Starting phenix.real_space_refine on Mon Mar 11 06:53:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/03_2024/8kgk_37224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/03_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_37224/03_2024/8kgk_37224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/03_2024/8kgk_37224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/03_2024/8kgk_37224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgk_37224/03_2024/8kgk_37224.pdb" } 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-5265/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: 5.49, per 1000 atoms: 0.73 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: 2.88 Conformation dependent library (CDL) restraints added in 1.8 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: 0.82 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: 2.17 Time building geometry restraints manager: 3.21 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 2.440 nonbonded pdb=" NH1 ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.146 2.520 nonbonded pdb=" OG SER C 279 " pdb=" OD1 ASP D 48 " model vdw 2.200 2.440 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.203 2.440 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.240 2.520 ... (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 ========== 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: 0.440 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: 0.000 Extract box with map and model: 1.720 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.220 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- 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 : 0.872 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: 0.2004 time to fit residues: 55.2077 Evaluate side-chains 176 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 40.0000 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7630 Z= 0.329 Angle : 0.595 7.691 10396 Z= 0.313 Chirality : 0.044 0.232 1207 Planarity : 0.005 0.047 1336 Dihedral : 4.440 27.202 1086 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.29 % Allowed : 11.32 % Favored : 86.39 % 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: 1.02 (0.27), residues: 991 helix: 2.24 (0.25), residues: 404 sheet: -0.48 (0.36), residues: 207 loop : -0.30 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.006 0.002 HIS B 220 PHE 0.016 0.002 PHE D 61 TYR 0.016 0.002 TYR E 95 ARG 0.005 0.000 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 198 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 0.840 Fit side-chains REVERT: A 355 GLN cc_start: 0.6231 (mp10) cc_final: 0.5953 (mp10) REVERT: C 179 THR cc_start: 0.8899 (m) cc_final: 0.8412 (p) REVERT: C 217 MET cc_start: 0.7292 (ttp) cc_final: 0.7030 (ttm) REVERT: C 293 ASN cc_start: 0.7622 (m-40) cc_final: 0.7372 (m-40) REVERT: C 334 SER cc_start: 0.8985 (m) cc_final: 0.8710 (m) REVERT: E 82 GLN cc_start: 0.7055 (tm-30) cc_final: 0.6655 (tm-30) outliers start: 17 outliers final: 12 residues processed: 188 average time/residue: 0.1937 time to fit residues: 49.4413 Evaluate side-chains 180 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 B residue 283 LYS Chi-restraints excluded: chain B residue 371 ASP 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 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: 0.8980 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7630 Z= 0.321 Angle : 0.579 7.889 10396 Z= 0.306 Chirality : 0.043 0.184 1207 Planarity : 0.004 0.045 1336 Dihedral : 4.536 28.066 1086 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.37 % Allowed : 14.02 % Favored : 82.61 % 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 (0.27), residues: 991 helix: 2.23 (0.25), residues: 404 sheet: -0.54 (0.35), residues: 210 loop : -0.36 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 82 HIS 0.009 0.001 HIS B 220 PHE 0.016 0.002 PHE D 61 TYR 0.018 0.002 TYR B 381 ARG 0.006 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 205 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 0.850 Fit side-chains REVERT: A 337 ASN cc_start: 0.8624 (m-40) cc_final: 0.8420 (m110) REVERT: A 355 GLN cc_start: 