e-02 8.12e+03 2.84e+02 bond pdb=" C LE1 C 2 " pdb=" N PHE C 3 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" C TRP C 4 " pdb=" N LYS C 5 " ideal model delta sigma weight residual 1.335 1.489 -0.154 1.36e-02 5.41e+03 1.28e+02 bond pdb=" C ASP C 1 " pdb=" N LE1 C 2 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.28e+02 bond pdb=" C TYR C 6 " pdb=" N CYS C 7 " ideal model delta sigma weight residual 1.331 1.472 -0.141 1.29e-02 6.01e+03 1.19e+02 ... (remaining 8053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.16: 10955 6.16 - 12.32: 6 12.32 - 18.48: 1 18.48 - 24.63: 1 24.63 - 30.79: 2 Bond angle restraints: 10965 Sorted by residual: angle pdb=" C12 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C18 CHO R 402 " ideal model delta sigma weight residual 111.09 80.30 30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C17 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C18 CHO R 402 " ideal model delta sigma weight residual 110.09 79.72 30.37 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C14 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C18 CHO R 402 " ideal model delta sigma weight residual 112.35 89.88 22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C12 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C17 CHO R 402 " ideal model delta sigma weight residual 116.19 130.74 -14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CA ASP C 1 " pdb=" C ASP C 1 " pdb=" N LE1 C 2 " ideal model delta sigma weight residual 116.20 124.11 -7.91 2.00e+00 2.50e-01 1.56e+01 ... (remaining 10960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 4799 35.19 - 70.37: 69 70.37 - 105.56: 0 105.56 - 140.75: 0 140.75 - 175.93: 5 Dihedral angle restraints: 4873 sinusoidal: 1921 harmonic: 2952 Sorted by residual: dihedral pdb=" C18 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C17 CHO R 402 " pdb=" C20 CHO R 402 " ideal model delta sinusoidal sigma weight residual 313.44 137.51 175.93 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C17 CHO R 402 " pdb=" C18 CHO R 402 " ideal model delta sinusoidal sigma weight residual -78.55 97.34 -175.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 CHO R 402 " pdb=" C13 CHO R 402 " pdb=" C14 CHO R 402 " pdb=" C18 CHO R 402 " ideal model delta sinusoidal sigma weight residual 69.82 -103.53 173.35 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 1266 0.352 - 0.704: 0 0.704 - 1.056: 0 1.056 - 1.408: 0 1.408 - 1.760: 1 Chirality restraints: 1267 Sorted by residual: chirality pdb=" C13 CHO R 402 " pdb=" C12 CHO R 402 " pdb=" C14 CHO R 402 " pdb=" C17 CHO R 402 " both_signs ideal model delta sigma weight residual False -2.94 -1.18 -1.76 2.00e-01 2.50e+01 7.74e+01 chirality pdb=" CA LE1 C 2 " pdb=" N LE1 C 2 " pdb=" C LE1 C 2 " pdb=" CB LE1 C 2 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL C 8 " pdb=" N VAL C 8 " pdb=" C VAL C 8 " pdb=" CB VAL C 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1264 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 272 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO R 273 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 273 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 273 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 173 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR R 173 " -0.023 2.00e-02 2.50e+03 pdb=" O THR R 173 " 0.009 2.00e-02 2.50e+03 pdb=" N TRP R 174 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 170 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C ALA R 170 " -0.022 2.00e-02 2.50e+03 pdb=" O ALA R 170 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU R 171 " 0.007 2.00e-02 2.50e+03 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 4966 3.04 - 3.51: 8129 3.51 - 3.97: 12352 3.97 - 4.44: 14629 4.44 - 4.90: 23270 Nonbonded interactions: 63346 Sorted by model distance: nonbonded pdb=" N VAL C 8 " pdb=" OXT VAL C 8 " model vdw 