Starting phenix.real_space_refine on Sat Jun 7 05:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqc_34947/06_2025/8hqc_34947.cif" } resolution = 3.89 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5429 2.51 5 N 1471 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1984 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1544 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2488 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "D" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 472 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 384 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1666 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.73, per 1000 atoms: 0.67 Number of scatterers: 8538 At special positions: 0 Unit cell: (87.1755, 126.025, 147.819, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1580 8.00 N 1471 7.00 C 5429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 41.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 40 through 62 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 96 Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 140 removed outlier: 3.762A pdb=" N MET A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 149 through 175 Proline residue: A 170 - end of helix removed outlier: 3.694A pdb=" N ARG A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.539A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.561A pdb=" N ARG A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 269 removed outlier: 4.803A pdb=" N ALA A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.756A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.901A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.778A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.738A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.835A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 262 " --> pdb=" O PHE B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.848A pdb=" N GLY B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.848A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 removed outlier: 3.968A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.633A pdb=" N ARG D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 44 through 63 removed outlier: 4.243A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.552A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.697A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 7.260A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.739A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.654A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.601A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.711A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.632A 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: 3.752A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.464A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (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: 7.173A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.894A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1236 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: 3.46 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2781 1.34 - 1.46: 2030 1.46 - 1.58: 3818 1.58 - 1.70: 1 1.70 - 1.82: 75 Bond restraints: 8705 Sorted by residual: bond pdb=" CB PRO B 294 " pdb=" CG PRO B 294 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.72e+00 bond pdb=" CG PRO B 294 " pdb=" CD PRO B 294 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.04e+00 bond pdb=" CA ILE B 335 " pdb=" CB ILE B 335 " ideal model delta sigma weight residual 1.540 1.522 0.018 1.39e-02 5.18e+03 1.75e+00 bond pdb=" CA GLU B 8 " pdb=" C GLU B 8 " ideal model delta sigma weight residual 1.523 1.544 -0.020 1.80e-02 3.09e+03 1.27e+00 bond pdb=" CA ILE A 169 " pdb=" C ILE A 169 " ideal model delta sigma weight residual 1.524 1.536 -0.011 1.05e-02 9.07e+03 1.19e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11442 1.55 - 3.10: 344 3.10 - 4.65: 61 4.65 - 6.20: 23 6.20 - 7.75: 6 Bond angle restraints: 11876 Sorted by residual: angle pdb=" CA PRO B 294 " pdb=" N PRO B 294 " pdb=" CD PRO B 294 " ideal model delta sigma weight residual 112.00 105.88 6.12 1.40e+00 5.10e-01 1.91e+01 angle pdb=" C MET B 53 " pdb=" N LYS B 54 " pdb=" CA LYS B 54 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" CB ASN C 119 " ideal model delta sigma weight residual 114.17 110.39 3.78 1.14e+00 7.69e-01 1.10e+01 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 113.53 110.47 3.06 9.80e-01 1.04e+00 9.72e+00 angle pdb=" C ASP A 180 " pdb=" N PHE A 181 " pdb=" CA PHE A 181 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.59e+00 ... (remaining 11871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4771 17.92 - 35.83: 275 35.83 - 53.75: 46 53.75 - 71.67: 5 71.67 - 89.58: 3 Dihedral angle restraints: 5100 sinusoidal: 1684 harmonic: 3416 Sorted by residual: dihedral pdb=" CA ALA C 56 " pdb=" C ALA C 56 " pdb=" N LYS C 57 " pdb=" CA LYS C 57 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 55.70 37.30 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual 93.00 58.21 34.79 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 857 0.033 - 0.066: 385 0.066 - 0.099: 131 0.099 - 0.132: 45 0.132 - 0.165: 5 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA LYS B 54 " pdb=" N LYS B 54 " pdb=" C LYS B 54 " pdb=" CB LYS B 54 