0.6265 (mp10) cc_final: 0.6060 (mp10) REVERT: C 179 THR cc_start: 0.8906 (m) cc_final: 0.8423 (p) REVERT: C 217 MET cc_start: 0.7346 (ttp) cc_final: 0.7102 (ttm) REVERT: C 298 ASP cc_start: 0.8026 (t0) cc_final: 0.7823 (t0) REVERT: C 334 SER cc_start: 0.8973 (m) cc_final: 0.8745 (m) REVERT: E 82 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6596 (tm-30) outliers start: 25 outliers final: 16 residues processed: 190 average time/residue: 0.1955 time to fit residues: 49.4598 Evaluate side-chains 184 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 254 ASN Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS 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: 0.9980 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7630 Z= 0.183 Angle : 0.529 8.390 10396 Z= 0.272 Chirality : 0.042 0.293 1207 Planarity : 0.004 0.042 1336 Dihedral : 4.341 23.879 1086 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.29 % Allowed : 17.25 % Favored : 80.46 % 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: 2.50 (0.26), residues: 404 sheet: -0.69 (0.34), residues: 219 loop : -0.39 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 82 HIS 0.007 0.001 HIS B 220 PHE 0.010 0.001 PHE C 199 TYR 0.020 0.001 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 199 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 0.855 Fit side-chains REVERT: A 173 MET cc_start: 0.8603 (mmm) cc_final: 0.8177 (mmm) REVERT: A 337 ASN cc_start: 0.8576 (m-40) cc_final: 0.8283 (m110) REVERT: C 179 THR cc_start: 0.8899 (m) cc_final: 0.8412 (p) REVERT: C 217 MET cc_start: 0.7368 (ttp) cc_final: 0.7118 (ttm) REVERT: C 334 SER cc_start: 0.8954 (m) cc_final: 0.8722 (m) REVERT: E 82 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6578 (tm-30) REVERT: E 83 MET cc_start: 0.2376 (mtp) cc_final: 0.2026 (mtp) REVERT: E 95 TYR cc_start: 0.7733 (m-80) cc_final: 0.7016 (m-80) outliers start: 17 outliers final: 12 residues processed: 186 average time/residue: 0.1984 time to fit residues: 49.8417 Evaluate side-chains 190 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN 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: 3.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7454 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7630 Z= 0.264 Angle : 0.554 7.872 10396 Z= 0.289 Chirality : 0.043 0.300 1207 Planarity : 0.004 0.041 1336 Dihedral : 4.381 23.879 1086 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.91 % Allowed : 17.92 % Favored : 78.17 % 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 (0.27), residues: 991 helix: 2.42 (0.26), residues: 403 sheet: -0.75 (0.35), residues: 208 loop : -0.39 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 82 HIS 0.008 0.001 HIS B 220 PHE 0.013 0.002 PHE D 61 TYR 0.020 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 204 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 0.973 Fit side-chains REVERT: A 88 LEU cc_start: 0.8746 (mp) cc_final: 0.8475 (mp) REVERT: A 337 ASN cc_start: 0.8556 (m-40) cc_final: 0.8264 (m-40) REVERT: C 179 THR cc_start: 0.8885 (m) cc_final: 0.8395 (p) REVERT: C 217 MET cc_start: 0.7350 (ttp) cc_final: 0.7087 (ttm) REVERT: C 334 SER cc_start: 0.8924 (m) cc_final: 0.8706 (m) REVERT: E 82 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6715 (tm-30) REVERT: E 83 MET cc_start: 0.2706 (mtp) cc_final: 0.2057 (mtp) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.1930 time to fit residues: 48.9195 Evaluate side-chains 192 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 229 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN 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: 0.5980 chunk 84 optimal weight: 0.0000 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7630 Z= 0.176 Angle : 0.518 8.317 10396 Z= 0.266 Chirality : 0.041 0.270 1207 Planarity : 0.004 0.040 1336 Dihedral : 4.206 19.747 1086 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.37 % Allowed : 19.41 % Favored : 77.22 % 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: 1.24 (0.27), residues: 991 helix: 2.73 (0.26), residues: 395 sheet: -0.57 (0.36), residues: 206 loop : -0.35 (0.31), residues: 390 