Starting phenix.real_space_refine on Sat Dec 28 05:55:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyw_35831/12_2024/8iyw_35831.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 C 4980 2.51 5 N 1381 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7849 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1475 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2393 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 119 Chain: "G" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 379 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1655 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 1930 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 12, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 263 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.68 Number of scatterers: 7849 At special positions: 0 Unit cell: (87.8, 116.335, 132.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 43 16.00 O 1444 8.00 N 1381 7.00 C 4980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 208 through 213 removed outlier: 4.074A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 removed outlier: 4.376A pdb=" N ASP B 218 " --> pdb=" O CYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.605A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.463A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.569A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.144A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.931A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'R' and resid 24 through 55 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 89 Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.690A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.092A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.624A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 262 removed outlier: 4.797A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 238 " --> pdb=" O MET R 234 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.619A pdb=" N GLY R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 268 removed outlier: 3.806A pdb=" N VAL R 268 " --> pdb=" O ASN R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.787A pdb=" N SER R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 290 Processing helix chain 'R' and resid 290 through 295 removed outlier: 4.099A pdb=" N TYR R 294 " --> pdb=" O ASP R 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.314A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.776A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.749A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.957A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.737A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.654A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.316A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.992A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 5.862A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 170 424 hydrogen bonds defined for protein. 1182 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: 2.50 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1407 1.33 - 1.45: 2209 1.45 - 1.58: 4347 1.58 - 1.71: 0 1.71 - 1.83: 55 Bond restraints: 8018 Sorted by residual: bond pdb=" C PHE R 282 " pdb=" N THR R 283 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.38e-02 5.25e+03 7.15e+01 bond pdb=" C VAL R 88 " pdb=" N ARG R 89 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.52e-02 4.33e+03 2.02e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.07e+01 bond pdb=" N ILE R 212 " pdb=" CA ILE R 212 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 7.98e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.35e-02 5.49e+03 7.75e+00 ... (remaining 8013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10465 1.74 - 3.48: 385 3.48 - 5.22: 70 5.22 - 6.96: 21 6.96 - 8.69: 13 Bond angle restraints: 10954 Sorted by residual: angle pdb=" CA CYS R 177 " pdb=" C CYS R 177 " pdb=" O CYS R 177 " ideal model delta sigma weight residual 120.40 113.07 7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N TYR R 284 " pdb=" CA TYR R 284 " pdb=" C TYR R 284 " ideal model delta sigma weight residual 111.36 104.59 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 111.14 104.57 6.57 1.08e+00 8.57e-01 3.70e+01 angle pdb=" C PHE R 282 " pdb=" N THR R 283 " pdb=" CA THR R 283 " ideal model delta sigma weight residual 120.31 111.62 8.69 1.52e+00 4.33e-01 3.27e+01 angle pdb=" C ILE R 116 " pdb=" N PHE R 117 " pdb=" CA PHE R 117 " ideal model delta sigma weight residual 120.65 113.16 7.49 1.32e+00 5.74e-01 3.22e+01 ... (remaining 10949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4453 23.42 - 46.83: 176 46.83 - 70.25: 18 70.25 - 93.67: 4 93.67 - 117.08: 1 Dihedral angle restraints: 4652 sinusoidal: 1421 harmonic: 3231 Sorted by residual: dihedral pdb=" CA GLN H 82 " pdb=" C GLN H 82 " pdb=" N MET H 83 " pdb=" CA MET H 83 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA B 7 " pdb=" C ALA B 7 " pdb=" N GLU B 8 " pdb=" CA GLU B 8 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C03 