2.577 2.496 nonbonded pdb=" N THR A 143 " pdb=" OG1 THR A 143 " model vdw 2.596 2.496 nonbonded pdb=" O TYR N 94 " pdb=" CA GLY N 121 " model vdw 2.613 2.752 nonbonded pdb=" O ASP A 163 " pdb=" OG1 THR A 164 " model vdw 2.627 3.040 nonbonded pdb=" N ASP A 153 " pdb=" O ASP A 153 " model vdw 2.628 2.496 ... (remaining 63341 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 0.189 8063 Z= 0.411 Angle : 0.757 30.793 10971 Z= 0.365 Chirality : 0.063 1.760 1267 Planarity : 0.003 0.056 1386 Dihedral : 13.291 175.933 2960 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.32 % Allowed : 5.06 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.94 (0.27), residues: 1001 helix: 2.46 (0.28), residues: 361 sheet: 0.19 (0.34), residues: 209 loop : -0.76 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.007 0.001 TYR N 80 PHE 0.008 0.001 PHE N 68 TRP 0.005 0.001 TRP R 203 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8058) covalent geometry : angle 0.75708 (10965) SS BOND : bond 0.00416 ( 3) SS BOND : angle 0.99457 ( 6) hydrogen bonds : bond 0.14526 ( 389) hydrogen bonds : angle 5.77456 ( 1125) Misc. bond : bond 0.05877 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7802 (mtp-110) REVERT: A 78 LYS cc_start: 0.8860 (mptt) cc_final: 0.8007 (mmmt) REVERT: A 124 TYR cc_start: 0.8925 (m-80) cc_final: 0.8365 (m-80) REVERT: A 226 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 243 THR cc_start: 0.8596 (m) cc_final: 0.8350 (p) REVERT: A 262 MET cc_start: 0.8590 (tpp) cc_final: 0.8264 (ttm) REVERT: A 264 TYR cc_start: 0.8669 (m-80) cc_final: 0.7944 (m-10) REVERT: A 301 LYS cc_start: 0.9258 (mmmt) cc_final: 0.9038 (mmmm) REVERT: B 10 LYS cc_start: 0.9275 (mtpt) cc_final: 0.8976 (mtpp) REVERT: B 17 LYS cc_start: 0.9296 (tptt) cc_final: 0.8990 (ptpt) REVERT: B 21 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8743 (tttp) REVERT: B 130 ASN cc_start: 0.9385 (m-40) cc_final: 0.9023 (m-40) REVERT: B 151 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 194 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8622 (ttp80) REVERT: B 196 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 222 GLU cc_start: 0.8168 (pt0) cc_final: 0.7881 (pm20) REVERT: B 242 GLU cc_start: 0.8658 (tt0) cc_final: 0.8350 (tt0) REVERT: D 21 MET cc_start: 0.9087 (mmm) cc_final: 0.8859 (mmp) REVERT: N 1 GLN cc_start: 0.8566 (mt0) cc_final: 0.8345 (mp10) REVERT: N 46 GLU cc_start: 0.8731 (pt0) cc_final: 0.8491 (mp0) REVERT: N 73 ASP cc_start: 0.7423 (t0) cc_final: 0.6955 (t0) REVERT: N 84 ASN cc_start: 0.9298 (m-40) cc_final: 0.8660 (m-40) REVERT: N 87 LYS cc_start: 0.9089 (mttt) cc_final: 0.8630 (mttt) REVERT: N 90 ASP cc_start: 0.7965 (m-30) cc_final: 0.7659 (m-30) REVERT: N 109 ASP cc_start: 0.8018 (m-30) cc_final: 0.7774 (m-30) REVERT: N 114 THR cc_start: 0.9213 (p) cc_final: 0.8967 (t) REVERT: R 218 THR cc_start: 0.8939 (m) cc_final: 0.8711 (p) REVERT: R 307 ASN cc_start: 0.6679 (OUTLIER) cc_final: 0.6420 (t0) REVERT: R 321 ASN cc_start: 0.8663 (m110) cc_final: 0.8326 (m-40) outliers start: 35 outliers final: 10 residues processed: 346 average time/residue: 0.1050 time to fit residues: 46.0934 Evaluate side-chains 205 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 31 ASN R 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.130440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101858 restraints weight = 15725.423| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.81 r_work: 0.3286 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8063 Z= 0.195 Angle : 0.834 30.680 10971 Z= 0.379 Chirality : 0.067 1.746 1267 Planarity : 0.004 0.045 1386 Dihedral : 12.837 177.747 1274 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.81 % Allowed : 15.29 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.27), residues: 1001 helix: 2.37 (0.27), residues: 366 sheet: 0.19 (0.35), residues: 200 loop : -0.80 