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 0.010 0.001 PHE A 340 TYR 0.014 0.001 TYR E 117 ARG 0.007 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 206 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 0.820 Fit side-chains REVERT: A 88 LEU cc_start: 0.8713 (mp) cc_final: 0.8469 (mp) REVERT: A 173 MET cc_start: 0.8585 (mmm) cc_final: 0.8287 (mmm) REVERT: A 337 ASN cc_start: 0.8612 (m-40) cc_final: 0.8287 (m-40) REVERT: B 252 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7106 (p0) REVERT: C 156 GLN cc_start: 0.7730 (tt0) cc_final: 0.7466 (tt0) REVERT: C 179 THR cc_start: 0.8886 (m) cc_final: 0.8406 (p) REVERT: C 334 SER cc_start: 0.8938 (m) cc_final: 0.8700 (m) REVERT: E 82 GLN cc_start: 0.6841 (tm-30) cc_final: 0.6529 (tm-30) REVERT: E 83 MET cc_start: 0.2628 (mtp) cc_final: 0.2016 (mtp) outliers start: 25 outliers final: 20 residues processed: 192 average time/residue: 0.1960 time to fit residues: 50.1277 Evaluate side-chains 194 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 111 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: 4.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7630 Z= 0.287 Angle : 0.560 7.244 10396 Z= 0.294 Chirality : 0.044 0.316 1207 Planarity : 0.004 0.040 1336 Dihedral : 4.403 21.443 1086 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.91 % Allowed : 18.87 % Favored : 77.22 % 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: 1.03 (0.27), residues: 991 helix: 2.51 (0.26), residues: 397 sheet: -0.74 (0.35), residues: 212 loop : -0.36 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 82 HIS 0.008 0.001 HIS B 220 PHE 0.012 0.002 PHE D 61 TYR 0.016 0.002 TYR B 381 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: 29 poor density : 176 time to evaluate : 0.802 Fit side-chains REVERT: A 88 LEU cc_start: 0.8697 (mp) cc_final: 0.8460 (mp) REVERT: A 337 ASN cc_start: 0.8592 (m-40) cc_final: 0.8212 (m-40) REVERT: C 156 GLN cc_start: 0.7765 (tt0) cc_final: 0.7457 (tt0) REVERT: C 179 THR cc_start: 0.8884 (m) cc_final: 0.8441 (p) REVERT: E 47 TRP cc_start: 0.8199 (t60) cc_final: 0.7925 (t60) REVERT: E 50 ASP cc_start: 0.7251 (m-30) cc_final: 0.7033 (m-30) REVERT: E 82 GLN cc_start: 0.6778 (tm-30) cc_final: 0.6489 (tm-30) REVERT: E 83 MET cc_start: 0.3223 (mtp) cc_final: 0.2321 (mtp) outliers start: 29 outliers final: 21 residues processed: 191 average time/residue: 0.1910 time to fit residues: 48.8130 Evaluate side-chains 195 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 111 THR 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: 0.8980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7630 Z= 0.186 Angle : 0.536 13.969 10396 Z= 0.274 Chirality : 0.042 0.283 1207 Planarity : 0.004 0.040 1336 Dihedral : 4.279 19.609 1086 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.96 % Allowed : 20.35 % Favored : 76.68 % 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: 1.15 (0.27), residues: 991 helix: 2.56 (0.26), residues: 399 sheet: -0.45 (0.36), residues: 203 loop : -0.42 (0.30), residues: 389 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 0.010 0.001 PHE C 241 TYR 0.015 0.001 TYR E 117 ARG 0.006 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 197 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 0.915 Fit side-chains REVERT: A 88 LEU cc_start: 0.8708 (mp) cc_final: 0.8399 (mp) REVERT: A 337 ASN cc_start: 0.8613 (m-40) cc_final: 0.8273 (m-40) REVERT: C 156 GLN cc_start: 0.7717 (tt0) cc_final: 0.7450 (tt0) REVERT: C 179 THR cc_start: 0.8865 (m) cc_final: 0.8430 (p) REVERT: E 82 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6700 (tm-30) REVERT: E 83 MET cc_start: 0.3180 (mtp) cc_final: 0.1399 (mtp) REVERT: E 95 TYR cc_start: 0.7534 (m-80) cc_final: 0.6912 (m-80) outliers start: 22 outliers final: 20 residues processed: 183 average time/residue: 0.1976 time to fit residues: 48.5972 Evaluate side-chains 191 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 82 GLN 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: 0.1980 chunk 89 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 92 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7630 Z= 0.176 Angle : 0.538 12.088 10396 