Starting phenix.real_space_refine on Fri Aug 22 23:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqc_34947/08_2025/8hqc_34947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqc_34947/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hqc_34947/08_2025/8hqc_34947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqc_34947/08_2025/8hqc_34947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hqc_34947/08_2025/8hqc_34947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqc_34947/08_2025/8hqc_34947.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} 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, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 1} 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, 'GLU:plan': 5, 'TYR:plan': 2, 'HIS:plan': 1, 'ASP:plan': 2, '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: {'ARG:plan': 2, 'GLU:plan': 3} 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, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.81, per 1000 atoms: 0.21 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: 0.75 Conformation dependent library (CDL) restraints added in 393.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.40 Time building geometry restraints manager: 0.98 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: 2.940 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG C 96 TYR 0.015 0.001 TYR A 44 PHE 0.035 0.002 PHE A 139 TRP 0.019 0.002 TRP C 63 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8705) covalent geometry : angle 0.68571 (11876) SS BOND : bond 0.00448 ( 5) SS BOND : angle 0.79737 ( 10) hydrogen bonds : bond 0.17556 ( 446) hydrogen bonds : angle 6.55078 ( 1236) *********************** 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 : 0.267 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: 0.6881 (m) REVERT: B 255 CYS cc_start: 0.8373 (t) cc_final: 0.7946 (t) REVERT: B 295 ASN cc_start: 0.7856 (t0) cc_final: 0.7635 (t0) 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: 0.0740 time to fit residues: 20.2713 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 347 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125654 restraints weight = 12594.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123043 restraints weight = 21763.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123783 restraints weight = 22861.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123835 restraints weight = 17719.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123897 restraints weight = 15410.826| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8710 Z= 0.158 Angle : 0.660 8.067 11886 Z= 0.343 Chirality : 0.044 0.149 1423 Planarity : 0.004 0.043 1507 Dihedral : 4.726 23.078 1249 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.93 % Allowed : 9.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1162 helix: 0.77 (0.27), residues: 416 sheet: 0.03 (0.31), residues: 265 loop : -0.39 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 18 TYR 0.015 0.002 TYR H 60 PHE 0.015 0.002 PHE C 199 TRP 0.016 0.001 TRP C 211 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8705) covalent geometry : angle 0.65910 (11876) SS BOND : bond 0.01064 ( 5) SS BOND : angle 1.54283 ( 10) hydrogen bonds : bond 0.04291 ( 446) hydrogen bonds : angle 5.07433 ( 1236) *********************** 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 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6898 (t) cc_final: 0.6628 (t) REVERT: B 207 SER cc_start: 0.7238 (t) cc_final: 0.6717 (m) REVERT: B 255 CYS cc_start: 0.8159 (t) cc_final: 0.7938 (t) REVERT: B 322 HIS cc_start: 0.7798 (t-90) cc_final: 0.7475 (t-90) REVERT: C 223 THR cc_start: 0.7725 (p) cc_final: 0.7522 (p) REVERT: D 29 ASN cc_start: 0.8519 (t0) cc_final: 0.8189 (t0) REVERT: G 36 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7116 (t0) REVERT: H 230 MET cc_start: 0.8385 (ttt) cc_final: 0.8118 (ttt) outliers start: 16 outliers final: 10 residues processed: 172 average time/residue: 0.0781 time to fit residues: 19.1403 Evaluate side-chains 170 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 C residue 265 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 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120787 restraints weight = 12582.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120179 restraints weight = 20982.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119296 restraints weight = 19329.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117931 restraints weight = 19264.