Starting phenix.real_space_refine on Wed Mar 12 12:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyw_35831/03_2025/8iyw_35831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyw_35831/03_2025/8iyw_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_35831/03_2025/8iyw_35831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyw_35831/03_2025/8iyw_35831.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyw_35831/03_2025/8iyw_35831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyw_35831/03_2025/8iyw_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.40, per 1000 atoms: 0.69 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: 1.65 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: 1.05 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: 2.16 Time building geometry restraints manager: 1.95 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: 37.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.680 ------------------------------------------------------------------------------- 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 : 1.398 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: 0.2492 time to fit residues: 46.2279 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 : 0.792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132811 restraints weight = 9663.477| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.39 r_work: 0.3328 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1244 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 6.597 10954 Z= 0.313 Chirality : 0.044 0.148 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.916 146.992 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 : 0.856 Fit side-chains revert: symmetry clash REVERT: G 44 HIS cc_start: 0.7974 (m-70) cc_final: 0.7569 (m-70) REVERT: G 48 ASP cc_start: 0.7683 (t0) cc_final: 0.7121 (t0) REVERT: R 198 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: R 213 TRP cc_start: 0.8089 (t60) cc_final: 0.7875 (t60) REVERT: R 216 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6950 (mtt-85) REVERT: R 284 TYR cc_start: 0.7830 (m-80) cc_final: 0.7330 (m-80) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.1804 time to fit residues: 33.6366 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 : 0.764 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 0.0570 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131687 restraints weight = 9928.218| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.33 r_work: 0.3324 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8018 Z= 0.193 Angle : 0.541 6.401 10954 Z= 0.291 Chirality : 0.043 0.153 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.494 139.242 1186 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.34 % Allowed : 12.92 % Favored : 83.74 % 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: 0.87 (0.26), residues: 1100 helix: 1.99 (0.28), residues: 363 sheet: -0.05 (0.30), residues: 253 loop : -0.07 (0.30), residues: 484 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 0.014 0.001 PHE C 199 TYR 0.018 0.001 TYR B 297 ARG 0.002 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 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8365 (tp30) cc_final: 0.8155 (tp30) REVERT: B 290 GLU cc_start: 0.8185 (pm20) cc_final: 0.7801 (pm20) REVERT: C 98 SER cc_start: 0.8110 (m) cc_final: 0.7556 (t) REVERT: G 44 HIS cc_start: 0.7881 (m-70) cc_final: 0.7557 (m-70) REVERT: G 48 ASP cc_start: 0.7939 (t0) cc_final: 0.7139 (t0) REVERT: H 237 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8351 (mp) REVERT: R 198 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: R 216 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6823 (mtt-85) REVERT: R 284 TYR cc_start: 0.7897 (m-80) cc_final: 0.7561 (m-80) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.1673 time to fit residues: 30.6278 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 H residue 237 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 37 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131552 restraints weight = 9807.514| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.33 r_work: 0.3316 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1977 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= 0.200 Angle : 0.522 6.451 10954 Z= 0.282 Chirality : 0.043 0.160 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.425 141.165 1186 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.06 % Allowed : 13.21 % 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: 0.92 (0.26), residues: 1100 helix: 2.19 (0.28), residues: 370 sheet: -0.19 (0.30), residues: 256 loop : -0.11 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.005 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 146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: C 98 SER cc_start: 0.8151 (m) cc_final: 0.7598 (t) REVERT: G 44 HIS cc_start: 0.7909 (m-70) cc_final: 0.7549 (m-70) REVERT: G 48 ASP cc_start: 0.8121 (t0) cc_final: 0.7295 (t0) REVERT: R 111 ARG cc_start: 0.5482 (mtm-85) cc_final: 0.5037 (mtm-85) REVERT: R 198 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: R 216 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6854 (mtt-85) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.1803 time to fit residues: 34.2396 Evaluate side-chains 131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3124 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121440 restraints weight = 9741.515| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.74 r_work: 0.3374 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8018 