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.013 0.002 TYR R 305 PHE 0.018 0.002 PHE A 292 TRP 0.020 0.002 TRP R 116 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8058) covalent geometry : angle 0.83182 (10965) SS BOND : bond 0.00416 ( 3) SS BOND : angle 2.56534 ( 6) hydrogen bonds : bond 0.04220 ( 389) hydrogen bonds : angle 4.52740 ( 1125) Misc. bond : bond 0.00199 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7674 (mtp-110) REVERT: A 82 TRP cc_start: 0.8847 (m100) cc_final: 0.8444 (m100) REVERT: A 188 MET cc_start: 0.8757 (mtp) cc_final: 0.8503 (mtp) REVERT: A 226 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7451 (pt0) REVERT: B 35 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7781 (mtm180) REVERT: B 196 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 242 GLU cc_start: 0.8750 (tt0) cc_final: 0.8532 (tt0) REVERT: D 29 LYS cc_start: 0.8503 (tppt) cc_final: 0.8234 (tppt) REVERT: D 47 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8671 (mp0) REVERT: N 1 GLN cc_start: 0.8523 (mt0) cc_final: 0.8056 (pm20) REVERT: N 53 GLN cc_start: 0.8736 (mt0) cc_final: 0.8517 (mt0) REVERT: N 69 THR cc_start: 0.8825 (m) cc_final: 0.8599 (p) REVERT: N 73 ASP cc_start: 0.7834 (t0) cc_final: 0.7525 (t0) REVERT: N 87 LYS cc_start: 0.8983 (mttt) cc_final: 0.8428 (mttp) REVERT: N 90 ASP cc_start: 0.8275 (m-30) cc_final: 0.7798 (m-30) REVERT: N 114 THR cc_start: 0.9277 (p) cc_final: 0.9019 (t) REVERT: R 102 LEU cc_start: 0.9187 (mt) cc_final: 0.8926 (mt) REVERT: R 179 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9008 (tt) REVERT: R 188 MET cc_start: 0.6240 (tmm) cc_final: 0.5819 (tmm) REVERT: R 218 THR cc_start: 0.8932 (m) cc_final: 0.8617 (p) REVERT: R 278 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8777 (mm-40) REVERT: R 297 ASN cc_start: 0.6993 (t0) cc_final: 0.6730 (t0) REVERT: R 307 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6428 (t0) REVERT: R 322 TYR cc_start: 0.7298 (t80) cc_final: 0.7066 (t80) outliers start: 39 outliers final: 21 residues processed: 230 average time/residue: 0.0759 time to fit residues: 23.5815 Evaluate side-chains 205 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 163 LYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 160 GLN R 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099822 restraints weight = 15525.333| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.81 r_work: 0.3314 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8063 Z= 0.127 Angle : 0.786 30.835 10971 Z= 0.349 Chirality : 0.065 1.737 1267 Planarity : 0.004 0.040 1386 Dihedral : 12.745 177.966 1270 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 3.82 % Allowed : 16.65 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.93 (0.27), residues: 1001 helix: 2.46 (0.27), residues: 365 sheet: 0.13 (0.35), residues: 215 loop : -0.78 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.013 0.001 TYR R 305 PHE 0.012 0.001 PHE A 292 TRP 0.026 0.002 TRP A 339 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8058) covalent geometry : angle 0.78457 (10965) SS BOND : bond 0.00449 ( 3) SS BOND : angle 2.11781 ( 6) hydrogen bonds : bond 0.03647 ( 389) hydrogen bonds : angle 4.31527 ( 1125) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7732 (mtp-110) REVERT: A 57 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8152 (ptpp) REVERT: A 226 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7573 (pt0) REVERT: A 301 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9103 (mmmm) REVERT: B 35 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7608 (mtm180) REVERT: B 170 TYR cc_start: 0.8587 (t80) cc_final: 0.8381 (t80) REVERT: B 196 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 47 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8664 (mp0) REVERT: N 1 GLN cc_start: 0.8497 (mt0) cc_final: 0.8044 (pm20) REVERT: N 53 GLN cc_start: 0.8685 (mt0) cc_final: 0.8470 (mt0) REVERT: N 70 ILE cc_start: 0.8406 (tt) cc_final: 0.8146 (tp) REVERT: N 73 ASP cc_start: 0.7880 (t0) cc_final: 0.7536 (t0) REVERT: N 87 LYS cc_start: 0.9067 (mttt) cc_final: 0.8761 (mttt) REVERT: N 90 ASP cc_start: 0.8245 (m-30) cc_final: 0.7884 (m-30) REVERT: N 94 TYR cc_start: 0.8831 (m-80) cc_final: 0.8540 (m-80) REVERT: R 86 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5940 (mtp) REVERT: R 188 MET cc_start: 0.6569 (tmm) cc_final: 0.6359 (tmm) REVERT: R 218 THR cc_start: 0.8768 (m) cc_final: 0.8565 (p) REVERT: R 297 ASN cc_start: 0.6809 (t0) cc_final: 0.6563 (t0) outliers start: 31 outliers final: 20 residues processed: 219 average time/residue: 0.0842 time to fit residues: 24.6568 Evaluate side-chains 198 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 87 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100608 restraints weight = 16209.228| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.79 r_work: 0.3283 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8063 Z= 0.147 Angle : 0.789 30.749 10971 Z= 0.351 Chirality : 0.065 1.738 1267 Planarity : 0.004 0.035 1386 Dihedral : 12.635 177.682 1265 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 4.44 % Allowed : 17.88 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.99 (0.27), residues: 1001 helix: 2.47 (0.28), residues: 360 sheet: 0.11 (0.34), residues: 225 loop : -0.66 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 129 TYR 0.011 0.001 TYR R 305 PHE 0.013 0.001 PHE R 271 TRP 0.016 0.001 TRP R 116 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8058) covalent geometry : angle 0.78726 (10965) SS BOND : bond 0.00398 ( 3) SS BOND : angle 2.27779 ( 6) hydrogen bonds : bond 0.03594 ( 389) hydrogen bonds : angle 4.26800 ( 1125) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8766 (mt0) cc_final: 0.8400 (mp10) REVERT: A 46 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7755 (mtp-110) REVERT: A 57 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8142 (ptpp) REVERT: A 215 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8972 (tt0) REVERT: A 226 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7647 (pt0) REVERT: A 262 MET cc_start: 0.8138 (ttm) cc_final: 0.7851 (ttm) REVERT: B 35 ARG cc_start: 0.8373 (ttm110) cc_final: 0.7703 (mtm180) REVERT: D 47 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8695 (mp0) REVERT: N 1 GLN cc_start: 0.8518 (mt0) cc_final: 0.8077 (pm20) REVERT: N 53 GLN cc_start: 0.8648 (mt0) cc_final: 0.8439 (mt0) REVERT: N 70 ILE cc_start: 0.8538 (tt) cc_final: 0.8163 (tp) REVERT: N 82 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7558 (tp-100) REVERT: N 87 LYS cc_start: 0.9078 (mttt) cc_final: 0.8790 (mttt) REVERT: N 90 ASP cc_start: 0.8321 (m-30) cc_final: 0.7953 (m-30) REVERT: R 86 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6039 (mtp) REVERT: R 297 ASN cc_start: 0.7031 (t0) cc_final: 0.6761 (t0) outliers start: 36 outliers final: 24 residues processed: 212 average time/residue: 0.0714 time to fit residues: 20.7696 Evaluate side-chains 201 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.129869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102161 restraints weight = 16028.986| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.87 r_work: 0.3331 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8063 Z= 0.119 Angle : 0.771 30.825 10971 Z= 0.342 Chirality : 0.064 1.736 1267 Planarity : 0.004 0.038 1386 Dihedral : 12.570 178.224 1265 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 4.07 % Allowed : 18.99 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.27), residues: 1001 helix: 2.55 (0.28), residues: 359 sheet: 0.19 (0.34), residues: 219 loop : -0.64 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 129 TYR 0.017 0.001 TYR R 111 PHE 0.012 0.001 PHE A 292 TRP 0.016 0.001 TRP R 116 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8058) covalent