Starting phenix.real_space_refine on Mon May 12 17:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.map" model { file = "/net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jis_36326/05_2025/8jis_36326.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 57 5.16 5 C 5828 2.51 5 N 1574 2.21 5 O 1699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9158 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3104 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 5.69, per 1000 atoms: 0.62 Number of scatterers: 9158 At special positions: 0 Unit cell: (86.751, 95.319, 173.502, 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 57 16.00 O 1699 8.00 N 1574 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 40.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.643A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.723A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.648A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.796A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 4.051A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.074A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.655A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 139 through 169 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.683A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 216 through 221 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.584A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix removed outlier: 3.963A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.830A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.587A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 354 removed outlier: 4.145A pdb=" N CYS R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 377 through 404 removed outlier: 3.762A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.814A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.630A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.763A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.742A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.978A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.734A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.980A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.516A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 112 through 114 removed outlier: 4.646A pdb=" N ASP R 114 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 443 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1496 1.31 - 1.44: 2689 1.44 - 1.56: 5100 1.56 - 1.69: 1 1.69 - 1.82: 78 Bond restraints: 9364 Sorted by residual: bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.331 1.385 -0.054 8.70e-03 1.32e+04 3.87e+01 bond pdb=" C GLU A 311 " pdb=" O GLU A 311 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.26e-02 6.30e+03 2.01e+01 bond pdb=" CA ALA R 368 " pdb=" C ALA R 368 " ideal model delta sigma weight residual 1.523 1.487 0.036 8.20e-03 1.49e+04 1.97e+01 bond pdb=" CA ALA B 328 " pdb=" C ALA B 328 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.18e-02 7.18e+03 1.90e+01 bond pdb=" CA SER B 191 " pdb=" C SER B 191 " ideal model delta sigma weight residual 1.520 1.472 0.048 1.12e-02 7.97e+03 1.83e+01 ... (remaining 9359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 12304 2.97 - 5.93: 343 5.93 - 8.90: 65 8.90 - 11.86: 10 11.86 - 14.83: 2 Bond angle restraints: 12724 Sorted by residual: angle pdb=" N HIS R 374 " pdb=" CA HIS R 374 " pdb=" C HIS R 374 " ideal model delta sigma weight residual 114.12 99.29 14.83 1.39e+00 5.18e-01 1.14e+02 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 113.19 101.25 11.94 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 112.34 101.39 10.95 1.30e+00 5.92e-01 7.09e+01 angle pdb=" N ILE R 345 " pdb=" CA ILE R 345 " pdb=" C ILE R 345 " ideal model delta sigma weight residual 110.42 102.95 7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" N SER R 93 " pdb=" CA SER R 93 " pdb=" C SER R 93 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 ... (remaining 12719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4676 17.50 - 35.01: 523 35.01 - 52.51: 231 52.51 - 70.02: 75 70.02 - 87.52: 20 Dihedral angle restraints: 5525 sinusoidal: 2097 harmonic: 3428 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 -179.90 -87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS R 46 " pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " ideal model delta sinusoidal sigma weight residual -73.00 -6.57 -66.43 1 2.00e+01 2.50e-03 1.44e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1140 0.081 - 0.161: 214 0.161 - 0.242: 52 0.242 - 0.322: 18 0.322 - 0.402: 7 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA THR N 111 " pdb=" N THR N 111 " pdb=" C THR N 111 " pdb=" CB THR N 111 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA SER B 136 " pdb=" N SER