Z= 0.147 Angle : 0.508 8.664 10954 Z= 0.269 Chirality : 0.042 0.189 1281 Planarity : 0.003 0.038 1415 Dihedral : 6.241 140.723 1186 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.48 % Allowed : 15.24 % Favored : 81.28 % 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: 1.03 (0.26), residues: 1100 helix: 2.35 (0.28), residues: 370 sheet: -0.22 (0.30), residues: 258 loop : -0.05 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE R 197 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 142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8223 (pm20) cc_final: 0.7825 (pm20) REVERT: C 98 SER cc_start: 0.8237 (m) cc_final: 0.7745 (t) REVERT: G 44 HIS cc_start: 0.7916 (m-70) cc_final: 0.7644 (m-70) REVERT: G 48 ASP cc_start: 0.8068 (t0) cc_final: 0.7313 (t0) REVERT: H 183 GLN cc_start: 0.7749 (mt0) cc_final: 0.7313 (tt0) REVERT: H 231 GLN cc_start: 0.8443 (pp30) cc_final: 0.8158 (pp30) REVERT: R 111 ARG cc_start: 0.5710 (mtm-85) cc_final: 0.5243 (mtm-85) REVERT: R 198 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: R 216 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6862 (mtt-85) outliers start: 24 outliers final: 19 residues processed: 131 average time/residue: 0.1794 time to fit residues: 32.8441 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 : 0.809 ------------------------------------------------------------------------------- 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 228 LEU 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 100 VAL 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 C residue 234 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 60 optimal weight: 0.5980 chunk 4 optimal weight: 0.0010 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.182515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140028 restraints weight = 9724.947| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.73 r_work: 0.3506 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8018 Z= 0.173 Angle : 0.510 7.128 10954 Z= 0.271 Chirality : 0.042 0.172 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.256 142.751 1186 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.48 % Allowed : 15.82 % Favored : 80.70 % 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: 1.04 (0.26), residues: 1100 helix: 2.48 (0.28), residues: 369 sheet: -0.34 (0.30), residues: 260 loop : -0.06 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE C 199 TYR 0.020 0.001 TYR B 297 ARG 0.006 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: 24 poor density : 116 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: B 270 ASN cc_start: 0.8660 (m-40) cc_final: 0.8442 (m-40) REVERT: B 290 GLU cc_start: 0.8258 (pm20) cc_final: 0.7920 (pm20) REVERT: C 98 SER cc_start: 0.8183 (m) cc_final: 0.7762 (t) REVERT: G 44 HIS cc_start: 0.7998 (m-70) cc_final: 0.7766 (m-70) REVERT: G 48 ASP cc_start: 0.8044 (t0) cc_final: 0.7370 (t0) REVERT: H 106 SER cc_start: 0.8995 (t) cc_final: 0.8503 (p) REVERT: H 183 GLN cc_start: 0.7861 (mt0) cc_final: 0.7518 (tt0) REVERT: H 231 GLN cc_start: 0.8305 (pp30) cc_final: 0.8008 (pp30) REVERT: R 111 ARG cc_start: 0.5942 (mtm-85) cc_final: 0.5464 (mtm-85) REVERT: R 198 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: R 216 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6906 (mtt-85) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.1710 time to fit residues: 31.9569 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 : 0.859 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.182235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139283 restraints weight = 9756.946| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.89 r_work: 0.3502 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2400 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= 0.185 Angle : 0.511 9.624 10954 Z= 0.272 Chirality : 0.042 0.156 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.266 143.834 1186 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.63 % Allowed : 15.53 % Favored : 80.84 % 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: 1.06 (0.26), residues: 1100 helix: 2.58 (0.28), residues: 369 sheet: -0.39 (0.30), residues: 260 loop : -0.09 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.026 0.001 PHE B 336 TYR 0.021 0.001 TYR B 297 ARG 0.007 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 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: B 270 ASN cc_start: 0.8661 (m-40) cc_final: 0.8446 (m-40) REVERT: C 98 SER cc_start: 0.8302 (m) cc_final: 0.7817 (t) REVERT: G 44 HIS cc_start: 0.8113 (m-70) cc_final: 0.7838 (m-70) REVERT: G 48 ASP cc_start: 0.8095 (t0) cc_final: 0.7410 (t0) REVERT: H 106 SER cc_start: 0.9011 (t) cc_final: 0.8493 (p) REVERT: H 183 GLN cc_start: 0.7848 (mt0) cc_final: 0.7512 (tt0) REVERT: H 231 GLN cc_start: 0.8330 (pp30) cc_final: 0.7997 (pp30) REVERT: R 111 ARG cc_start: 0.5895 (mtm-85) cc_final: 0.5445 (mtm-85) REVERT: R 216 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6891 (mtt-85) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.1740 time to fit residues: 32.9893 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 THR 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 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER 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 83 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113967 restraints weight = 9710.172| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.89 r_work: 0.3250 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8018 Z= 0.233 Angle : 0.532 6.373 10954 