OKL R 401 " pdb=" C04 OKL R 401 " pdb=" C05 OKL R 401 " pdb=" N06 OKL R 401 " ideal model delta sinusoidal sigma weight residual 183.45 66.37 117.08 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 962 0.050 - 0.100: 245 0.100 - 0.150: 66 0.150 - 0.200: 4 0.200 - 0.250: 4 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA HIS B 196 " pdb=" N HIS B 196 " pdb=" C HIS B 196 " pdb=" CB HIS B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PHE R 105 " pdb=" N PHE R 105 " pdb=" C PHE R 105 " pdb=" CB PHE R 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA HIS R 161 " pdb=" N HIS R 161 " pdb=" C HIS R 161 " pdb=" CB HIS R 161 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1278 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 401 " -0.012 2.00e-02 2.50e+03 4.04e-02 5.30e+01 pdb=" C07 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 401 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 401 " 0.041 2.00e-02 2.50e+03 pdb=" C13 OKL R 401 " 0.053 2.00e-02 2.50e+03 pdb=" C15 OKL R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N06 OKL R 401 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 401 " 0.054 2.00e-02 2.50e+03 pdb=" N16 OKL R 401 " 0.024 2.00e-02 2.50e+03 pdb=" O08 OKL R 401 " -0.041 2.00e-02 2.50e+03 pdb=" O11 OKL R 401 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 401 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 177 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C CYS R 177 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS R 177 " -0.025 2.00e-02 2.50e+03 pdb=" N SER R 178 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 210 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C LYS B 210 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 210 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS B 211 " -0.017 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1783 2.78 - 3.31: 7637 3.31 - 3.84: 12456 3.84 - 4.37: 14149 4.37 - 4.90: 25163 Nonbonded interactions: 61188 Sorted by model distance: nonbonded pdb=" O LYS B 193 " pdb=" ND2 ASN B 194 " model vdw 2.252 3.120 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.260 3.040 nonbonded pdb=" O ARG R 228 " pdb=" OG1 THR R 231 " model vdw 2.278 3.040 nonbonded pdb=" NE ARG H 98 " pdb=" OD1 ASP H 109 " model vdw 2.295 3.120 nonbonded pdb=" O ASN R 17 " pdb=" ND2 ASN R 17 " model vdw 2.298 3.120 ... (remaining 61183 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.005 0.117 8018 Z= 0.311 Angle : 0.837 8.695 10954 Z= 0.518 Chirality : 0.049 0.250 1281 Planarity : 0.005 0.047 1415 Dihedral : 12.733 117.085 2547 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.45 % Allowed : 11.76 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1100 helix: 0.47 (0.27), residues: 353 sheet: 0.06 (0.32), residues: 250 loop : -0.09 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 152 HIS 0.006 0.001 HIS H 35 PHE 0.017 0.002 PHE C 199 TYR 0.025 0.002 TYR R 284 ARG 0.003 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.971 Fit side-chains REVERT: H 68 PHE cc_start: 0.7828 (m-10) cc_final: 0.7427 (m-10) REVERT: R 216 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7067 (mtt-85) outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 0.2096 time to fit residues: 38.7254 Evaluate side-chains 119 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain R residue 17 ASN Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN H 113 GLN R 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8018 Z= 0.190 Angle : 0.576 6.598 10954 Z= 0.313 Chirality : 0.044 0.148 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.916 146.988 1192 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 12.92 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1100 helix: 1.59 (0.28), residues: 360 sheet: 0.05 (0.31), residues: 249 loop : -0.05 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE C 199 TYR 0.020 0.001 TYR R 269 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: G 44 HIS cc_start: 0.8181 (m-70) cc_final: 0.7829 (m-70) REVERT: G 48 ASP cc_start: 0.7789 (t0) cc_final: 0.7345 (t0) REVERT: R 198 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: R 213 TRP cc_start: 0.8188 (t60) cc_final: 0.7917 (t60) REVERT: R 216 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7037 (mtt-85) REVERT: R 284 TYR cc_start: 0.7981 (m-80) cc_final: 0.7565 (m-80) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.1851 time to fit residues: 34.7042 Evaluate side-chains 127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8018 Z= 0.221 Angle : 0.551 6.408 10954 Z= 0.297 Chirality : 0.043 0.156 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.547 138.918 1186 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.48 % Allowed : 13.06 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1100 helix: 1.88 (0.28), residues: 369 sheet: -0.09 (0.30), residues: 253 loop : -0.10 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.002 PHE C 199 TYR 0.018 0.002 TYR B 297 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: B 252 ASP cc_start: 