Z= 0.273 Chirality : 0.042 0.271 1207 Planarity : 0.004 0.040 1336 Dihedral : 4.219 20.780 1086 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.10 % Allowed : 20.49 % Favored : 76.42 % 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: 1.18 (0.27), residues: 991 helix: 2.61 (0.26), residues: 400 sheet: -0.45 (0.37), residues: 205 loop : -0.44 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.011 0.001 PHE C 241 TYR 0.013 0.001 TYR C 111 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 194 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 0.845 Fit side-chains REVERT: A 337 ASN cc_start: 0.8593 (m-40) cc_final: 0.8248 (m-40) REVERT: C 156 GLN cc_start: 0.7675 (tt0) cc_final: 0.7418 (tt0) REVERT: C 179 THR cc_start: 0.8932 (m) cc_final: 0.8484 (p) REVERT: E 82 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6983 (tm-30) REVERT: E 83 MET cc_start: 0.2943 (mtp) cc_final: 0.2243 (mtp) REVERT: E 95 TYR cc_start: 0.7448 (m-80) cc_final: 0.6959 (m-80) outliers start: 23 outliers final: 20 residues processed: 181 average time/residue: 0.1951 time to fit residues: 47.4362 Evaluate side-chains 193 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 219 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 254 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 SER 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: 5.9990 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 96 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 81 optimal weight: 40.0000 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 7630 Z= 0.158 Angle : 0.548 12.447 10396 Z= 0.269 Chirality : 0.040 0.229 1207 Planarity : 0.004 0.045 1336 Dihedral : 4.033 18.024 1086 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.43 % Allowed : 21.56 % 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: 1.34 (0.27), residues: 991 helix: 2.69 (0.26), residues: 402 sheet: -0.04 (0.38), residues: 199 loop : -0.53 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.017 0.001 PHE A 306 TYR 0.014 0.001 TYR C 111 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 204 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 0.882 Fit side-chains REVERT: A 337 ASN cc_start: 0.8595 (m-40) cc_final: 0.8258 (m-40) REVERT: C 52 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: C 101 MET cc_start: 0.9126 (mtt) cc_final: 0.8917 (mtt) REVERT: C 156 GLN cc_start: 0.7657 (tt0) cc_final: 0.7442 (tt0) REVERT: C 179 THR cc_start: 0.8923 (m) cc_final: 0.8460 (p) REVERT: C 334 SER cc_start: 0.8773 (m) cc_final: 0.8521 (m) REVERT: E 39 GLN cc_start: 0.8390 (tt0) cc_final: 0.8166 (tt0) REVERT: E 80 TYR cc_start: 0.7232 (m-80) cc_final: 0.7027 (m-80) REVERT: E 82 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7033 (tm-30) REVERT: E 83 MET cc_start: 0.2783 (mtp) cc_final: 0.0877 (mtp) REVERT: E 95 TYR cc_start: 0.7044 (m-80) cc_final: 0.6679 (m-80) outliers start: 18 outliers final: 18 residues processed: 192 average time/residue: 0.1948 time to fit residues: 50.2101 Evaluate side-chains 196 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 B residue 57 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 37 VAL 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: 0.9980 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 220 GLN D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.160395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118542 restraints weight = 22299.868| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 4.85 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7630 Z= 0.196 Angle : 0.581 14.518 10396 Z= 0.287 Chirality : 0.042 0.305 1207 Planarity : 0.004 0.042 1336 Dihedral : 4.117 18.919 1086 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.43 % Allowed : 21.02 % 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: 1.26 (0.27), residues: 991 helix: 2.60 (0.26), residues: 401 sheet: -0.19 (0.36), residues: 212 loop : -0.45 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.017 0.001 PHE A 306 TYR 0.014 0.001 TYR C 111 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: 1949.04 seconds wall clock time: 36 minutes 4.31 seconds (2164.31 seconds total)