geometry : angle 0.77021 (10965) SS BOND : bond 0.00437 ( 3) SS BOND : angle 1.89435 ( 6) hydrogen bonds : bond 0.03387 ( 389) hydrogen bonds : angle 4.20041 ( 1125) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8785 (mt0) cc_final: 0.8409 (mp10) REVERT: A 46 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7713 (mtp-110) REVERT: A 57 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8159 (ptpp) REVERT: A 215 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8972 (tt0) REVERT: A 226 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7672 (pt0) REVERT: A 243 THR cc_start: 0.8638 (m) cc_final: 0.8412 (p) REVERT: A 301 LYS cc_start: 0.9337 (mmmm) cc_final: 0.8851 (mmtp) REVERT: B 35 ARG cc_start: 0.8315 (ttm110) cc_final: 0.7607 (mtm180) REVERT: D 29 LYS cc_start: 0.8157 (tppt) cc_final: 0.7915 (tppt) REVERT: D 47 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8647 (mp0) REVERT: N 1 GLN cc_start: 0.8522 (mt0) cc_final: 0.8119 (pm20) REVERT: N 60 TYR cc_start: 0.8030 (m-80) cc_final: 0.7826 (m-80) REVERT: N 87 LYS cc_start: 0.9083 (mttt) cc_final: 0.8859 (mttt) REVERT: R 86 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.6032 (mtp) REVERT: R 297 ASN cc_start: 0.6857 (t0) cc_final: 0.6580 (t0) outliers start: 33 outliers final: 23 residues processed: 213 average time/residue: 0.0695 time to fit residues: 20.1958 Evaluate side-chains 211 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 73 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101088 restraints weight = 16003.755| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.74 r_work: 0.3292 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8063 Z= 0.136 Angle : 0.781 30.852 10971 Z= 0.348 Chirality : 0.065 1.733 1267 Planarity : 0.004 0.040 1386 Dihedral : 12.570 178.344 1265 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 4.44 % Allowed : 19.85 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.97 (0.28), residues: 1001 helix: 2.44 (0.27), residues: 366 sheet: 0.11 (0.34), residues: 225 loop : -0.70 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 129 TYR 0.011 0.001 TYR N 95 PHE 0.012 0.001 PHE R 271 TRP 0.014 0.001 TRP R 116 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8058) covalent geometry : angle 0.78038 (10965) SS BOND : bond 0.00283 ( 3) SS BOND : angle 1.60918 ( 6) hydrogen bonds : bond 0.03461 ( 389) hydrogen bonds : angle 4.18794 ( 1125) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7611 (mt0) cc_final: 0.7034 (mt0) REVERT: A 35 ASN cc_start: 0.8319 (m-40) cc_final: 0.7956 (m110) REVERT: A 44 GLN cc_start: 0.8751 (mt0) cc_final: 0.8341 (mp10) REVERT: A 46 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7652 (ttm-80) REVERT: A 57 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8239 (ptpp) REVERT: A 215 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8988 (tt0) REVERT: A 226 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7653 (pt0) REVERT: A 243 THR cc_start: 0.8659 (m) cc_final: 0.8432 (p) REVERT: A 262 MET cc_start: 0.8059 (ttm) cc_final: 0.7826 (ttm) REVERT: A 301 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9056 (mmtp) REVERT: B 35 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7696 (mtm180) REVERT: D 29 LYS cc_start: 0.8167 (tppt) cc_final: 0.7941 (tppt) REVERT: N 1 GLN cc_start: 0.8528 (mt0) cc_final: 0.8136 (pm20) REVERT: N 32 TYR cc_start: 0.8667 (m-80) cc_final: 0.8263 (m-80) REVERT: N 46 GLU cc_start: 0.8681 (pm20) cc_final: 0.8467 (pm20) REVERT: N 87 LYS cc_start: 0.8937 (mttt) cc_final: 0.8573 (mttp) REVERT: R 242 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7761 (mm-40) REVERT: R 297 ASN cc_start: 0.7050 (t0) cc_final: 0.6773 (t0) REVERT: R 307 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6642 (t0) outliers start: 36 outliers final: 26 residues processed: 211 average time/residue: 0.0719 time to fit residues: 20.3221 Evaluate