B 136 " pdb=" C SER B 136 " pdb=" CB SER B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1428 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 90 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PRO R 90 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO R 90 " -0.024 2.00e-02 2.50e+03 pdb=" N TRP R 91 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 280 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C PRO A 280 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO A 280 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 42 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLU G 42 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU G 42 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA G 43 " 0.018 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2581 2.79 - 3.32: 8268 3.32 - 3.85: 15774 3.85 - 4.37: 18580 4.37 - 4.90: 30732 Nonbonded interactions: 75935 Sorted by model distance: nonbonded pdb=" OD2 ASP A 26 " pdb=" NZ LYS B 78 " model vdw 2.266 3.120 nonbonded pdb=" O SER A 44 " pdb=" OG SER A 44 " model vdw 2.294 3.040 nonbonded pdb=" O LEU R 349 " pdb=" OG1 THR R 353 " model vdw 2.303 3.040 nonbonded pdb=" N HIS R 374 " pdb=" N ALA R 375 " model vdw 2.320 2.560 nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS B 89 " model vdw 2.346 3.120 ... (remaining 75930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.009 0.057 9369 Z= 0.659 Angle : 1.200 14.827 12734 Z= 0.787 Chirality : 0.077 0.402 1431 Planarity : 0.005 0.067 1619 Dihedral : 19.441 87.521 3292 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.91 % Favored : 92.23 % Rotamer: Outliers : 14.75 % Allowed : 17.86 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1158 helix: 0.00 (0.25), residues: 418 sheet: -0.37 (0.33), residues: 215 loop : -1.64 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 211 HIS 0.006 0.001 HIS A 324 PHE 0.024 0.002 PHE B 199 TYR 0.027 0.002 TYR R 148 ARG 0.008 0.001 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.22854 ( 443) hydrogen bonds : angle 7.47247 ( 1275) SS BOND : bond 0.00619 ( 5) SS BOND : angle 1.57858 ( 10) covalent geometry : bond 0.00921 ( 9364) covalent geometry : angle 1.19965 (12724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 171 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (m) REVERT: A 324 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (p-80) REVERT: A 359 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 175 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7625 (mp10) REVERT: B 186 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: B 228 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: B 292 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: P 21 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8520 (tm-30) REVERT: G 21 MET cc_start: 0.6642 (ppp) cc_final: 0.6419 (ppp) REVERT: G 46 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8699 (tppt) REVERT: G 50 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (mm) REVERT: N 34 MET cc_start: 0.8307 (mmm) cc_final: 0.8043 (mmm) REVERT: N 46 GLU cc_start: 0.8158 (pt0) cc_final: 0.7764 (mm-30) REVERT: N 53 GLN cc_start: 0.8153 (mp10) cc_final: 0.7910 (mp10) REVERT: R 31 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8264 (p) REVERT: R 42 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: R 107 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: R 261 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6972 (t) REVERT: R 346 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5609 (mmtt) REVERT: R 351 LYS cc_start: 0.8762 (tmtp) cc_final: 0.8389 (tptp) REVERT: R 369 PHE cc_start: 0.8034 (m-80) cc_final: 0.7719 (m-80) outliers start: 142 outliers final: 20 residues processed: 272 average time/residue: 1.1872 time to fit residues: 344.7934 Evaluate side-chains 173 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 190 GLN B 230 ASN G 44 HIS R 63 ASN R 180 HIS R 406 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086227 restraints weight = 15289.205| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.07 r_work: 0.3048 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9369 Z= 0.150 Angle : 0.649 12.226 12734 Z= 0.345 Chirality : 0.042 0.159 1431 Planarity : 0.005 0.064 1619 Dihedral : 8.547 85.235 1332 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.68 % Rotamer: Outliers : 6.02 % Allowed : 23.68 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1158 helix: 1.36 (0.25), residues: 442 sheet: 0.19 (0.34), residues: 211 loop : -1.44 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 110 HIS 0.004 0.001 HIS A 197 PHE 0.018 0.002 PHE A 307 TYR 0.024 0.001 TYR R 148 ARG 0.013 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 443) hydrogen bonds : angle 4.86222 ( 1275) SS BOND : bond 0.00207 ( 5) SS BOND : angle 1.47844 ( 