Starting phenix.real_space_refine on Sat Aug 3 06:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/08_2024/8kgk_37224.cif" } resolution = 3.16 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= 0.001 sd= 0.098 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 53 5.16 5 C 4738 2.51 5 N 1298 2.21 5 O 1387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7476 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1888 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1804 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 2503 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2497 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 78 Conformer: "B" Number of residues, atoms: 339, 2497 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 78 bond proxies already assigned to first conformer: 2537 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 353 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 928 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS C 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 233 " occ=0.50 Time building chain proxies: 5.59, per 1000 atoms: 0.75 Number of scatterers: 7476 At special positions: 0 Unit cell: (71.28, 95.04, 128.52, 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 53 16.00 O 1387 8.00 N 1298 7.00 C 4738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 43 through 70 removed outlier: 3.533A pdb=" N THR A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.677A pdb=" N ARG A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 75' Processing helix chain 'A' and resid 76 through 102 removed outlier: 4.638A pdb=" N MET A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 112 through 145 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.696A pdb=" N GLU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 284 through 314 Proline residue: A 302 - end of helix removed outlier: 3.525A pdb=" N ALA A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 341 removed outlier: 3.519A pdb=" N SER A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.703A pdb=" N GLN B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.535A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 237 " --> pdb=" O TRP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.733A pdb=" N ARG B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.785A pdb=" N TYR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 removed outlier: 3.915A pdb=" N ALA B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 306' Processing helix chain 'B' and resid 321 through 343 removed outlier: 3.681A pdb=" N ILE B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 381 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.860A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.656A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.587A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 209 through 214 removed outlier: 6.039A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.154A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 340 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 62 removed outlier: 3.811A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 72 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.955A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.219A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.116A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.543A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.444A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.940A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1185 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: 2.37 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1222 1.26 - 1.40: 1961 1.40 - 1.54: 4350 1.54 - 1.68: 24 1.68 - 1.82: 73 Bond restraints: 7630 Sorted by residual: bond pdb=" N CYS A 115 " pdb=" CA CYS A 115 " ideal model delta sigma weight residual 1.459 1.318 0.141 1.21e-02 6.83e+03 1.36e+02 bond pdb=" C LEU A 117 " pdb=" O LEU A 117 " ideal model delta sigma weight residual 1.237 1.122 0.114 1.19e-02 7.06e+03 9.20e+01 bond pdb=" C ALA A 114 " pdb=" O ALA A 114 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.22e+01 bond pdb=" C GLU A 112 " pdb=" O GLU A 112 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.62e+01 bond pdb=" C VAL A 113 " pdb=" O VAL A 113 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.09e+01 ... (remaining 7625 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.81: 121 105.81 - 112.90: 4102 112.90 - 119.99: 2575 119.99 - 127.08: 3519 127.08 - 134.17: 79 Bond angle restraints: 10396 Sorted by residual: angle pdb=" O CYS A 115 " pdb=" C CYS A 115 " pdb=" N ARG A 116 " ideal model delta sigma weight residual 122.12 114.14 7.98 1.06e+00 8.90e-01 5.66e+01 angle pdb=" N GLU A 112 " pdb=" CA GLU A 112 " pdb=" C GLU A 112 " ideal model delta sigma weight residual 111.28 103.25 8.03 1.09e+00 8.42e-01 5.43e+01 angle pdb=" CA CYS A 115 " pdb=" C CYS A 115 " pdb=" N ARG A 116 " ideal model delta sigma weight residual 117.30 125.55 -8.25 1.16e+00 7.43e-01 5.05e+01 angle pdb=" N CYS A 115 " pdb=" CA CYS A 115 " pdb=" CB CYS A 115 " ideal model delta sigma weight residual 110.12 120.38 -10.26 1.47e+00 4.63e-01 4.87e+01 angle pdb=" C PRO A 192 " pdb=" N PRO A 193 " pdb=" CA PRO A 193 " ideal model delta sigma weight residual 119.84 111.81 8.03 1.25e+00 6.40e-01 4.13e+01 ... (remaining 10391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4076 17.42 - 34.83: 331 34.83 - 52.25: 62 52.25 - 69.66: 10 69.66 - 87.08: 6 Dihedral angle restraints: 4485 sinusoidal: 1561 harmonic: 2924 Sorted by residual: dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 195 " pdb=" CB CYS A 195 " ideal model delta sinusoidal sigma weight residual -86.00 -166.54 80.54 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" N CYS A 115 " pdb=" C CYS A 115 " pdb=" CA CYS A 115 " pdb=" CB CYS A 115 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.67 33.33 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 4482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1196 0.150 - 0.301: 7 0.301 - 0.451: 3 0.451 - 0.601: 0 0.601 - 0.751: 1 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CA CYS A 115 " pdb=" N CYS A 115 " pdb=" C CYS A 115 " pdb=" CB CYS A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA PHE A 125 " pdb=" N PHE A 125 " pdb=" C PHE A 125 " pdb=" CB PHE A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LEU A 121 " pdb=" N LEU A 121 " pdb=" C LEU A 121 " pdb=" CB LEU A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1204 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 122 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C SER A 122 " -0.079 2.00e-02 2.50e+03 pdb=" O SER A 122 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL A 123 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 192 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO A 193 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 113 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL A 113 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 113 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 114 " 0.016 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 162 2.68 - 3.23: 7282 3.23 - 3.79: 12160 3.79 - 4.34: 15905 4.34 - 4.90: 26492 Nonbonded interactions: 62001 Sorted by model distance: nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.122 3.040 nonbonded pdb=" NH1 ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.146 3.120 nonbonded pdb=" OG SER C 279 " pdb=" OD1 ASP D 48 " model vdw 2.200 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.203 3.040 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.240 3.120 ... (remaining 61996 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=0.50 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: 0.470 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 7630 Z= 0.352 Angle : 0.688 10.262 10396 Z= 0.416 Chirality : 0.051 0.751 1207 Planarity : 0.005 0.071 1336 Dihedral : 13.366 87.077 2586 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 0.40 % Allowed : 0.67 % Favored : 98.92 % Cbeta Deviations : 0.11 % 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: 0.89 (0.27), residues: 991 helix: 2.09 (0.26), residues: 398 sheet: -0.39 (0.36), residues: 206 loop : -0.36 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.016 0.001 PHE A 120 TYR 0.019 0.001 TYR A 303 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 0.864 Fit side-chains REVERT: C 179 THR cc_start: 0.8973 (m) cc_final: 0.8696 (t) REVERT: C 217 MET cc_start: 0.7308 (ttp) cc_final: 0.6900 (ttm) REVERT: C 297 TRP cc_start: 0.7994 (m100) cc_final: 0.7268 (m100) outliers start: 3 outliers final: 0 residues processed: 207 average time/residue: 0.1933 time to fit residues: 