Z= 0.287 Chirality : 0.043 0.155 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.358 143.624 1186 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.48 % Allowed : 15.97 % Favored : 80.55 % 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: 1.00 (0.26), residues: 1100 helix: 2.54 (0.28), residues: 369 sheet: -0.44 (0.31), residues: 253 loop : -0.14 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE B 336 TYR 0.020 0.002 TYR B 297 ARG 0.006 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 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8364 (pm20) cc_final: 0.7979 (pm20) REVERT: C 98 SER cc_start: 0.8094 (m) cc_final: 0.7361 (t) REVERT: G 44 HIS cc_start: 0.7865 (m-70) cc_final: 0.7546 (m-70) REVERT: G 48 ASP cc_start: 0.8310 (t0) cc_final: 0.7428 (t0) REVERT: H 106 SER cc_start: 0.9292 (t) cc_final: 0.8741 (p) REVERT: H 231 GLN cc_start: 0.8641 (pp30) cc_final: 0.8125 (pp30) REVERT: R 111 ARG cc_start: 0.5361 (mtm-85) cc_final: 0.4950 (mtm-85) REVERT: R 216 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6704 (mtt-85) outliers start: 24 outliers final: 21 residues processed: 130 average time/residue: 0.1746 time to fit residues: 31.7864 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 189 SER 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 83 MET 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 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114273 restraints weight = 9721.721| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.87 r_work: 0.3249 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8018 Z= 0.227 Angle : 0.543 10.005 10954 Z= 0.289 Chirality : 0.042 0.154 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.348 144.035 1186 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.34 % Allowed : 16.98 % Favored : 79.68 % 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: 0.97 (0.26), residues: 1100 helix: 2.59 (0.28), residues: 369 sheet: -0.49 (0.31), residues: 253 loop : -0.21 (0.29), residues: 478 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 0.019 0.001 PHE B 336 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 138 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8521 (pm20) cc_final: 0.8098 (pm20) REVERT: B 331 ASN cc_start: 0.7397 (m-40) cc_final: 0.7083 (p0) REVERT: C 98 SER cc_start: 0.8109 (m) cc_final: 0.7388 (t) REVERT: C 339 TRP cc_start: 0.7468 (m-10) cc_final: 0.7177 (m-10) REVERT: G 44 HIS cc_start: 0.7896 (m-70) cc_final: 0.7575 (m-70) REVERT: G 48 ASP cc_start: 0.8347 (t0) cc_final: 0.7462 (t0) REVERT: H 106 SER cc_start: 0.9310 (t) cc_final: 0.8988 (t) REVERT: H 231 GLN cc_start: 0.8617 (pp30) cc_final: 0.8117 (pp30) REVERT: R 111 ARG cc_start: 0.5401 (mtm-85) cc_final: 0.5000 (mtm-85) REVERT: R 216 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6667 (mtt-85) outliers start: 23 outliers final: 20 residues processed: 131 average time/residue: 0.1846 time to fit residues: 33.4459 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 THR 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 157 ILE Chi-restraints excluded: chain C residue 189 SER 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 83 MET 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.0307 > 50: distance: 54 - 74: 8.398 distance: 59 - 81: 8.500 distance: 62 - 67: 3.608 distance: 63 - 86: 7.673 distance: 67 - 68: 3.299 distance: 68 - 69: 3.963 distance: 68 - 71: 4.450 distance: 69 - 70: 5.019 distance: 69 - 74: 6.788 distance: 70 - 93: 6.761 distance: 71 - 73: 4.673 distance: 74 - 75: 9.021 distance: 75 - 76: 4.389 distance: 75 - 78: 6.596 distance: 76 - 77: 6.120 distance: 76 - 81: 10.311 distance: 77 - 101: 11.065 distance: 78 - 79: 14.462 distance: 78 - 80: 16.730 distance: 81 - 82: 7.374 distance: 82 - 83: 8.274 distance: 82 - 85: 12.448 distance: 83 - 84: 12.753 distance: 83 - 86: 6.609 distance: 84 - 112: 17.303 distance: 86 - 87: 6.247 distance: 87 - 88: 3.140 distance: 87 - 90: 3.911 distance: 88 - 89: 7.212 distance: 88 - 93: 3.976 distance: 89 - 124: 18.008 distance: 90 - 91: 7.203 distance: 90 - 92: 10.689 distance: 94 - 95: 3.661 distance: 94 - 97: 5.471 distance: 95 - 101: 7.582 distance: 96 - 135: 19.683 distance: 98 - 99: 4.609 distance: 101 - 102: 6.232 distance: 102 - 103: 14.120 distance: 102 - 105: 4.923 distance: 103 - 104: 24.772 distance: 103 - 112: 41.504 distance: 104 - 146: 33.178 distance: 105 - 106: 8.788 distance: 106 - 107: 7.646 distance: 107 - 108: 6.066 distance: 108 - 109: 4.184 distance: 109 - 110: 3.277 distance: 109 - 111: 3.962 distance: 112 - 113: 28.912 distance: 113 - 114: 13.069 distance: 113 - 116: 14.971 distance: 114 - 115: 7.709 distance: 114 - 124: 9.601 distance: 115 - 153: 23.857 distance: 116 - 117: 11.440 distance: 117 - 118: 10.293 distance: 117 - 119: 18.867 distance: 118 - 120: 4.963 distance: 119 - 121: 6.295 distance: 120 - 122: 8.350 distance: 121 - 122: 15.997 distance: 124 - 125: 4.532 distance: 125 - 126: 7.223 distance: 125 - 128: 3.652 distance: 126 - 127: 9.960 distance: 126 - 135: 3.199 distance: 128 - 129: 3.793 distance: 129 - 131: 12.508 distance: 132 - 134: 8.575 distance: 133 - 134: 7.435 distance: 135 - 136: 3.997 distance: 137 - 138: 12.747 distance: 137 - 146: 3.088 distance: 139 - 140: 4.545 distance: 141 - 142: 3.524 distance: 142 - 143: 3.807 distance: 143 - 144: 3.800 distance: 143 - 145: 3.921 distance: 146 - 147: 7.183 distance: 147 - 148: 3.002 distance: 147 - 150: 4.981 distance: 148 - 149: 10.253 distance: 148 - 153: 4.330 distance: 150 - 151: 8.475 distance: 150 - 152: 6.072 distance: 199 - 210: 3.321