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA PRO B 294 " pdb=" N PRO B 294 " pdb=" C PRO B 294 " pdb=" CB PRO B 294 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA PHE A 139 " pdb=" N PHE A 139 " pdb=" C PHE A 139 " pdb=" CB PHE A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1420 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 293 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO B 294 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 314 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 315 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 139 " 0.013 2.00e-02 2.50e+03 1.52e-02 4.02e+00 pdb=" CG PHE A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 139 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1328 2.76 - 3.29: 8721 3.29 - 3.83: 13369 3.83 - 4.36: 15081 4.36 - 4.90: 26644 Nonbonded interactions: 65143 Sorted by model distance: nonbonded pdb=" OG SER C 147 " pdb=" O MET C 188 " model vdw 2.223 3.040 nonbonded pdb=" ND2 ASN A 55 " pdb=" OD2 ASP A 82 " model vdw 2.249 3.120 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.294 3.120 nonbonded pdb=" NH1 ARG H 202 " pdb=" OD2 ASP H 223 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU A 176 " pdb=" OG SER D 66 " model vdw 2.314 3.040 ... (remaining 65138 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 105.570 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.980 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.003 0.096 8710 Z= 0.147 Angle : 0.686 7.754 11886 Z= 0.369 Chirality : 0.043 0.165 1423 Planarity : 0.005 0.096 1507 Dihedral : 11.767 89.582 2877 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.25), residues: 1162 helix: 0.58 (0.26), residues: 407 sheet: -0.16 (0.30), residues: 269 loop : -0.23 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.007 0.001 HIS A 309 PHE 0.035 0.002 PHE A 139 TYR 0.015 0.001 TYR A 44 ARG 0.009 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.17556 ( 446) hydrogen bonds : angle 6.55078 ( 1236) SS BOND : bond 0.00448 ( 5) SS BOND : angle 0.79737 ( 10) covalent geometry : bond 0.00322 ( 8705) covalent geometry : angle 0.68571 (11876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6874 (t) cc_final: 0.6539 (t) REVERT: B 207 SER cc_start: 0.7336 (t) cc_final: 0.6882 (m) REVERT: B 255 CYS cc_start: 0.8373 (t) cc_final: 0.7946 (t) REVERT: B 305 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 223 THR cc_start: 0.7828 (p) cc_final: 0.7618 (p) REVERT: C 339 TRP cc_start: 0.8841 (m100) cc_final: 0.8543 (m100) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1837 time to fit residues: 49.5427 Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 295 ASN B 347 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127433 restraints weight = 12343.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124697 restraints weight = 22551.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124489 restraints weight = 23897.968| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8710 Z= 0.155 Angle : 0.658 8.104 11886 Z= 0.341 Chirality : 0.044 0.150 1423 Planarity : 0.004 0.043 1507 Dihedral : 4.712 23.046 1249 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.81 % Allowed : 9.89 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.25), residues: 1162 helix: 0.76 (0.27), residues: 416 sheet: 0.03 (0.31), residues: 265 loop : -0.38 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.003 0.001 HIS A 99 PHE 0.015 0.002 PHE C 199 TYR 0.015 0.002 TYR H 60 ARG 0.006 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 446) hydrogen bonds : angle 5.04891 ( 1236) SS BOND : bond 0.00782 ( 5) SS BOND : angle 1.51571 ( 10) covalent geometry : bond 0.00350 ( 8705) covalent geometry : angle 0.65672 (11876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6888 (t) cc_final: 0.6616 (t) REVERT: B 207 SER cc_start: 0.7238 (t) cc_final: 0.6737 (m) REVERT: B 255 CYS cc_start: 0.8118 (t) cc_final: 0.7860 (t) REVERT: B 322 HIS cc_start: 0.7770 (t-90) cc_final: 0.7453 (t-90) REVERT: C 223 THR cc_start: 0.7711 (p) cc_final: 0.7505 (p) REVERT: D 29 ASN cc_start: 0.8518 (t0) cc_final: 0.8181 (t0) REVERT: G 36 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7061 (t0) REVERT: H 230 MET cc_start: 0.8358 (ttt) cc_final: 0.8130 (ttt) outliers start: 15 outliers final: 9 residues processed: 169 average time/residue: 0.1905 time to fit residues: 45.3316 Evaluate side-chains 167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 0.0670 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 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 = 0.3684 r_free = 0.3684 target = 0.147643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128362 restraints weight = 12381.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122360 restraints weight = 20017.