0.8506 (t0) cc_final: 0.8271 (t0) REVERT: B 290 GLU cc_start: 0.8191 (pm20) cc_final: 0.7824 (pm20) REVERT: C 98 SER cc_start: 0.8278 (m) cc_final: 0.7888 (t) REVERT: G 44 HIS cc_start: 0.8110 (m-70) cc_final: 0.7809 (m-70) REVERT: G 48 ASP cc_start: 0.8042 (t0) cc_final: 0.7429 (t0) REVERT: R 198 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: R 216 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6933 (mtt-85) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 0.1725 time to fit residues: 31.8677 Evaluate side-chains 129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 269 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0270 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8018 Z= 0.173 Angle : 0.509 6.398 10954 Z= 0.274 Chirality : 0.042 0.160 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.337 140.975 1186 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.92 % Allowed : 13.35 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1100 helix: 2.24 (0.28), residues: 369 sheet: -0.23 (0.30), residues: 259 loop : -0.06 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.002 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: C 98 SER cc_start: 0.8252 (m) cc_final: 0.7834 (t) REVERT: G 44 HIS cc_start: 0.8040 (m-70) cc_final: 0.7766 (m-70) REVERT: G 48 ASP cc_start: 0.8118 (t0) cc_final: 0.7507 (t0) REVERT: R 111 ARG cc_start: 0.5767 (mtm-85) cc_final: 0.5312 (mtm-85) REVERT: R 154 ILE cc_start: 0.8697 (mm) cc_final: 0.8493 (mt) REVERT: R 198 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: R 216 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6947 (mtt-85) outliers start: 27 outliers final: 19 residues processed: 135 average time/residue: 0.1921 time to fit residues: 35.8544 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8018 Z= 0.191 Angle : 0.521 8.619 10954 Z= 0.276 Chirality : 0.042 0.171 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.276 140.655 1186 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.92 % Allowed : 14.22 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1100 helix: 2.39 (0.28), residues: 369 sheet: -0.31 (0.30), residues: 257 loop : -0.06 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.006 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8235 (pm20) cc_final: 0.7848 (pm20) REVERT: C 98 SER cc_start: 0.8288 (m) cc_final: 0.7804 (t) REVERT: G 44 HIS cc_start: 0.8050 (m-70) cc_final: 0.7786 (m-70) REVERT: G 48 ASP cc_start: 0.8198 (t0) cc_final: 0.7566 (t0) REVERT: H 231 GLN cc_start: 0.8433 (pp30) cc_final: 0.8210 (pp30) REVERT: R 111 ARG cc_start: 0.5784 (mtm-85) cc_final: 0.5319 (mtm-85) REVERT: R 198 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: R 216 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6918 (mtt-85) outliers start: 27 outliers final: 22 residues processed: 134 average time/residue: 0.1848 time to fit residues: 34.8438 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8018 Z= 0.224 Angle : 0.530 6.904 10954 Z= 0.283 Chirality : 0.042 0.163 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.409 143.768 1186 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.92 % Allowed : 15.67 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1100 helix: 2.46 (0.28), residues: 369 sheet: -0.41 (0.30), residues: 257 loop : -0.14 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.016 0.001 PHE C 199 TYR 0.020 0.001 TYR B 297 ARG 0.005 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: B 270 ASN cc_start: 0.8568 (m-40) cc_final: 0.8360 (m-40) REVERT: C 98 SER cc_start: 0.8346 (m) cc_final: 0.7810 (t) REVERT: G 44 HIS cc_start: 0.8122 (m-70) cc_final: 0.7844 (m-70) REVERT: G 48 ASP cc_start: 0.8279 (t0) cc_final: 0.7629 (t0) REVERT: H 106 SER cc_start: 0.9188 (t) cc_final: 0.8698 (p) REVERT: H 231 GLN cc_start: 0.8489 (pp30) cc_final: 0.8216 (pp30) REVERT: R 111 ARG cc_start: 0.5844 (mtm-85) cc_final: 0.5389 (mtm-85) REVERT: R 198 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: R 216 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6928 (mtt-85) outliers start: 27 outliers final: 21 residues processed: 133 average time/residue: 0.1893 time to fit residues: 34.7625 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8018 Z= 0.349 Angle : 0.588 8.976 10954 Z= 0.316 Chirality : 0.044 0.158 1281 Planarity : 0.004 0.040 1415 Dihedral : 6.614 143.529 1186 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.92 % Allowed : 15.82 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1100 helix: 2.34 (0.28), residues: 370 sheet: -0.76 (0.30), residues: 264 loop : -0.18 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 PHE 0.023 0.002 PHE C 199 TYR 0.020 0.002 TYR B 297 ARG 0.006 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8481 (pm20) cc_final: 0.8103 (pm20) REVERT: G 44 HIS cc_start: 0.8196 (m-70) cc_final: 0.7866 (m-70) REVERT: G 48 ASP cc_start: 0.8267 (t0) cc_final: 0.7551 (t0) REVERT: H 231 GLN cc_start: 0.8535 (pp30) cc_final: 0.8200 (pp30) REVERT: R 111 ARG cc_start: 0.5836 (mtm-85) cc_final: 0.5393 (mtm-85) REVERT: R 198 