side-chains 212 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099444 restraints weight = 16110.133| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.69 r_work: 0.3268 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8063 Z= 0.162 Angle : 0.804 30.996 10971 Z= 0.358 Chirality : 0.065 1.721 1267 Planarity : 0.005 0.098 1386 Dihedral : 12.607 178.158 1265 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 5.06 % Allowed : 20.10 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.89 (0.28), residues: 1001 helix: 2.33 (0.28), residues: 372 sheet: 0.03 (0.34), residues: 225 loop : -0.71 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 129 TYR 0.012 0.001 TYR R 305 PHE 0.014 0.001 PHE R 271 TRP 0.019 0.002 TRP R 116 HIS 0.003 0.001 HIS R 117 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8058) covalent geometry : angle 0.80331 (10965) SS BOND : bond 0.00299 ( 3) SS BOND : angle 1.85116 ( 6) hydrogen bonds : bond 0.03541 ( 389) hydrogen bonds : angle 4.23265 ( 1125) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7638 (mt0) cc_final: 0.7090 (mt0) REVERT: A 35 ASN cc_start: 0.8329 (m-40) cc_final: 0.7950 (m110) REVERT: A 44 GLN cc_start: 0.8738 (mt0) cc_final: 0.8363 (mp10) REVERT: A 46 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7703 (ttm-80) REVERT: A 57 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8205 (ptpp) REVERT: A 82 TRP cc_start: 0.8842 (m100) cc_final: 0.8426 (m100) REVERT: A 215 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9002 (tt0) REVERT: A 226 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7662 (pt0) REVERT: A 243 THR cc_start: 0.8660 (m) cc_final: 0.8438 (p) REVERT: A 301 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9103 (mmmm) REVERT: B 35 ARG cc_start: 0.8418 (ttm110) cc_final: 0.7729 (mtm180) REVERT: D 29 LYS cc_start: 0.8170 (tppt) cc_final: 0.7952 (tppt) REVERT: N 1 GLN cc_start: 0.8546 (mt0) cc_final: 0.8176 (pm20) REVERT: N 32 TYR cc_start: 0.8698 (m-80) cc_final: 0.8263 (m-80) REVERT: N 46 GLU cc_start: 0.8670 (pm20) cc_final: 0.8401 (pm20) REVERT: N 114 THR cc_start: 0.9373 (p) cc_final: 0.9083 (t) REVERT: R 121 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7342 (p) REVERT: R 203 TRP cc_start: 0.6069 (p-90) cc_final: 0.5708 (p-90) REVERT: R 242 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7699 (mm-40) REVERT: R 297 ASN cc_start: 0.7158 (t0) cc_final: 0.6877 (t0) REVERT: R 307 ASN cc_start: 0.7089 (OUTLIER) cc_final: 0.6862 (t0) outliers start: 41 outliers final: 32 residues processed: 213 average time/residue: 0.0650 time to fit residues: 18.8708 Evaluate side-chains 217 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 304 THR Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.128123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100349 restraints weight = 16184.165| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.72 r_work: 0.3281 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8063 Z= 0.140 Angle : 0.816 30.959 10971 Z= 0.360 Chirality : 0.065 1.724 1267 Planarity : 0.004 0.054 1386 Dihedral : 12.591 178.451 1265 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 4.19 % Allowed : 21.09 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.28), residues: 1001 helix: 2.34 (0.28), residues: 371 sheet: 0.02 (0.34), residues: 225 loop : -0.67 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 129 TYR 0.010 0.001 TYR N 95 PHE 0.013 0.001 PHE R 271 TRP 0.017 0.001 TRP R 116 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8058) covalent geometry : angle 0.81508 (10965) SS BOND : bond 0.00257 ( 3) SS BOND : angle 1.52212 ( 6) hydrogen bonds : bond 0.03496 ( 389) hydrogen bonds : angle 4.21912 ( 1125) Misc. bond : bond 0.00198 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7645 (mt0) cc_final: 0.7152 (mt0) REVERT: A 35 ASN cc_start: 0.8355 (m-40) cc_final: 0.7979 (m110) REVERT: A 