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117590 restraints weight = 19722.262| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1852 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= 0.154 Angle : 0.621 8.515 11886 Z= 0.322 Chirality : 0.043 0.145 1423 Planarity : 0.004 0.041 1507 Dihedral : 4.499 23.609 1249 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.26 % Allowed : 11.46 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1162 helix: 0.80 (0.27), residues: 416 sheet: -0.04 (0.31), residues: 266 loop : -0.40 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.014 0.002 TYR C 105 PHE 0.016 0.002 PHE C 199 TRP 0.018 0.001 TRP C 211 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8705) covalent geometry : angle 0.62031 (11876) SS BOND : bond 0.00549 ( 5) SS BOND : angle 1.26154 ( 10) hydrogen bonds : bond 0.03955 ( 446) hydrogen bonds : angle 4.85843 ( 1236) *********************** 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 197 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.251 Fit side-chains REVERT: B 14 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 255 CYS cc_start: 0.8036 (t) cc_final: 0.7780 (t) REVERT: B 322 HIS cc_start: 0.7786 (t-90) cc_final: 0.7409 (t-90) REVERT: C 234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: G 36 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7099 (t0) REVERT: H 192 MET cc_start: 0.8068 (tmm) cc_final: 0.7699 (tmm) REVERT: H 230 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (ttt) outliers start: 27 outliers final: 20 residues processed: 178 average time/residue: 0.0657 time to fit residues: 16.9831 Evaluate side-chains 179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 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 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR 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 36 ASP Chi-restraints excluded: chain G residue 54 VAL 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 77 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120292 restraints weight = 12939.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116712 restraints weight = 21945.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116892 restraints weight = 22123.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117042 restraints weight = 20207.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116987 restraints weight = 16404.874| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2134 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 : 0.604 8.179 11886 Z= 0.311 Chirality : 0.042 0.140 1423 Planarity : 0.004 0.043 1507 Dihedral : 4.348 23.329 1249 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.26 % Allowed : 14.60 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1162 helix: 0.88 (0.27), residues: 415 sheet: -0.13 (0.31), residues: 265 loop : -0.34 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.012 0.001 TYR C 105 PHE 0.014 0.001 PHE B 190 TRP 0.015 0.001 TRP C 211 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8705) covalent geometry : angle 0.60330 (11876) SS BOND : bond 0.00432 ( 5) SS BOND : angle 1.17493 ( 10) hydrogen bonds : bond 0.03644 ( 446) hydrogen bonds : angle 4.73923 ( 1236) *********************** 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 190 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 99 HIS cc_start: 0.6391 (m-70) cc_final: 0.6074 (m90) REVERT: B 14 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 207 SER cc_start: 0.7471 (t) cc_final: 0.6962 (m) REVERT: B 255 CYS cc_start: 0.8013 (t) cc_final: 0.7734 (t) REVERT: B 322 HIS cc_start: 0.7722 (t-90) cc_final: 0.7458 (t-90) REVERT: C 234 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: H 192 MET cc_start: 0.8038 (tmm) cc_final: 0.7664 (tmm) REVERT: H 204 SER cc_start: 0.8524 (t) cc_final: 0.8201 (m) REVERT: H 230 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8089 (ttt) outliers start: 27 outliers final: 19 residues processed: 172 average time/residue: 0.0699 time to fit residues: 17.6513 Evaluate side-chains 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 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 G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3578 r_free = 0.3578 target = 0.138016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117289 restraints weight = 13132.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115222 restraints weight = 27472.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115048 restraints weight = 27268.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114687 restraints weight = 22283.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115131 restraints weight = 21390.714| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8710 Z= 0.189 Angle : 0.639 8.506 11886 Z= 0.333 Chirality : 0.044 0.151 1423 Planarity : 0.004 0.045 1507 Dihedral : 4.505 23.819 1249 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.07 % Allowed : 15.56 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1162 helix: 0.90 (0.27), residues: 416 sheet: -0.28 (0.31), residues: 263 loop : -0.53 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 229 TYR 0.015 0.002 TYR C 105 PHE 0.020 0.002 PHE A 255 TRP 0.017 0.001 TRP C 211 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8705) covalent geometry : angle 0.63827 (11876) SS BOND : bond 0.00635 ( 5) SS BOND : angle 1.20818 ( 10) hydrogen bonds : bond 0.04000 ( 446) hydrogen bonds : angle 4.87459 ( 1236) *********************** 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 196 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.239 Fit side-chains REVERT: A 139 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7641 (t80) REVERT: B 14 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 207 SER cc_start: 0.7556 (t) cc_final: 0.7023 (m) REVERT: B 322 HIS cc_start: 0.7838 (t-90) cc_final: 0.7307 (t-90) REVERT: C 211 TRP cc_start: 0.9144 (OUTLIER) cc_final: 0.8835 (m100) REVERT: C 234 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: H 204 SER cc_start: 0.8669 (t) cc_final: 0.8319 (m) REVERT: H 230 MET cc_start: 0.8543 (ttt) cc_final: 0.8325 (ttt) outliers start: 42 outliers final: 31 residues processed: 175 average time/residue: 0.0651 time to fit residues: 16.7075 Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 227 LEU 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 61 MET 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 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.0170 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 0.0000 chunk 72 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113608 restraints weight = 12588.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112257 restraints weight = 20676.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112039 restraints weight = 20887.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111022 restraints weight = 17146.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111110 restraints weight = 16873.913| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8710 Z= 0.134 Angle : 0.601 8.723 11886 Z= 0.310 Chirality : 0.042 0.134 1423 Planarity : 0.004 0.046 1507 Dihedral : 4.319 23.425 1249 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.95 % Allowed : 17.37 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1162 helix: 1.01 (0.27), residues: 413 sheet: -0.40 (0.30), residues: 269 loop : -0.44 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 229 TYR 0.011 0.001 TYR A 301 PHE 0.022 0.001 PHE H 212 TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8705) covalent geometry : angle 0.60068 (11876) SS BOND : bond 0.00361 ( 5) SS BOND : angle 1.11858 ( 10) hydrogen bonds : bond 0.03519 ( 446) hydrogen bonds : angle 4.71036 ( 1236) *********************** 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 202 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.255 Fit side-chains REVERT: A 139 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 14 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 207 SER cc_start: 0.7529 (t) cc_final: 0.7001 (m) REVERT: B 322 HIS cc_start: 0.7804 (t-90) cc_final: 0.7422 (t-90) REVERT: C 147 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8747 (t) REVERT: C 211 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8802 (m100) REVERT: C 234 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: H 138 ILE cc_start: 0.6452 (pt) cc_final: 0.6186 (pt) REVERT: H 204 SER cc_start: 0.8536 (t) cc_final: 0.8194 (m) REVERT: H 223 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7311 (t0) REVERT: H 230 MET cc_start: 0.8579 (ttt) cc_final: 0.8329 (ttt) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 0.0717 time to fit residues: 18.4785 Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 58 ILE 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 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 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 Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 223 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 312 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 340 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110598 restraints weight = 12961.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109457 restraints weight = 20819.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109665 restraints weight = 21704.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109121 restraints weight = 16905.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109227 restraints weight = 16840.404| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8710 Z= 0.203 Angle : 0.674 13.751 11886 Z= 0.346 Chirality : 0.045 0.148 1423 Planarity : 0.004 0.052 1507 Dihedral : 4.556 23.646 1249 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.67 % Allowed : 17.97 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1162 helix: 0.94 (0.27), residues: 417 sheet: -0.45 (0.31), residues: 256 loop : -0.60 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 229 TYR 0.015 0.002 TYR C 105 PHE 0.020 0.002 PHE C 199 TRP 0.019 0.002 TRP C 211 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8705) covalent geometry : angle 0.67342 (11876) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.37791 ( 10) hydrogen bonds : bond 0.04047 ( 446) hydrogen bonds : angle 4.86667 ( 1236) *********************** 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 195 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.338 Fit side-chains REVERT: A 139 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 14 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 207 SER cc_start: 0.7533 (t) cc_final: 0.6992 (m) REVERT: B 322 HIS cc_start: 0.7871 (t-90) cc_final: 0.7346 (t-90) REVERT: B 341 ASP cc_start: 0.8903 (t0) cc_final: 0.8632 (t70) REVERT: C 211 TRP cc_start: 0.9155 (OUTLIER) cc_final: 0.8862 (m100) REVERT: C 234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: G 44 HIS cc_start: 0.8209 (m90) cc_final: 0.8002 (m-70) REVERT: H 230 MET cc_start: 0.8597 (ttt) cc_final: 0.8388 (ttt) outliers start: 47 outliers final: 35 residues processed: 171 average time/residue: 0.0793 time to fit residues: 19.4036 Evaluate side-chains 183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 264 VAL 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 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 C residue 340 ASN 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 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.131900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111153 restraints weight = 12736.