Starting phenix.real_space_refine on Sat Aug 3 07:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/08_2024/8kh4_37236.cif" } resolution = 3.1 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= 0.118 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 51 5.16 5 C 4814 2.51 5 N 1286 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7521 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2048 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1809 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 2435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 2458 Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 936 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 265 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.73, per 1000 atoms: 0.76 Number of scatterers: 7521 At special positions: 0 Unit cell: (72.36, 95.04, 126.36, 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 51 16.00 O 1370 8.00 N 1286 7.00 C 4814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 178 " distance=2.04 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: 3.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 43.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 27 through 55 removed outlier: 3.838A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 96 through 131 removed outlier: 3.655A pdb=" N GLY A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 140 through 160 removed outlier: 3.593A pdb=" N TRP A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.815A pdb=" N PHE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 297 removed outlier: 3.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 302 through 327 removed outlier: 4.122A pdb=" N ALA A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Proline residue: A 321 - end of helix removed outlier: 3.550A pdb=" N TRP A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.691A pdb=" N ALA B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.658A pdb=" N MET B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.039A pdb=" N TYR B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.683A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.739A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.563A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.657A pdb=" N VAL A 179 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 172 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 177 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 214 removed outlier: 9.660A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP B 249 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.625A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.555A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.579A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.112A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.737A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.747A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.833A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1212 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: 2.38 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1208 1.29 - 1.42: 2106 1.42 - 1.56: 4303 1.56 - 1.69: 3 1.69 - 1.83: 73 Bond restraints: 7693 Sorted by residual: bond pdb=" CA PHE A 201 " pdb=" C PHE A 201 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.29e-02 6.01e+03 7.08e+01 bond pdb=" CA SER A 62 " pdb=" C SER A 62 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.26e-02 6.30e+03 6.04e+01 bond pdb=" CA VAL A 179 " pdb=" C VAL A 179 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.27e-02 6.20e+03 5.74e+01 bond pdb=" C PHE A 201 " pdb=" O PHE A 201 " ideal model delta sigma weight residual 1.237 1.156 0.080 1.19e-02 7.06e+03 4.57e+01 bond pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 1.459 1.377 0.082 1.25e-02 6.40e+03 4.26e+01 ... (remaining 7688 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.62: 84 103.62 - 111.74: 3681 111.74 - 119.85: 3034 119.85 - 127.97: 3623 127.97 - 136.08: 81 Bond angle restraints: 10503 Sorted by residual: angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" C ARG A 213 " ideal model delta sigma weight residual 111.07 100.56 10.51 1.07e+00 8.73e-01 9.65e+01 angle pdb=" N ILE A 211 " pdb=" CA ILE A 211 " pdb=" C ILE A 211 " ideal model delta sigma weight residual 110.62 102.37 8.25 1.02e+00 9.61e-01 6.55e+01 angle pdb=" N ALA D 34 " pdb=" CA ALA D 34 " pdb=" C ALA D 34 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N TYR D 40 " pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 111.28 102.91 8.37 1.09e+00 8.42e-01 5.90e+01 angle pdb=" C PHE A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta sigma weight residual 119.05 110.58 8.47 1.11e+00 8.12e-01 5.82e+01 ... (remaining 10498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 4320 24.19 - 48.38: 190 48.38 - 72.57: 13 72.57 - 96.76: 10 96.76 - 120.95: 1 Dihedral angle restraints: 4534 sinusoidal: 1614 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -2.52 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" C ASN A 63 " pdb=" N ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual -122.60 -138.96 16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 4531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1181 0.163 - 0.327: 29 0.327 - 0.490: 7 0.490 - 0.653: 4 0.653 - 0.817: 2 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ALA A 219 " pdb=" N ALA A 219 " pdb=" C ALA A 219 " pdb=" CB ALA A 219 " both_signs ideal model delta sigma weight residual False 2.48 1.77 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 1220 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO C 236 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 213 " -0.018 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG A 213 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 214 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 57 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C TYR A 57 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 57 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 58 " 0.017 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 6873 3.19 - 3.76: 12272 3.76 - 4.33: 16918 4.33 - 4.90: 28357 Nonbonded interactions: 64548 Sorted by model distance: nonbonded pdb=" CD2 LEU A 61 " pdb=" CB ALA A 144 " model vdw 2.049 3.880 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.150 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.180 3.040 nonbonded pdb=" N VAL A 179 " pdb=" O VAL A 179 " model vdw 2.218 2.496 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.219 3.120 ... (remaining 64543 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=0.38 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: 0.370 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.150 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 7693 Z= 0.581 Angle : 1.014 13.493 10503 Z= 0.632 Chirality : 0.081 0.817 1223 Planarity : 0.007 0.098 1324 Dihedral : 14.018 120.945 2639 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.40 % Allowed : 1.48 % Favored : 98.12 % Cbeta Deviations : 0.95 % 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: 0.62 (0.27), residues: 988 helix: 1.63 (0.26), residues: 402 sheet: 0.16 (0.35), residues: 204 loop : -0.73 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 99 HIS 0.007 0.002 HIS D 44 PHE 0.028 0.002 PHE A 65 TYR 0.025 0.002 TYR C 85 ARG 0.008 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: B 34 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7618 (tttt) REVERT: B 280 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7821 (ttt90) REVERT: B 317 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7476 (ptp90) REVERT: C 101 MET cc_start: 0.8895 (mtp) cc_final: 0.8644 (mtp) REVERT: C 290 ASP cc_start: 0.6802 (m-30) cc_final: 0.6572 (m-30) REVERT: E 60 TYR cc_start: 0.7386 (m-80) cc_final: 0.7036 (m-80) REVERT: E 80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7066 (m-80) outliers start: 3 outliers final: 0 residues processed: 170 average time/residue: 0.1955 time to fit residues: 44.8952 Evaluate side-chains 150 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7693 Z= 0.279 Angle : 0.649 10.841 10503 Z= 0.341 Chirality : 0.046 0.199 1223 Planarity : 0.006 0.077 1324 Dihedral : 5.911 57.344 1149 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.94 % Allowed : 10.77 % Favored : 88.29 % 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: 0.72 (0.27), residues: 988 helix: 1.91 (0.26), residues: 384 sheet: 0.05 (0.34), residues: 217 loop : -0.69 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 99 HIS 0.005 0.002 HIS C 225 PHE 0.018 0.002 PHE B 212 TYR 0.033 0.002 TYR C 85 ARG 0.005 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.6279 (ppp) REVERT: A 327 TRP cc_start: 0.7733 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: B 266 LEU cc_start: 0.8451 (tp) cc_final: 0.8126 (tp) REVERT: B 274 LYS cc_start: 0.7574 (tttp) cc_final: 0.7308 (ttmt) REVERT: B 280 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7689 (ttt90) REVERT: C 111 TYR cc_start: 0.8215 (m-80) cc_final: 0.7785 (m-80) REVERT: E 80 TYR cc_start: 0.7475 (m-80) cc_final: 0.6925 (m-80) REVERT: E 93 VAL cc_start: 0.7350 (t) cc_final: 0.7054 (t) REVERT: E 115 TYR cc_start: 0.8034 (t80) cc_final: 0.7748 (t80) outliers start: 7 outliers final: 3 residues processed: 158 average time/residue: 0.1946 time to fit residues: 41.3596 Evaluate side-chains 148 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 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: 8.