44 GLN cc_start: 0.8728 (mt0) cc_final: 0.8407 (mp10) REVERT: A 46 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7684 (ttm-80) REVERT: A 57 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8243 (ptpp) REVERT: A 215 GLU cc_start: 0.9235 (mm-30) cc_final: 0.9013 (tt0) REVERT: A 226 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7673 (pt0) REVERT: A 243 THR cc_start: 0.8629 (m) cc_final: 0.8408 (p) REVERT: A 301 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9099 (mmmm) REVERT: B 35 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7662 (mtm180) REVERT: D 29 LYS cc_start: 0.8191 (tppt) cc_final: 0.7990 (tppt) REVERT: D 47 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8630 (mp0) REVERT: N 32 TYR cc_start: 0.8655 (m-80) cc_final: 0.8294 (m-80) REVERT: N 46 GLU cc_start: 0.8692 (pm20) cc_final: 0.8423 (pm20) REVERT: N 76 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8996 (mtmm) REVERT: N 114 THR cc_start: 0.9359 (p) cc_final: 0.9086 (t) REVERT: R 121 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7389 (p) REVERT: R 188 MET cc_start: 0.7071 (tmm) cc_final: 0.6708 (tmm) REVERT: R 203 TRP cc_start: 0.5910 (p-90) cc_final: 0.5585 (p-90) REVERT: R 242 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7774 (mm-40) REVERT: R 297 ASN cc_start: 0.7118 (t0) cc_final: 0.6849 (t0) outliers start: 34 outliers final: 29 residues processed: 209 average time/residue: 0.0793 time to fit residues: 22.5309 Evaluate side-chains 212 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 304 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100866 restraints weight = 16012.696| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.75 r_work: 0.3288 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8063 Z= 0.133 Angle : 0.818 30.941 10971 Z= 0.360 Chirality : 0.065 1.727 1267 Planarity : 0.004 0.052 1386 Dihedral : 12.566 178.522 1264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 3.82 % Allowed : 21.58 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.92 (0.28), residues: 1001 helix: 2.34 (0.28), residues: 371 sheet: 0.04 (0.34), residues: 225 loop : -0.67 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 129 TYR 0.012 0.001 TYR N 80 PHE 0.010 0.001 PHE R 271 TRP 0.019 0.001 TRP R 116 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8058) covalent geometry : angle 0.81753 (10965) SS BOND : bond 0.00240 ( 3) SS BOND : angle 1.38893 ( 6) hydrogen bonds : bond 0.03372 ( 389) hydrogen bonds : angle 4.15745 ( 1125) Misc. bond : bond 0.00155 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7620 (mt0) cc_final: 0.7303 (mt0) REVERT: A 35 ASN cc_start: 0.8373 (m-40) cc_final: 0.8133 (m-40) REVERT: A 44 GLN cc_start: 0.8736 (mt0) cc_final: 0.8405 (mp10) REVERT: A 46 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7683 (ttm-80) REVERT: A 57 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8183 (ptpp) REVERT: A 215 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9001 (tt0) REVERT: A 226 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7683 (pt0) REVERT: A 243 THR cc_start: 0.8603 (m) cc_final: 0.8397 (p) REVERT: A 301 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9181 (mmmm) REVERT: B 35 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7636 (mtm180) REVERT: D 47 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8620 (mp0) REVERT: N 32 TYR cc_start: 0.8626 (m-80) cc_final: 0.8299 (m-80) REVERT: N 46 GLU cc_start: 0.8692 (pm20) cc_final: 0.8405 (pm20) REVERT: N 76 LYS cc_start: 0.9252 (mtmm) cc_final: 0.9005 (mtmm) REVERT: N 114 THR cc_start: 0.9362 (p) cc_final: 0.9096 (t) REVERT: R 121 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7337 (p) REVERT: R 203 TRP cc_start: 0.5843 (p-90) cc_final: 0.5560 (p-90) REVERT: R 242 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7751 (mm-40) REVERT: R 297 ASN cc_start: 0.7114 (t0) cc_final: 0.6884 (t0) outliers