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109817 restraints weight = 20327.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109687 restraints weight = 21511.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109272 restraints weight = 17398.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109101 restraints weight = 16376.768| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8710 Z= 0.189 Angle : 0.672 12.164 11886 Z= 0.345 Chirality : 0.044 0.148 1423 Planarity : 0.005 0.069 1507 Dihedral : 4.597 24.127 1249 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.07 % Allowed : 18.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.25), residues: 1162 helix: 0.95 (0.27), residues: 417 sheet: -0.54 (0.30), residues: 262 loop : -0.69 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 229 TYR 0.013 0.002 TYR C 105 PHE 0.017 0.002 PHE C 199 TRP 0.018 0.001 TRP C 211 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8705) covalent geometry : angle 0.67063 (11876) SS BOND : bond 0.00538 ( 5) SS BOND : angle 1.44598 ( 10) hydrogen bonds : bond 0.03949 ( 446) hydrogen bonds : angle 4.85590 ( 1236) *********************** 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 192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.257 Fit side-chains REVERT: A 139 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7676 (t80) REVERT: B 14 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 207 SER cc_start: 0.7531 (t) cc_final: 0.6983 (m) REVERT: B 322 HIS cc_start: 0.7829 (t-90) cc_final: 0.7351 (t-90) REVERT: B 341 ASP cc_start: 0.8904 (t0) cc_final: 0.8658 (t70) REVERT: C 211 TRP cc_start: 0.9132 (OUTLIER) cc_final: 0.8866 (m100) REVERT: C 234 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: G 11 GLN cc_start: 0.7608 (pp30) cc_final: 0.7158 (pp30) REVERT: H 138 ILE cc_start: 0.6565 (pt) cc_final: 0.6238 (pt) REVERT: H 230 MET cc_start: 0.8606 (ttt) cc_final: 0.8334 (ttt) outliers start: 42 outliers final: 37 residues processed: 168 average time/residue: 0.0719 time to fit residues: 17.5082 Evaluate side-chains 186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 227 LEU 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 80 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 218 CYS 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 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 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.140174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120334 restraints weight = 12741.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118657 restraints weight = 25021.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119296 restraints weight = 24197.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118979 restraints weight = 19287.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118896 restraints weight = 17931.700| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8710 Z= 0.163 Angle : 0.687 19.233 11886 Z= 0.344 Chirality : 0.044 0.150 1423 Planarity : 0.004 0.053 1507 Dihedral : 4.469 24.037 1249 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.55 % Allowed : 18.46 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.25), residues: 1162 helix: 0.97 (0.27), residues: 417 sheet: -0.62 (0.30), residues: 264 loop : -0.66 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 229 TYR 0.012 0.002 TYR A 301 PHE 0.016 0.002 PHE A 139 TRP 0.016 0.001 TRP C 211 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8705) covalent geometry : angle 0.68593 (11876) SS BOND : bond 0.00463 ( 5) SS BOND : angle 1.38941 ( 10) hydrogen bonds : bond 0.03757 ( 446) hydrogen bonds : angle 4.78704 ( 1236) *********************** 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 199 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.227 Fit side-chains REVERT: A 139 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 14 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 207 SER cc_start: 0.7548 (t) cc_final: 0.6929 (m) REVERT: B 322 HIS cc_start: 0.7775 (t-90) cc_final: 0.7402 (t-90) REVERT: B 341 ASP cc_start: 0.8852 (t0) cc_final: 0.8593 (t70) REVERT: C 211 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.8837 (m100) REVERT: C 234 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: G 11 GLN cc_start: 0.7473 (pp30) cc_final: 0.7049 (pp30) REVERT: H 138 ILE cc_start: 0.6448 (pt) cc_final: 