10) covalent geometry : bond 0.00329 ( 9364) covalent geometry : angle 0.64807 (12724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8711 (mt0) cc_final: 0.8430 (mt0) REVERT: A 209 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8671 (ptp-170) REVERT: B 59 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: B 175 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7824 (mp10) REVERT: B 186 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: B 217 MET cc_start: 0.8967 (pmt) cc_final: 0.8558 (pmm) REVERT: P 21 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8548 (tm-30) REVERT: G 21 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6297 (ppp) REVERT: G 46 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8580 (tppt) REVERT: G 50 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7420 (mm) REVERT: N 46 GLU cc_start: 0.8242 (pt0) cc_final: 0.7978 (mm-30) REVERT: N 53 GLN cc_start: 0.8235 (mp10) cc_final: 0.7867 (mp10) REVERT: N 122 THR cc_start: 0.7344 (m) cc_final: 0.6926 (p) REVERT: R 31 SER cc_start: 0.9070 (m) cc_final: 0.8809 (p) REVERT: R 42 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: R 107 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6804 (pm20) REVERT: R 112 GLN cc_start: 0.7553 (mm110) cc_final: 0.7144 (mm110) REVERT: R 261 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6602 (t) REVERT: R 346 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.5211 (mmtt) REVERT: R 351 LYS cc_start: 0.8723 (tmtp) cc_final: 0.8363 (tptp) REVERT: R 370 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4859 (t) REVERT: R 371 MET cc_start: 0.8595 (mpp) cc_final: 0.8082 (mpp) outliers start: 58 outliers final: 16 residues processed: 205 average time/residue: 1.1793 time to fit residues: 258.2104 Evaluate side-chains 168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 230 ASN R 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084562 restraints weight = 15179.904| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.10 r_work: 0.3033 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9369 Z= 0.159 Angle : 0.590 8.291 12734 Z= 0.316 Chirality : 0.041 0.153 1431 Planarity : 0.004 0.050 1619 Dihedral : 7.049 81.839 1307 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.30 % Allowed : 25.44 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1158 helix: 1.81 (0.25), residues: 440 sheet: 0.26 (0.34), residues: 225 loop : -1.21 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.002 0.001 HIS B 225 PHE 0.016 0.001 PHE A 307 TYR 0.025 0.001 TYR R 148 ARG 0.006 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 443) hydrogen bonds : angle 4.51053 ( 1275) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.16716 ( 10) covalent geometry : bond 0.00363 ( 9364) covalent geometry : angle 0.58942 (12724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 209 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (ptp-170) REVERT: A 297 GLU cc_start: 0.8952 (pt0) cc_final: 0.8723 (pp20) REVERT: B 37 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6543 (pp) REVERT: B 59 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: B 175 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8010 (mp10) REVERT: B 217 MET cc_start: 0.9076 (pmt) cc_final: 0.8672 (pmm) REVERT: B 336 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8882 (mp) REVERT: P 16 GLU cc_start: 0.8709 (tp30) cc_final: 0.8277 (mm-30) REVERT: P 17 GLN cc_start: 0.8579 (tt0) cc_final: 0.8237 (tt0) REVERT: P 21 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8562 (tm-30) REVERT: G 38 MET cc_start: 0.7693 (mtp) cc_final: 0.7477 (mtm) REVERT: N 46 GLU cc_start: 0.8371 (pt0) cc_final: 0.8023 (mm-30) REVERT: N 53 GLN cc_start: 0.8395 (mp10) cc_final: 0.7846 (mp10) REVERT: N 122 THR cc_start: 0.7369 (m) cc_final: 0.7023 (p) REVERT: R 42 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: R 107 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: R 112 GLN cc_start: 0.7837 (mm110) cc_final: 0.7396 (mm110) REVERT: R 221 GLN cc_start: 0.8014 (mm110) cc_final: 0.7747 (mm110) REVERT: R 371 MET cc_start: 0.8574 (mpp) cc_final: 0.8103 (mpp) outliers start: 51 outliers final: 20 residues processed: 188 average time/residue: 1.2148 time to fit residues: 243.5158 Evaluate side-chains 162 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 213 GLN Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 37 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.125775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081568 restraints weight = 15390.741| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.07 r_work: 0.2946 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9369 Z= 0.169 Angle : 0.589 8.031 12734 Z= 0.314 Chirality : 0.041 0.153 1431 Planarity : 0.004 0.052 1619 Dihedral : 6.442 82.060 1291 