start: 31 outliers final: 29 residues processed: 206 average time/residue: 0.0703 time to fit residues: 19.5966 Evaluate side-chains 215 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102820 restraints weight = 16072.711| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.78 r_work: 0.3341 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8063 Z= 0.117 Angle : 0.819 30.825 10971 Z= 0.358 Chirality : 0.064 1.739 1267 Planarity : 0.004 0.057 1386 Dihedral : 12.539 178.775 1264 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 3.08 % Allowed : 23.06 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.98 (0.28), residues: 1001 helix: 2.35 (0.28), residues: 371 sheet: 0.17 (0.35), residues: 219 loop : -0.65 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 129 TYR 0.011 0.001 TYR N 80 PHE 0.009 0.001 PHE N 29 TRP 0.018 0.001 TRP R 116 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8058) covalent geometry : angle 0.81844 (10965) SS BOND : bond 0.00310 ( 3) SS BOND : angle 1.33053 ( 6) hydrogen bonds : bond 0.03183 ( 389) hydrogen bonds : angle 4.10310 ( 1125) Misc. bond : bond 0.00108 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7621 (mt0) cc_final: 0.7097 (mt0) REVERT: A 35 ASN cc_start: 0.8375 (m-40) cc_final: 0.8016 (m110) REVERT: A 44 GLN cc_start: 0.8724 (mt0) cc_final: 0.8506 (mp10) REVERT: A 46 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7756 (mtp-110) REVERT: A 57 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8235 (ptpp) REVERT: A 215 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8985 (tt0) REVERT: A 226 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7626 (pt0) REVERT: A 301 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9093 (mmmm) REVERT: B 35 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7619 (mtm180) REVERT: B 75 GLN cc_start: 0.9005 (tt0) cc_final: 0.8714 (tm-30) REVERT: D 47 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8620 (mp0) REVERT: N 32 TYR cc_start: 0.8563 (m-80) cc_final: 0.8153 (m-80) REVERT: N 46 GLU cc_start: 0.8685 (pm20) cc_final: 0.8384 (pm20) REVERT: N 76 LYS cc_start: 0.9268 (mtmm) cc_final: 0.9042 (mtmm) REVERT: N 114 THR cc_start: 0.9331 (p) cc_final: 0.9085 (t) REVERT: R 203 TRP cc_start: 0.5714 (p-90) cc_final: 0.5434 (p-90) REVERT: R 242 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7777 (mm-40) REVERT: R 297 ASN cc_start: 0.7066 (t0) cc_final: 0.6841 (t0) outliers start: 25 outliers final: 24 residues processed: 204 average time/residue: 0.0693 time to fit residues: 19.3221 Evaluate side-chains 207 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 270 CYS Chi-restraints excluded: chain R residue 275 TRP Chi-restraints excluded: chain R residue 304 THR Chi-restraints excluded: chain C residue 3 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.100491 restraints weight = 16004.101| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.75 r_work: 0.3282 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8063 Z= 0.146 Angle : 0.840 30.980 10971 Z= 0.371 Chirality : 0.065 1.724 1267 Planarity : 0.004 0.058 1386 Dihedral : 12.599 178.744 1264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 3.58 % Allowed : 23.30 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.93 (0.28), residues: 1001 helix: 2.27 (0.28), residues: 372 sheet: 0.12 (0.34), residues: 230 loop : -0.64 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 129 TYR 0.015 0.001 TYR R 111 PHE 0.011 0.001 PHE R 271 TRP 0.018 0.002 TRP R 116 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8058) covalent geometry : angle 0.84002 (10965) SS BOND : bond 0.00195 ( 3) SS BOND : angle 1.42801 ( 6) hydrogen bonds : bond 0.03364 ( 389) hydrogen bonds : angle 4.15724 ( 1125) Misc. bond : bond 0.00124 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.30 seconds wall clock time: 31 minutes 11.85 seconds (1871.85 seconds total)