0.6210 (pt) REVERT: H 230 MET cc_start: 0.8521 (ttt) cc_final: 0.8294 (ttt) REVERT: H 231 GLN cc_start: 0.8519 (pp30) cc_final: 0.8274 (pp30) outliers start: 46 outliers final: 39 residues processed: 171 average time/residue: 0.0768 time to fit residues: 18.8655 Evaluate side-chains 189 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 57 LEU 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 227 LEU Chi-restraints excluded: chain A residue 264 VAL 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 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 218 CYS 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 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 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 44 HIS 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 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 99 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122966 restraints weight = 12886.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115510 restraints weight = 19698.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114218 restraints weight = 21758.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114234 restraints weight = 19092.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114851 restraints weight = 16398.722| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8710 Z= 0.135 Angle : 0.665 17.735 11886 Z= 0.334 Chirality : 0.043 0.143 1423 Planarity : 0.004 0.061 1507 Dihedral : 4.326 24.685 1249 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.46 % Allowed : 19.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1162 helix: 1.09 (0.27), residues: 414 sheet: -0.70 (0.30), residues: 270 loop : -0.51 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 229 TYR 0.012 0.001 TYR A 301 PHE 0.017 0.001 PHE A 139 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8705) covalent geometry : angle 0.66433 (11876) SS BOND : bond 0.00379 ( 5) SS BOND : angle 1.24397 ( 10) hydrogen bonds : bond 0.03492 ( 446) hydrogen bonds : angle 4.69657 ( 1236) ********************** 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 191 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.230 Fit side-chains REVERT: A 139 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 14 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 207 SER cc_start: 0.7593 (t) cc_final: 0.7077 (m) REVERT: B 322 HIS cc_start: 0.7902 (t-90) cc_final: 0.7462 (t-90) REVERT: B 341 ASP cc_start: 0.9035 (t0) cc_final: 0.8730 (t70) REVERT: C 211 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8780 (m100) REVERT: C 234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: G 11 GLN cc_start: 0.8323 (pp30) cc_final: 0.7972 (pp30) REVERT: H 138 ILE cc_start: 0.6052 (pt) cc_final: 0.5710 (pt) REVERT: H 204 SER cc_start: 0.8644 (t) cc_final: 0.8231 (m) REVERT: H 230 MET cc_start: 0.8410 (ttt) cc_final: 0.8169 (ttt) outliers start: 37 outliers final: 31 residues processed: 169 average time/residue: 0.0779 time to fit residues: 18.7356 Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 57 LEU 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 139 PHE Chi-restraints excluded: chain A residue 227 LEU 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 148 CYS Chi-restraints excluded: chain C residue 179 THR 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 218 CYS 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 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 44 HIS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 111 optimal weight: 0.0010 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** 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 340 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 = 0.3592 r_free = 0.3592 target = 0.139081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120150 restraints weight = 12905.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112280 restraints weight = 21433.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112706 restraints weight = 25300.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112499 restraints weight = 22086.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113354 restraints weight = 18434.434| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8710 Z= 0.149 Angle : 0.682 19.114 11886 Z= 0.341 Chirality : 0.043 0.164 1423 Planarity : 0.004 0.053 1507 Dihedral : 4.301 29.401 1249 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.98 % Allowed : 20.27 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.25), residues: 1162 helix: 1.18 (0.27), residues: 408 sheet: -0.73 (0.30), residues: 270 loop : -0.47 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 229 TYR 0.015 0.001 TYR A 301 PHE 0.022 0.002 PHE H 212 TRP 0.022 0.001 TRP C 339 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8705) covalent geometry : angle 0.68167 (11876) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.04454 ( 10) hydrogen bonds : bond 0.03617 ( 446) hydrogen bonds : angle 4.74295 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1332.27 seconds wall clock time: 23 minutes 46.08 seconds (1426.08 seconds total)