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: R 216 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6993 (mtt-85) outliers start: 27 outliers final: 23 residues processed: 131 average time/residue: 0.1827 time to fit residues: 33.3442 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8018 Z= 0.205 Angle : 0.540 9.125 10954 Z= 0.287 Chirality : 0.042 0.156 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.458 145.101 1186 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.77 % Allowed : 16.84 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1100 helix: 2.50 (0.28), residues: 369 sheet: -0.70 (0.31), residues: 258 loop : -0.22 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (tt) REVERT: B 270 ASN cc_start: 0.8558 (m-40) cc_final: 0.8344 (m-40) REVERT: B 290 GLU cc_start: 0.8513 (pm20) cc_final: 0.8152 (pm20) REVERT: B 331 ASN cc_start: 0.7945 (m-40) cc_final: 0.7698 (p0) REVERT: C 339 TRP cc_start: 0.7878 (m-10) cc_final: 0.7504 (m-10) REVERT: G 44 HIS cc_start: 0.8145 (m-70) cc_final: 0.7839 (m-70) REVERT: G 48 ASP cc_start: 0.8244 (t0) cc_final: 0.7554 (t0) REVERT: H 106 SER cc_start: 0.9155 (t) cc_final: 0.8857 (t) REVERT: H 230 MET cc_start: 0.7799 (ttt) cc_final: 0.7515 (ttt) REVERT: H 231 GLN cc_start: 0.8431 (pp30) cc_final: 0.8118 (pp30) REVERT: R 111 ARG cc_start: 0.5944 (mtm-85) cc_final: 0.5516 (mtm-85) REVERT: R 216 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6921 (mtt-85) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.1939 time to fit residues: 34.9512 Evaluate side-chains 128 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8018 Z= 0.197 Angle : 0.538 9.404 10954 Z= 0.285 Chirality : 0.042 0.155 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.403 145.286 1186 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.19 % Allowed : 17.56 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1100 helix: 2.59 (0.28), residues: 369 sheet: -0.72 (0.30), residues: 258 loop : -0.18 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE C 199 TYR 0.021 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 270 ASN cc_start: 0.8553 (m-40) cc_final: 0.8329 (m-40) REVERT: C 339 TRP cc_start: 0.7885 (m-10) cc_final: 0.7521 (m-10) REVERT: G 44 HIS cc_start: 0.8120 (m-70) cc_final: 0.7841 (m-70) REVERT: G 48 ASP cc_start: 0.8233 (t0) cc_final: 0.7571 (t0) REVERT: H 106 SER cc_start: 0.9171 (t) cc_final: 0.8875 (t) REVERT: H 230 MET cc_start: 0.7724 (ttt) cc_final: 0.7450 (ttt) REVERT: H 231 GLN cc_start: 0.8410 (pp30) cc_final: 0.8103 (pp30) REVERT: R 111 ARG cc_start: 0.5964 (mtm-85) cc_final: 0.5509 (mtm-85) REVERT: R 216 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6883 (mtt-85) outliers start: 22 outliers final: 20 residues processed: 128 average time/residue: 0.1786 time to fit residues: 32.0692 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8018 Z= 0.248 Angle : 0.566 9.480 10954 Z= 0.301 Chirality : 0.043 0.155 1281 Planarity : 0.004 0.040 1415 Dihedral : 6.432 145.001 1186 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.34 % Allowed : 17.56 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1100 helix: 2.52 (0.28), residues: 369 sheet: -0.80 (0.30), residues: 258 loop : -0.22 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE C 199 TYR 0.020 0.002 TYR B 297 ARG 0.007 0.000 ARG R 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8161 (tt) REVERT: B 270 ASN cc_start: 0.8563 (m-40) cc_final: 0.8350 (m-40) REVERT: B 290 GLU cc_start: 0.8596 (pm20) cc_final: 0.8322 (pm20) REVERT: C 339 TRP cc_start: 0.7892 (m-10) cc_final: 0.7534 (m-10) REVERT: G 44 HIS cc_start: 0.8128 (m-70) cc_final: 0.7838 (m-70) REVERT: G 48 ASP cc_start: 0.8274 (t0) cc_final: 0.7613 (t0) REVERT: H 106 SER cc_start: 0.9189 (t) cc_final: 0.8866 (t) REVERT: H 231 GLN cc_start: 0.8458 (pp30) cc_final: 0.8037 (pp30) REVERT: R 111 ARG cc_start: 0.5992 (mtm-85) cc_final: 0.5543 (mtm-85) REVERT: R 216 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6873 (mtt-85) outliers start: 23 outliers final: 22 residues processed: 126 average time/residue: 0.2007 time to fit residues: 35.4354 Evaluate side-chains 131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.0020 chunk 4 optimal weight: 0.2980 chunk 63 optimal weight: 0.0970 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132360 restraints weight = 9705.187| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.31 r_work: 0.3335 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8018 Z= 0.150 Angle : 0.532 9.612 10954 Z= 0.280 Chirality : 0.041 0.153 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.234 145.956 1186 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.47 % Allowed : 18.58 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1100 helix: 2.66 (0.28), residues: 369 sheet: -0.78 (0.30), residues: 259 loop : -0.10 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 169 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.020 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.95 seconds wall clock time: 34 minutes 14.18 seconds (2054.18 seconds total)