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120377 restraints weight = 19461.729| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8710 Z= 0.122 Angle : 0.600 8.239 11886 Z= 0.309 Chirality : 0.042 0.144 1423 Planarity : 0.004 0.040 1507 Dihedral : 4.331 23.040 1249 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 12.42 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.25), residues: 1162 helix: 0.88 (0.27), residues: 414 sheet: 0.06 (0.31), residues: 260 loop : -0.22 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS A 99 PHE 0.014 0.001 PHE B 190 TYR 0.013 0.001 TYR H 60 ARG 0.003 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 446) hydrogen bonds : angle 4.74705 ( 1236) SS BOND : bond 0.00323 ( 5) SS BOND : angle 2.02907 ( 10) covalent geometry : bond 0.00259 ( 8705) covalent geometry : angle 0.59729 (11876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: B 255 CYS cc_start: 0.8054 (t) cc_final: 0.7760 (t) REVERT: B 322 HIS cc_start: 0.7823 (t-90) cc_final: 0.7508 (t-90) REVERT: C 234 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: H 192 MET cc_start: 0.7994 (tmm) cc_final: 0.7729 (tmm) REVERT: H 204 SER cc_start: 0.8485 (t) cc_final: 0.8079 (m) REVERT: H 230 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (ttt) outliers start: 21 outliers final: 14 residues processed: 186 average time/residue: 0.1777 time to fit residues: 47.6667 Evaluate side-chains 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123794 restraints weight = 12858.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121252 restraints weight = 20872.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119790 restraints weight = 22790.881| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8710 Z= 0.133 Angle : 0.605 8.246 11886 Z= 0.311 Chirality : 0.042 0.140 1423 Planarity : 0.004 0.045 1507 Dihedral : 4.259 22.868 1249 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.26 % Allowed : 13.75 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.25), residues: 1162 helix: 0.88 (0.27), residues: 418 sheet: -0.07 (0.31), residues: 265 loop : -0.31 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.003 0.001 HIS A 99 PHE 0.018 0.002 PHE A 255 TYR 0.012 0.001 TYR C 105 ARG 0.005 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 446) hydrogen bonds : angle 4.69427 ( 1236) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.25828 ( 10) covalent geometry : bond 0.00301 ( 8705) covalent geometry : angle 0.60430 (11876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 255 CYS cc_start: 0.7905 (t) cc_final: 0.7653 (t) REVERT: B 322 HIS cc_start: 0.7730 (t-90) cc_final: 0.7434 (t-90) REVERT: C 234 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: H 192 MET cc_start: 0.8035 (tmm) cc_final: 0.7658 (tmm) REVERT: H 204 SER cc_start: 0.8534 (t) cc_final: 0.8274 (m) REVERT: H 230 MET cc_start: 0.8364 (ttt) cc_final: 0.8099 (ttt) outliers start: 27 outliers final: 21 residues processed: 166 average time/residue: 0.1852 time to fit residues: 44.4021 Evaluate side-chains 170 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU 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 C residue 294 CYS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120628 restraints weight = 12950.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114596 restraints weight = 18639.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111029 restraints weight = 16540.574| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8710 Z= 0.174 Angle : 0.629 8.452 11886 Z= 0.326 Chirality : 0.044 0.142 1423 Planarity : 0.004 0.048 1507 Dihedral : 4.403 23.831 1249 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.19 % Allowed : 15.08 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.25), residues: 1162 helix: 0.94 (0.27), residues: 416 sheet: -0.21 (0.30), residues: 262 loop : -0.47 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 211 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.002 PHE C 199 TYR 0.016 0.002 TYR C 105 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 446) hydrogen bonds : angle 4.76220 ( 1236) SS BOND : bond 0.00666 ( 5) SS BOND : angle 1.00766 ( 10) covalent geometry : bond 0.00411 ( 8705) covalent geometry : angle 0.62851 (11876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 139 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 207 SER cc_start: 0.7619 (t) cc_final: 0.7160 (m) REVERT: B 322 HIS cc_start: 0.7989 (t-90) cc_final: 0.7399 (t-90) REVERT: C 211 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8821 (m100) REVERT: C 234 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: H 204 SER cc_start: 0.8636 (t) cc_final: 0.8255 (m) REVERT: H 230 MET cc_start: 0.8607 (ttt) cc_final: 0.8243 (ttt) outliers start: 43 outliers final: 31 residues processed: 174 average time/residue: 0.1995 time to fit residues: 50.2289 Evaluate side-chains 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 98 optimal weight: 0.0070 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.134840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113188 restraints weight = 12505.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111445 restraints weight = 22743.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111986 restraints weight = 22228.665| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8710 Z= 0.127 Angle : 0.593 8.570 11886 Z= 0.306 Chirality : 0.042 0.135 1423 Planarity : 0.004 0.049 1507 Dihedral : 4.230 23.262 1249 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.22 % Allowed : 17.85 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.25), residues: 1162 helix: 1.03 (0.27), residues: 412 sheet: -0.36 (0.30), residues: 269 loop : -0.38 (0.30), residues: 481 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 0.014 0.001 PHE B 190 TYR 0.010 0.001 TYR C 105 ARG 0.010 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 446) hydrogen bonds : angle 4.64732 ( 1236) SS BOND : bond 0.00350 ( 5) SS BOND : angle 1.02792 ( 10) covalent geometry : bond 0.00288 ( 8705) covalent geometry : angle 0.59297 (11876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 2.488 Fit side-chains REVERT: A 139 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7529 (t80) REVERT: B 14 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 207 SER cc_start: 0.7472 (t) cc_final: 0.6949 (m) REVERT: B 322 HIS cc_start: 0.7772 (t-90) cc_final: 0.7436 (t-90) REVERT: C 147 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8743 (t) REVERT: C 234 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: H 138 ILE cc_start: 0.6355 (pt) cc_final: 0.6106 (pt) REVERT: H 204 SER cc_start: 0.8475 (t) cc_final: 0.8245 (m) outliers start: 35 outliers final: 20 residues processed: 172 average time/residue: 0.2487 time to fit residues: 63.0381 Evaluate side-chains 170 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU 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 C residue 265 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.0270 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN H 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113677 restraints weight = 12701.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112186 restraints weight = 21620.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111998 restraints weight = 21775.337| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8710 Z= 0.152 Angle : 0.617 9.111 11886 Z= 0.319 Chirality : 0.043 0.139 1423 Planarity : 0.004 0.051 1507 Dihedral : 4.259 23.215 1249 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.43 % Allowed : 17.13 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.25), residues: 1162 helix: 1.07 (0.27), residues: 412 sheet: -0.44 (0.30), residues: 270 loop : -0.41 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.003 0.001 HIS A 99 PHE 0.015 0.002 PHE A 139 TYR 0.013 0.001 TYR C 105 ARG 0.008 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 446) hydrogen bonds : angle 4.69258 ( 1236) SS BOND : bond 0.00428 ( 5) SS BOND : angle 1.16706 ( 10) covalent geometry : bond 0.00354 ( 8705) covalent geometry : angle 0.61680 (11876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.996 Fit side-chains REVERT: A 139 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7580 (t80) REVERT: B 14 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 207 SER cc_start: 0.7545 (t) cc_final: 0.7018 (m) REVERT: B 322 HIS cc_start: 0.7841 (t-90) cc_final: 0.7393 (t-90) REVERT: C 147 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (t) REVERT: C 211 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8627 (m100) REVERT: C 234 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: G 11 GLN cc_start: 0.7530 (pp30) cc_final: 0.7097 (pp30) REVERT: H 138 ILE cc_start: 0.6431 (pt) cc_final: 0.6131 (pt) REVERT: H 204 SER cc_start: 0.8543 (t) cc_final: 0.8264 (m) REVERT: H 223 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7221 (t0) REVERT: H 230 MET cc_start: 0.8571 (ttt) cc_final: 0.8158 (ttt) outliers start: 45 outliers final: 29 residues processed: 179 average time/residue: 0.2589 time to fit residues: 68.9894 Evaluate side-chains 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** 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 = 0.3608 r_free = 0.3608 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120650 restraints weight = 12906.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117839 restraints weight = 24859.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117804 restraints weight = 25050.292| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8710 Z= 0.150 Angle : 0.625 9.085 11886 Z= 0.321 Chirality : 0.043 0.139 1423 Planarity : 0.004 0.077 1507 Dihedral : 4.251 23.340 1249 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.46 % Allowed : 18.70 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.25), residues: 1162 helix: 1.08 (0.27), residues: 412 sheet: -0.46 (0.30), residues: 266 loop : -0.47 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 211 HIS 0.003 0.001 HIS A 99 PHE 0.024 0.002 PHE H 212 TYR 0.012 0.001 TYR C 105 ARG 0.016 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 446) hydrogen bonds : angle 4.68222 ( 1236) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.09451 ( 10) covalent geometry : bond 0.00349 ( 8705) covalent geometry : angle 0.62480 (11876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.129 Fit side-chains REVERT: A 139 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 14 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 207 SER cc_start: 0.7565 (t) cc_final: 0.6993 (m) REVERT: B 322 HIS cc_start: 0.7739 (t-90) cc_final: 0.7409 (t-90) REVERT: C 147 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (t) REVERT: C 234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: H 138 ILE cc_start: 0.6516 (pt) cc_final: 0.6222 (pt) REVERT: H 204 SER cc_start: 0.8534 (t) cc_final: 0.8262 (m) REVERT: H 230 MET cc_start: 0.8487 (ttt) cc_final: 0.8087 (ttt) REVERT: H 231 GLN cc_start: 0.8582 (pp30) cc_final: 0.8279 (pp30) outliers start: 37 outliers final: 30 residues processed: 166 average time/residue: 0.2228 time to fit residues: 54.3930 Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 59 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: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** 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 = 0.3602 r_free = 0.3602 target = 0.140017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122126 restraints weight = 12917.