53.2793 Evaluate side-chains 176 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7630 Z= 0.357 Angle : 0.625 7.315 10396 Z= 0.332 Chirality : 0.045 0.243 1207 Planarity : 0.005 0.048 1336 Dihedral : 4.578 32.262 1086 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.29 % Allowed : 11.19 % Favored : 86.52 % 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: 0.92 (0.27), residues: 991 helix: 2.18 (0.25), residues: 402 sheet: -0.54 (0.35), residues: 210 loop : -0.36 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 82 HIS 0.007 0.002 HIS C 142 PHE 0.017 0.002 PHE D 61 TYR 0.017 0.002 TYR E 95 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 0.759 Fit side-chains REVERT: A 355 GLN cc_start: 0.6515 (mp10) cc_final: 0.6299 (mp10) REVERT: C 179 THR cc_start: 0.8904 (m) cc_final: 0.8407 (p) REVERT: C 215 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 217 MET cc_start: 0.7388 (ttp) cc_final: 0.7066 (ttp) REVERT: C 293 ASN cc_start: 0.7654 (m-40) cc_final: 0.7400 (m-40) REVERT: C 334 SER cc_start: 0.8871 (m) cc_final: 0.8595 (m) outliers start: 17 outliers final: 11 residues processed: 190 average time/residue: 0.1885 time to fit residues: 48.0294 Evaluate side-chains 178 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7630 Z= 0.373 Angle : 0.621 8.010 10396 Z= 0.329 Chirality : 0.045 0.194 1207 Planarity : 0.005 0.047 1336 Dihedral : 4.712 35.803 1086 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.50 % Allowed : 14.29 % Favored : 82.21 % 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: 0.84 (0.27), residues: 991 helix: 2.16 (0.25), residues: 404 sheet: -0.72 (0.34), residues: 213 loop : -0.37 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 82 HIS 0.009 0.002 HIS B 220 PHE 0.019 0.002 PHE D 61 TYR 0.019 0.002 TYR B 381 ARG 0.005 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 0.827 Fit side-chains REVERT: A 98 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6975 (mmt) REVERT: A 231 MET cc_start: 0.7962 (ttm) cc_final: 0.7589 (ttm) REVERT: A 337 ASN cc_start: 0.8681 (m-40) cc_final: 0.8461 (m110) REVERT: B 378 LEU cc_start: 0.8082 (mt) cc_final: 0.7822 (mt) REVERT: C 82 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.8283 (m-10) REVERT: C 217 MET cc_start: 0.7440 (ttp) cc_final: 0.7116 (ttm) outliers start: 26 outliers final: 15 residues processed: 185 average time/residue: 0.1985 time to fit residues: 49.5147 Evaluate side-chains 183 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7630 Z= 0.197 Angle : 0.551 8.270 10396 Z= 0.286 Chirality : 0.042 0.308 1207 Planarity : 0.004 0.045 1336 Dihedral : 4.454 31.625 1086 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 17.25 % Favored : 80.59 % 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: 1.01 (0.27), residues: 991 helix: 2.58 (0.26), residues: 397 sheet: -0.84 (0.34), residues: 221 loop : -0.40 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.011 0.001 PHE C 241 TYR 0.022 0.002 TYR B 381 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.834 Fit side-chains REVERT: A 98 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6901 (mmt) REVERT: A 168 VAL cc_start: 0.8865 (t) cc_final: 0.8664 (m) REVERT: A 173 MET cc_start: 0.8638 (mmm) cc_final: 0.8191 (mmm) REVERT: A 231 MET cc_start: 0.7950 (ttm) cc_final: 0.7588 (ttm) REVERT: A 337 ASN cc_start: 0.8700 (m-40) cc_final: 0.8457 (m110) REVERT: C 82 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.8328 (m-10) REVERT: C 101 MET cc_start: 0.9123 (mtt) cc_final: 0.8840 (mtt) REVERT: C 217 MET cc_start: 0.7442 (ttp) cc_final: 0.7136 (ttm) REVERT: C 334 SER cc_start: 0.8793 (m) cc_final: 0.8560 (m) REVERT: E 83 MET cc_start: 0.2690 (mtp) cc_final: 0.2148 (mtp) REVERT: E 95 TYR cc_start: 0.7743 (m-80) cc_final: 0.7010 (m-80) outliers start: 16 outliers final: 11 residues processed: 190 average time/residue: 0.2065 time to fit residues: 51.8845 Evaluate side-chains 185 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 0.0370 chunk 23 optimal weight: 0.9980 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS E 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7630 Z= 0.215 Angle : 0.554 8.840 10396 Z= 0.287 Chirality : 0.042 0.258 1207 Planarity : 0.004 0.044 1336 Dihedral : 4.386 30.863 1086 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.50 % Allowed : 17.65 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 