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 5.61 % Allowed : 24.51 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1158 helix: 2.09 (0.25), residues: 434 sheet: 0.40 (0.35), residues: 225 loop : -1.10 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 39 HIS 0.002 0.001 HIS B 225 PHE 0.014 0.001 PHE A 189 TYR 0.024 0.001 TYR R 148 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 443) hydrogen bonds : angle 4.37813 ( 1275) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.17010 ( 10) covalent geometry : bond 0.00390 ( 9364) covalent geometry : angle 0.58863 (12724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8280 (mm-30) REVERT: A 281 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: A 297 GLU cc_start: 0.8936 (pt0) cc_final: 0.8689 (pp20) REVERT: B 37 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.6628 (pt) REVERT: B 59 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: B 175 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7991 (mp10) REVERT: B 217 MET cc_start: 0.9097 (pmt) cc_final: 0.8661 (pmm) REVERT: B 220 GLN cc_start: 0.8404 (mp10) cc_final: 0.8204 (mp10) REVERT: B 336 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8807 (mt) REVERT: P 15 ASP cc_start: 0.8281 (t0) cc_final: 0.8029 (t0) REVERT: P 16 GLU cc_start: 0.8639 (tp30) cc_final: 0.8201 (mm-30) REVERT: P 17 GLN cc_start: 0.8574 (tt0) cc_final: 0.8320 (tp40) REVERT: P 21 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8509 (tm-30) REVERT: G 38 MET cc_start: 0.7673 (mtp) cc_final: 0.7460 (mtm) REVERT: N 46 GLU cc_start: 0.8312 (pt0) cc_final: 0.7980 (mm-30) REVERT: N 53 GLN cc_start: 0.8350 (mp10) cc_final: 0.7784 (mp10) REVERT: N 65 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8903 (ttpp) REVERT: N 120 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8296 (mm-40) REVERT: N 122 THR cc_start: 0.7196 (m) cc_final: 0.6800 (p) REVERT: R 31 SER cc_start: 0.9020 (m) cc_final: 0.8810 (p) REVERT: R 37 GLN cc_start: 0.9101 (pp30) cc_final: 0.8886 (pp30) REVERT: R 112 GLN cc_start: 0.7889 (mm110) cc_final: 0.7611 (mm110) REVERT: R 371 MET cc_start: 0.8651 (mpp) cc_final: 0.8046 (mpp) outliers start: 54 outliers final: 26 residues processed: 190 average time/residue: 1.1519 time to fit residues: 233.9117 Evaluate side-chains 168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 213 GLN Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 3 GLN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081354 restraints weight = 15435.003| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.06 r_work: 0.2924 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9369 Z= 0.176 Angle : 0.589 8.691 12734 Z= 0.314 Chirality : 0.041 0.153 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.607 82.344 1282 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 4.57 % Allowed : 25.23 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1158 helix: 2.14 (0.25), residues: 435 sheet: 0.45 (0.35), residues: 225 loop : -1.01 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 39 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.023 0.001 TYR R 148 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 443) hydrogen bonds : angle 4.34288 ( 1275) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.27259 ( 10) covalent geometry : bond 0.00408 ( 9364) covalent geometry : angle 0.58855 (12724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 281 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: B 37 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.6667 (pt) REVERT: B 59 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 127 LYS cc_start: 0.8675 (mptt) cc_final: 0.8461 (tppp) REVERT: B 175 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7896 (mp10) REVERT: B 186 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: B 217 MET cc_start: 0.9100 (pmt) cc_final: 0.8616 (pmm) REVERT: B 336 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8816 (mt) REVERT: P 15 ASP cc_start: 0.8239 (t0) cc_final: 0.7974 (t0) REVERT: P 16 GLU cc_start: 0.8673 (tp30) cc_final: 0.8458 (tp30) REVERT: P 17 GLN cc_start: 0.8590 (tt0) cc_final: 0.8307 (tp40) REVERT: P 21 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8520 (tm-30) REVERT: N 46 GLU cc_start: 0.8333 (pt0) cc_final: 0.7978 (mm-30) REVERT: N 53 GLN cc_start: 0.8362 (mp10) cc_final: 0.7795 (mp10) REVERT: N 87 LYS cc_start: 0.8282 (mttm) cc_final: 0.8022 (ptpp) REVERT: N 120 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8499 (mm-40) REVERT: N 122 THR cc_start: 0.7189 (m) cc_final: 0.6773 (p) REVERT: R 31 SER cc_start: 0.8995 (m) cc_final: 0.8782 (p) REVERT: R 37 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8906 (pp30) REVERT: R 112 GLN cc_start: 0.8163 (mm110) cc_final: 0.7875 (mm110) REVERT: R 371 MET cc_start: 0.8643 (mpp) cc_final: 0.8112 (mpp) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 1.1782 time to fit residues: 224.3898 Evaluate side-chains 167 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 0.0670 chunk 26 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.126694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082491 restraints weight = 15409.216| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.08 r_work: 0.2944 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9369 Z= 0.129 Angle : 0.574 8.920 12734 Z= 0.305 Chirality : 0.040 0.144 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.487 81.534 1282 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 4.47 % Allowed : 25.86 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1158 helix: 2.27 (0.25), residues: 434 sheet: 0.56 (0.35), residues: 223 loop : -1.00 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.001 0.000 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.021 0.001 TYR R 148 ARG 0.006 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 443) hydrogen bonds : angle 4.26131 ( 1275) SS BOND : bond 0.00194 ( 5) SS BOND : angle 1.29655 ( 10) covalent geometry : bond 0.00296 ( 9364) covalent geometry : angle 0.57266 (12724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 281 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: A 359 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8446 (mt-10) REVERT: B 37 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6693 (pt) REVERT: B 59 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: B 127 LYS cc_start: 0.8678 (mptt) cc_final: 0.8454 (tppp) REVERT: B 175 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7872 (mp10) REVERT: B 186 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: B 217 MET cc_start: 0.9125 (pmt) cc_final: 0.8690 (pmm) REVERT: B 280 LYS cc_start: 0.8901 (tppp) cc_final: 0.8498 (tptp) REVERT: B 336 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8778 (mp) REVERT: P 15 ASP cc_start: 0.8236 (t0) cc_final: 0.7911 (t0) REVERT: P 16 GLU cc_start: 0.8678 (tp30) cc_final: 0.8206 (mm-30) REVERT: P 17 GLN cc_start: 0.8607 (tt0) cc_final: 0.8331 (tp40) REVERT: P 21 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8517 (tm-30) REVERT: G 21 MET cc_start: 0.6746 (tmm) cc_final: 0.6480 (ttm) REVERT: N 46 GLU cc_start: 0.8279 (pt0) cc_final: 0.8004 (mm-30) REVERT: N 53 GLN cc_start: 0.8451 (mp10) cc_final: 0.7953 (mp10) REVERT: N 120 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8512 (mm-40) REVERT: N 122 THR cc_start: 0.7111 (m) cc_final: 0.6746 (p) REVERT: R 31 SER cc_start: 0.9039 (m) cc_final: 0.8795 (p) REVERT: R 112 GLN cc_start: 0.7903 (mm110) cc_final: 0.7604 (mm110) REVERT: R 371 MET cc_start: 0.8628 (mpp) cc_final: 0.8037 (mpp) outliers start: 43 outliers final: 24 residues processed: 178 average time/residue: 1.2188 time to fit residues: 231.5782 Evaluate side-chains 163 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 79 optimal weight: 40.0000 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 216 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080309 restraints weight = 15529.483| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.08 r_work: 0.2906 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9369 Z= 0.220 Angle : 0.638 12.841 12734 Z= 0.341 Chirality : 0.043 0.216 1431 Planarity : 0.004 0.054 1619 Dihedral : 5.640 81.041 1282 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.98 % Allowed : 25.55 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1158 helix: 2.20 (0.25), residues: 433 sheet: 0.50 (0.35), residues: 223 loop : -0.98 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.002 0.001 HIS B 225 PHE 0.016 0.001 PHE N 108 TYR 0.024 0.002 TYR R 148 ARG 0.006 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 443) hydrogen bonds : angle 4.36646 ( 1275) SS BOND : bond 0.00266 ( 5) SS BOND : angle 2.89507 ( 10) covalent geometry : bond 0.00512 ( 9364) covalent geometry : angle 0.63328 (12724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 281 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 297 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: B 37 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.6890 (pp) REVERT: B 59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: B 127 LYS cc_start: 0.8740 (mptt) cc_final: 0.8513 (tppp) REVERT: B 175 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7859 (mp10) REVERT: B 186 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: B 217 MET cc_start: 0.9113 (pmt) cc_final: 0.8676 (pmm) REVERT: B 336 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8813 (mp) REVERT: P 15 ASP cc_start: 0.8210 (t0) cc_final: 0.7877 (t0) REVERT: P 16 GLU cc_start: 0.8711 (tp30) cc_final: 0.8467 (tp30) REVERT: P 17 GLN cc_start: 0.8590 (tt0) cc_final: 0.8351 (tp40) REVERT: P 21 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8578 (tm-30) REVERT: G 21 MET cc_start: 0.6860 (tmm) cc_final: 0.6605 (ttm) REVERT: N 46 GLU cc_start: 0.8335 (pt0) cc_final: 0.8009 (mm-30) REVERT: N 53 GLN cc_start: 0.8384 (mp10) cc_final: 0.7854 (mp10) REVERT: N 65 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8914 (ttpp) REVERT: N 87 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7849 (ptpp) REVERT: N 120 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8635 (mm-40) REVERT: N 122 THR cc_start: 0.7222 (m) cc_final: 0.6801 (p) REVERT: R 31 SER cc_start: 0.9042 (m) cc_final: 0.8767 (p) REVERT: R 112 GLN cc_start: 0.7565 (mm110) cc_final: 0.7302 (mm110) outliers start: 48 outliers final: 28 residues processed: 181 average time/residue: 1.1944 time to fit residues: 231.4028 Evaluate side-chains 169 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 422 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 0.0000 chunk 4 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 47 GLN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.083509 restraints weight = 15614.061| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.11 r_work: 0.2961 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9369 Z= 0.121 Angle : 0.591 11.095 12734 Z= 0.313 Chirality : 0.040 0.162 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.386 80.091 1282 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.74 % Allowed : 26.69 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1158 helix: 2.44 (0.25), residues: 431 sheet: 0.58 (0.34), residues: 225 loop : -1.02 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.001 0.000 HIS G 44 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR R 148 ARG 0.013 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 443) hydrogen bonds : angle 4.20969 ( 1275) SS BOND : bond 0.00474 ( 5) SS BOND : angle 2.43840 ( 10) covalent geometry : bond 0.00276 ( 9364) covalent geometry : angle 0.58732 (12724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 281 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: B 37 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.6789 (pp) REVERT: B 59 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 127 LYS cc_start: 0.8665 (mptt) cc_final: 0.8418 (tppp) REVERT: B 175 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7855 (mp10) REVERT: B 186 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: B 217 MET cc_start: 0.9147 (pmt) cc_final: 0.8716 (pmm) REVERT: B 228 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: B 280 LYS cc_start: 0.8881 (tppp) cc_final: 0.8482 (tptp) REVERT: B 336 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8775 (mp) REVERT: P 15 ASP cc_start: 0.8259 (t0) cc_final: 0.7900 (t0) REVERT: P 16 GLU cc_start: 0.8704 (tp30) cc_final: 0.8213 (mm-30) REVERT: P 17 GLN cc_start: 0.8538 (tt0) cc_final: 0.8296 (tp40) REVERT: P 21 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8504 (tm-30) REVERT: N 46 GLU cc_start: 0.8255 (pt0) cc_final: 0.8018 (mm-30) REVERT: N 53 GLN cc_start: 0.8420 (mp10) cc_final: 0.7742 (mp10) REVERT: N 87 LYS cc_start: 0.8136 (ptpp) cc_final: 0.7840 (ptpp) REVERT: N 120 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8511 (mm-40) REVERT: N 122 THR cc_start: 0.7108 (m) cc_final: 0.6802 (p) REVERT: R 31 SER cc_start: 0.9031 (m) cc_final: 0.8771 (p) REVERT: R 112 GLN cc_start: 0.7723 (mm110) cc_final: 0.7490 (mm110) outliers start: 36 outliers final: 19 residues processed: 180 average time/residue: 1.1559 time to fit residues: 222.3289 Evaluate side-chains 164 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 246 ASN R 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.126578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082455 restraints weight = 15334.235| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.07 r_work: 0.2962 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9369 Z= 0.148 Angle : 0.599 10.657 12734 Z= 0.319 Chirality : 0.041 0.145 1431 Planarity : 0.004 0.054 1619 Dihedral : 5.336 78.788 1281 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 2.80 % Allowed : 28.35 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1158 helix: 2.49 (0.24), residues: 428 sheet: 0.58 (0.34), residues: 225 loop : -1.02 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS G 44 PHE 0.013 0.001 PHE A 189 TYR 0.021 0.001 TYR R 148 ARG 0.008 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 443) hydrogen bonds : angle 4.22066 ( 1275) SS BOND : bond 0.00394 ( 5) SS BOND : angle 2.22635 ( 10) covalent geometry : bond 0.00346 ( 9364) covalent geometry : angle 0.59639 (12724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 281 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: B 37 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.6807 (pp) REVERT: B 59 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: B 127 LYS cc_start: 0.8702 (mptt) cc_final: 0.8445 (tppp) REVERT: B 175 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7873 (mp10) REVERT: B 186 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: B 217 MET cc_start: 0.9176 (pmt) cc_final: 0.8730 (pmm) REVERT: B 226 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 228 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: B 280 LYS cc_start: 0.8906 (tppp) cc_final: 0.8451 (tptp) REVERT: B 336 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8790 (mp) REVERT: P 15 ASP cc_start: 0.8274 (t0) cc_final: 0.7973 (t0) REVERT: P 16 GLU cc_start: 0.8729 (tp30) cc_final: 0.8229 (mm-30) REVERT: P 17 GLN cc_start: 0.8472 (tt0) cc_final: 0.8260 (tp40) REVERT: P 21 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8561 (tm-30) REVERT: N 46 GLU cc_start: 0.8447 (pt0) cc_final: 0.8016 (mm-30) REVERT: N 53 GLN cc_start: 0.8437 (mp10) cc_final: 0.7723 (mp10) REVERT: N 87 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7582 (ptpp) REVERT: N 120 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8580 (mm-40) REVERT: N 122 THR cc_start: 0.7181 (m) cc_final: 0.6852 (p) REVERT: R 31 SER cc_start: 0.9054 (m) cc_final: 0.8797 (p) REVERT: R 112 GLN cc_start: 0.7567 (mm110) cc_final: 0.7322 (mm110) REVERT: R 415 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7500 (ptpt) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 1.2383 time to fit residues: 221.3893 Evaluate side-chains 161 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083019 restraints weight = 15597.636| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.11 r_work: 0.2973 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9369 Z= 0.135 Angle : 0.601 11.051 12734 Z= 0.320 Chirality : 0.041 0.144 1431 Planarity : 0.004 0.054 1619 Dihedral : 4.657 50.977 1278 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.70 % Allowed : 28.76 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1158 helix: 2.49 (0.24), residues: 431 sheet: 0.58 (0.34), residues: 225 loop : -0.99 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 PHE 0.018 0.001 PHE A 189 TYR 0.020 0.001 TYR R 148 ARG 0.010 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 443) hydrogen bonds : angle 4.18629 ( 1275) SS BOND : bond 0.00391 ( 5) SS BOND : angle 2.14890 ( 10) covalent geometry : bond 0.00315 ( 9364) covalent geometry : angle 0.59773 (12724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 37 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.6776 (pp) REVERT: B 59 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: B 186 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: B 217 MET cc_start: 0.9185 (pmt) cc_final: 0.8746 (pmm) REVERT: B 226 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 228 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: B 280 LYS cc_start: 0.8916 (tppp) cc_final: 0.8463 (tptp) REVERT: B 336 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8761 (mp) REVERT: P 15 ASP cc_start: 0.8280 (t0) cc_final: 0.7977 (t0) REVERT: P 16 GLU cc_start: 0.8765 (tp30) cc_final: 0.8263 (mm-30) REVERT: P 17 GLN cc_start: 0.8472 (tt0) cc_final: 0.8263 (tp40) REVERT: P 21 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8563 (tm-30) REVERT: N 53 GLN cc_start: 0.8513 (mp10) cc_final: 0.7839 (mp10) REVERT: N 120 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8577 (mm-40) REVERT: N 122 THR cc_start: 0.7163 (m) cc_final: 0.6826 (p) REVERT: R 31 SER cc_start: 0.9052 (m) cc_final: 0.8794 (p) REVERT: R 112 GLN cc_start: 0.7589 (mm110) cc_final: 0.7344 (mm110) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 1.2469 time to fit residues: 219.4516 Evaluate side-chains 162 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 246 ASN B 175 GLN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080284 restraints weight = 15497.387| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.08 r_work: 0.2925 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9369 Z= 0.214 Angle : 0.652 11.208 12734 Z= 0.346 Chirality : 0.043 0.155 1431 Planarity : 0.004 0.054 1619 Dihedral : 4.839 49.196 1278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.80 % Allowed : 28.76 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1158 helix: 2.38 (0.24), residues: 432 sheet: 0.53 (0.34), residues: 223 loop : -0.95 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.002 0.001 HIS B 225 PHE 0.014 0.001 PHE R 230 TYR 0.024 0.002 TYR R 148 ARG 0.011 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 443) hydrogen bonds : angle 4.29934 ( 1275) SS BOND : bond 0.00353 ( 5) SS BOND : angle 2.00276 ( 10) covalent geometry : bond 0.00505 ( 9364) covalent geometry : angle 0.65031 (12724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9365.40 seconds wall clock time: 161 minutes 4.07 seconds (9664.07 seconds total)