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113471 restraints weight = 20666.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111594 restraints weight = 19938.596| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8710 Z= 0.152 Angle : 0.655 14.141 11886 Z= 0.331 Chirality : 0.043 0.145 1423 Planarity : 0.004 0.056 1507 Dihedral : 4.273 23.318 1249 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.70 % Allowed : 19.18 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.25), residues: 1162 helix: 1.14 (0.27), residues: 413 sheet: -0.65 (0.30), residues: 271 loop : -0.41 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS B 189 PHE 0.028 0.002 PHE H 212 TYR 0.012 0.001 TYR C 105 ARG 0.014 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 446) hydrogen bonds : angle 4.72178 ( 1236) SS BOND : bond 0.00484 ( 5) SS BOND : angle 1.17191 ( 10) covalent geometry : bond 0.00354 ( 8705) covalent geometry : angle 0.65461 (11876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.900 Fit side-chains REVERT: A 139 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7651 (t80) REVERT: B 14 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 207 SER cc_start: 0.7637 (t) cc_final: 0.7137 (m) REVERT: B 322 HIS cc_start: 0.7959 (t-90) cc_final: 0.7494 (t-90) REVERT: C 147 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8745 (t) REVERT: C 234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: C 339 TRP cc_start: 0.9270 (m100) cc_final: 0.9001 (m100) REVERT: G 11 GLN cc_start: 0.8460 (pp30) cc_final: 0.8097 (pp30) REVERT: G 22 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 138 ILE cc_start: 0.6302 (pt) cc_final: 0.5969 (pt) REVERT: H 204 SER cc_start: 0.8466 (t) cc_final: 0.8151 (m) REVERT: H 230 MET cc_start: 0.8541 (ttt) cc_final: 0.8103 (ttt) outliers start: 39 outliers final: 30 residues processed: 167 average time/residue: 0.1755 time to fit residues: 41.7298 Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 68 optimal weight: 0.2980 chunk 26 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 0.0470 chunk 90 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 54 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127685 restraints weight = 12778.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123626 restraints weight = 17823.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121213 restraints weight = 20844.981| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8710 Z= 0.111 Angle : 0.628 12.927 11886 Z= 0.314 Chirality : 0.042 0.146 1423 Planarity : 0.004 0.055 1507 Dihedral : 3.992 22.296 1249 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 21.35 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.25), residues: 1162 helix: 1.08 (0.27), residues: 418 sheet: -0.27 (0.30), residues: 263 loop : -0.34 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 169 HIS 0.004 0.001 HIS A 99 PHE 0.026 0.001 PHE H 212 TYR 0.011 0.001 TYR A 301 ARG 0.014 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 446) hydrogen bonds : angle 4.53348 ( 1236) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.31055 ( 10) covalent geometry : bond 0.00235 ( 8705) covalent geometry : angle 0.62686 (11876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.030 Fit side-chains REVERT: A 118 LEU cc_start: 0.8428 (tp) cc_final: 0.8207 (tt) REVERT: A 139 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 14 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 207 SER cc_start: 0.7414 (t) cc_final: 0.6898 (m) REVERT: C 147 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8679 (t) REVERT: C 234 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: G 11 GLN cc_start: 0.7727 (pp30) cc_final: 0.7308 (pp30) REVERT: H 38 ARG cc_start: 0.8320 (ptt180) cc_final: 0.7677 (ptt180) REVERT: H 138 ILE cc_start: 0.5427 (pt) cc_final: 0.5104 (pt) REVERT: H 230 MET cc_start: 0.8393 (ttt) cc_final: 0.7923 (ttt) outliers start: 20 outliers final: 14 residues processed: 174 average time/residue: 0.1787 time to fit residues: 44.9077 Evaluate side-chains 162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 54 HIS C 88 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124593 restraints weight = 12901.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116747 restraints weight = 21557.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114333 restraints weight = 18720.121| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8710 Z= 0.129 Angle : 0.647 12.937 11886 Z= 0.328 Chirality : 0.042 0.145 1423 Planarity : 0.004 0.055 1507 Dihedral : 3.991 23.778 1249 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.41 % Allowed : 22.68 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.25), residues: 1162 helix: 1.14 (0.27), residues: 420 sheet: -0.46 (0.30), residues: 270 loop : -0.36 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 143 HIS 0.009 0.001 HIS B 322 PHE 0.024 0.002 PHE H 212 TYR 0.010 0.001 TYR H 102 ARG 0.013 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 446) hydrogen bonds : angle 4.56404 ( 1236) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.27155 ( 10) covalent geometry : bond 0.00292 ( 8705) covalent geometry : angle 0.64600 (11876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.31 seconds wall clock time: 64 minutes 21.04 seconds (3861.04 seconds total)