991 helix: 2.54 (0.26), residues: 406 sheet: -0.83 (0.34), residues: 221 loop : -0.34 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.011 0.001 PHE C 241 TYR 0.023 0.002 TYR B 381 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 0.853 Fit side-chains REVERT: A 88 LEU cc_start: 0.8717 (mp) cc_final: 0.8447 (mp) REVERT: A 98 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6841 (mmt) REVERT: A 168 VAL cc_start: 0.8857 (t) cc_final: 0.8653 (m) REVERT: A 173 MET cc_start: 0.8635 (mmm) cc_final: 0.8126 (mmm) REVERT: A 223 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6686 (tt) REVERT: A 231 MET cc_start: 0.7988 (ttm) cc_final: 0.7668 (ttm) REVERT: A 337 ASN cc_start: 0.8663 (m-40) cc_final: 0.8412 (m110) REVERT: B 252 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7062 (p0) REVERT: C 217 MET cc_start: 0.7331 (ttp) cc_final: 0.6946 (ttm) REVERT: C 334 SER cc_start: 0.8802 (m) cc_final: 0.8580 (m) REVERT: E 83 MET cc_start: 0.2870 (mtp) cc_final: 0.2163 (mtp) REVERT: E 90 ASP cc_start: 0.7605 (m-30) cc_final: 0.7401 (m-30) outliers start: 26 outliers final: 15 residues processed: 191 average time/residue: 0.1894 time to fit residues: 48.9499 Evaluate side-chains 192 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7630 Z= 0.253 Angle : 0.565 8.035 10396 Z= 0.296 Chirality : 0.043 0.271 1207 Planarity : 0.004 0.043 1336 Dihedral : 4.424 31.336 1086 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.91 % Allowed : 18.60 % Favored : 77.49 % 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: 1.05 (0.27), residues: 991 helix: 2.53 (0.26), residues: 406 sheet: -0.86 (0.33), residues: 226 loop : -0.31 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.012 0.001 PHE A 340 TYR 0.017 0.002 TYR B 381 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 0.836 Fit side-chains REVERT: A 88 LEU cc_start: 0.8715 (mp) cc_final: 0.8459 (mp) REVERT: A 98 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6896 (mmt) REVERT: A 173 MET cc_start: 0.8671 (mmm) cc_final: 0.8106 (mmm) REVERT: A 231 MET cc_start: 0.7997 (ttm) cc_final: 0.7650 (ttm) REVERT: A 337 ASN cc_start: 0.8668 (m-40) cc_final: 0.8399 (m110) REVERT: B 252 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7037 (p0) REVERT: E 83 MET cc_start: 0.3258 (mtp) cc_final: 0.1843 (mtp) outliers start: 29 outliers final: 21 residues processed: 189 average time/residue: 0.1870 time to fit residues: 47.6605 Evaluate side-chains 194 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7630 Z= 0.190 Angle : 0.558 8.021 10396 Z= 0.288 Chirality : 0.042 0.264 1207 Planarity : 0.004 0.043 1336 Dihedral : 4.336 29.270 1086 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.23 % Allowed : 20.49 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.27), residues: 991 helix: 2.53 (0.26), residues: 401 sheet: -0.79 (0.34), residues: 224 loop : -0.35 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.012 0.001 PHE A 340 TYR 0.017 0.001 TYR A 331 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 0.923 Fit side-chains REVERT: A 88 LEU cc_start: 0.8686 (mp) cc_final: 0.8458 (mp) REVERT: A 98 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6713 (mmt) REVERT: A 173 MET cc_start: 0.8679 (mmm) cc_final: 0.8122 (mmm) REVERT: A 231 MET cc_start: 0.7954 (ttm) cc_final: 0.7597 (ttm) REVERT: A 337 ASN cc_start: 0.8667 (m-40) cc_final: 0.8397 (m110) REVERT: B 252 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6937 (p0) REVERT: C 156 GLN cc_start: 0.7685 (tt0) cc_final: 0.7392 (tt0) REVERT: C 229 ILE cc_start: 0.8496 (mt) cc_final: 0.8206 (mm) REVERT: E 83 MET cc_start: 0.3015 (mtp) cc_final: 0.2160 (mtp) REVERT: E 90 ASP cc_start: 0.7615 (m-30) cc_final: 0.7387 (m-30) REVERT: E 95 TYR cc_start: 0.7516 (m-80) cc_final: 0.6809 (m-80) outliers start: 24 outliers final: 15 residues processed: 193 average time/residue: 0.1866 time to fit residues: 48.4772 Evaluate side-chains 190 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7630 Z= 0.292 Angle : 0.599 10.554 10396 Z= 0.312 Chirality : 0.044 0.286 1207 Planarity : 0.004 0.043 1336 Dihedral : 4.520 31.688 1086 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.50 % Allowed : 19.95 % Favored : 76.55 % 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: 0.97 (0.27), residues: 991 helix: 2.40 (0.26), residues: 406 sheet: -0.85 (0.34), residues: 224 loop : -0.32 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 82 HIS 0.008 0.001 HIS B 220 PHE 0.012 0.002 PHE D 61 TYR 0.023 0.002 TYR B 381 ARG 0.007 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 0.770 Fit side-chains REVERT: A 98 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6684 (mmt) REVERT: A 231 MET cc_start: 0.7950 (ttm) cc_final: 0.7584 (ttm) REVERT: A 337 ASN cc_start: 0.8672 (m-40) cc_final: 0.8411 (m110) REVERT: B 252 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6978 (p0) REVERT: C 101 MET cc_start: 0.9169 (mtt) cc_final: 0.8919 (mtt) REVERT: E 83 MET cc_start: 0.3285 (mtp) cc_final: 0.2251 (mtp) REVERT: E 90 ASP cc_start: 0.7578 (m-30) cc_final: 0.7364 (m-30) outliers start: 26 outliers final: 23 residues processed: 190 average time/residue: 0.1955 time to fit residues: 49.4552 Evaluate side-chains 195 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7630 Z= 0.210 Angle : 0.568 9.303 10396 Z= 0.296 Chirality : 0.042 0.258 1207 Planarity : 0.004 0.043 1336 Dihedral : 4.434 29.846 1086 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.37 % Allowed : 20.35 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.27), residues: 991 helix: 2.46 (0.26), residues: 401 sheet: -0.77 (0.34), residues: 221 loop : -0.34 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.013 0.001 PHE A 340 TYR 0.020 0.002 TYR A 331 ARG 0.007 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.753 Fit side-chains REVERT: A 98 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6605 (mmt) REVERT: A 173 MET cc_start: 0.8594 (mmm) cc_final: 0.8287 (mmm) REVERT: A 231 MET cc_start: 0.7962 (ttm) cc_final: 0.7624 (ttm) REVERT: A 337 ASN cc_start: 0.8667 (m-40) cc_final: 0.8405 (m110) REVERT: B 252 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6945 (p0) REVERT: C 101 MET cc_start: 0.9134 (mtt) cc_final: 0.8872 (mtt) REVERT: E 83 MET cc_start: 0.3250 (mtp) cc_final: 0.2248 (mtp) REVERT: E 90 ASP cc_start: 0.7595 (m-30) cc_final: 0.7376 (m-30) outliers start: 25 outliers final: 21 residues processed: 190 average time/residue: 0.1920 time to fit residues: 48.7326 Evaluate side-chains 196 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7630 Z= 0.226 Angle : 0.588 15.400 10396 Z= 0.304 Chirality : 0.043 0.319 1207 Planarity : 0.004 0.043 1336 Dihedral : 4.422 29.568 1086 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.37 % Allowed : 20.75 % Favored : 75.88 % 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: 1.06 (0.27), residues: 991 helix: 2.49 (0.26), residues: 402 sheet: -0.66 (0.34), residues: 215 loop : -0.38 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.013 0.001 PHE A 340 TYR 0.022 0.002 TYR A 331 ARG 0.007 0.000 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 0.852 Fit side-chains REVERT: A 98 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6605 (mmt) REVERT: A 173 MET cc_start: 0.8576 (mmm) cc_final: 0.8310 (mmm) REVERT: A 231 MET cc_start: 0.7958 (ttm) cc_final: 0.7592 (ttm) REVERT: A 337 ASN cc_start: 0.8653 (m-40) cc_final: 0.8409 (m110) REVERT: B 252 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6921 (p0) REVERT: C 101 MET cc_start: 0.9143 (mtt) cc_final: 0.8876 (mtt) REVERT: E 83 MET cc_start: 0.2805 (mtp) cc_final: 0.1865 (mtp) REVERT: E 90 ASP cc_start: 0.7440 (m-30) cc_final: 0.7234 (m-30) REVERT: E 95 TYR cc_start: 0.7632 (m-80) cc_final: 0.6859 (m-80) outliers start: 25 outliers final: 20 residues processed: 192 average time/residue: 0.1951 time to fit residues: 50.0371 Evaluate side-chains 197 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115151 restraints weight = 22144.567| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.68 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7630 Z= 0.236 Angle : 0.594 14.390 10396 Z= 0.307 Chirality : 0.043 0.318 1207 Planarity : 0.004 0.044 1336 Dihedral : 4.423 29.575 1086 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.50 % Allowed : 20.49 % Favored : 76.01 % 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: 1.05 (0.27), residues: 991 helix: 2.48 (0.26), residues: 402 sheet: -0.66 (0.35), residues: 215 loop : -0.40 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP C 211 HIS 0.007 0.001 HIS B 220 PHE 0.014 0.001 PHE A 340 TYR 0.028 0.002 TYR A 331 ARG 0.007 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.40 seconds wall clock time: 34 minutes 12.48 seconds (2052.48 seconds total)