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7693 Z= 0.214 Angle : 0.593 11.022 10503 Z= 0.310 Chirality : 0.044 0.166 1223 Planarity : 0.005 0.070 1324 Dihedral : 5.572 55.664 1149 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.88 % Allowed : 12.79 % Favored : 85.33 % 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: 988 helix: 2.06 (0.27), residues: 389 sheet: 0.03 (0.33), residues: 222 loop : -0.68 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 PHE 0.018 0.001 PHE B 222 TYR 0.028 0.002 TYR C 85 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6618 (ppp) REVERT: A 327 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: B 266 LEU cc_start: 0.8509 (tp) cc_final: 0.8206 (tp) REVERT: B 274 LYS cc_start: 0.7526 (tttp) cc_final: 0.7305 (ttmt) REVERT: B 280 ARG cc_start: 0.8060 (tpt90) cc_final: 0.7648 (ttt90) REVERT: E 3 GLN cc_start: 0.6094 (mp10) cc_final: 0.5688 (mp10) REVERT: E 50 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7911 (p0) REVERT: E 80 TYR cc_start: 0.7465 (m-80) cc_final: 0.6985 (m-80) REVERT: E 115 TYR cc_start: 0.8071 (t80) cc_final: 0.7815 (t80) REVERT: D 38 MET cc_start: 0.6584 (mtm) cc_final: 0.6287 (mtp) outliers start: 14 outliers final: 8 residues processed: 161 average time/residue: 0.1951 time to fit residues: 42.1644 Evaluate side-chains 154 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR 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: 0.0000 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7693 Z= 0.229 Angle : 0.592 11.451 10503 Z= 0.308 Chirality : 0.043 0.163 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.507 55.622 1149 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.15 % Allowed : 14.00 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 988 helix: 2.14 (0.27), residues: 391 sheet: -0.07 (0.33), residues: 224 loop : -0.67 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.006 0.001 HIS B 220 PHE 0.016 0.001 PHE B 222 TYR 0.027 0.002 TYR C 85 ARG 0.004 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8530 (m) cc_final: 0.8137 (p) REVERT: A 327 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: B 266 LEU cc_start: 0.8515 (tp) cc_final: 0.8220 (tp) REVERT: B 274 LYS cc_start: 0.7604 (tttp) cc_final: 0.7378 (ttmt) REVERT: B 280 ARG cc_start: 0.8066 (tpt90) cc_final: 0.7623 (ttt90) REVERT: C 263 THR cc_start: 0.8162 (m) cc_final: 0.7879 (p) REVERT: E 3 GLN cc_start: 0.6215 (mp10) cc_final: 0.5451 (mp10) REVERT: E 50 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.7997 (p0) REVERT: E 80 TYR cc_start: 0.7466 (m-80) cc_final: 0.6990 (m-80) REVERT: D 38 MET cc_start: 0.6605 (mtm) cc_final: 0.6305 (mtp) outliers start: 16 outliers final: 9 residues processed: 161 average time/residue: 0.1881 time to fit residues: 41.2274 Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 74 ASN E 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7693 Z= 0.194 Angle : 0.567 11.470 10503 Z= 0.295 Chirality : 0.043 0.182 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.360 55.087 1149 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 14.94 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 988 helix: 2.46 (0.27), residues: 382 sheet: -0.10 (0.32), residues: 234 loop : -0.64 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.015 0.001 PHE B 212 TYR 0.022 0.002 TYR C 85 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8489 (m) cc_final: 0.8115 (p) REVERT: A 140 THR cc_start: 0.6244 (OUTLIER) cc_final: 0.6043 (t) REVERT: A 327 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 266 LEU cc_start: 0.8533 (tp) cc_final: 0.8250 (tp) REVERT: B 274 LYS cc_start: 0.7610 (tttp) cc_final: 0.7390 (ttmt) REVERT: B 280 ARG cc_start: 0.8072 (tpt90) cc_final: 0.7609 (ttt90) REVERT: E 50 ASP cc_start: 0.8652 (p0) cc_final: 0.7958 (p0) REVERT: E 80 TYR cc_start: 0.7456 (m-80) cc_final: 0.7003 (m-80) REVERT: E 115 TYR cc_start: 0.8059 (t80) cc_final: 0.7856 (t80) outliers start: 16 outliers final: 10 residues processed: 161 average time/residue: 0.1881 time to fit residues: 41.2919 Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 77 ASN E 84 ASN E 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 0.038 7693 Z= 0.245 Angle : 0.594 11.977 10503 Z= 0.310 Chirality : 0.043 0.167 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.426 54.986 1149 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.10 % Allowed : 15.48 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 988 helix: 2.44 (0.27), residues: 381 sheet: 0.10 (0.33), residues: 222 loop : -0.73 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.007 0.001 HIS B 220 PHE 0.016 0.002 PHE E 108 TYR 0.027 0.002 TYR C 85 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8557 (m) cc_final: 0.8179 (p) REVERT: A 140 THR cc_start: 0.6287 (OUTLIER) cc_final: 0.6086 (t) REVERT: A 327 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6845 (m-10) REVERT: B 274 LYS cc_start: 0.7639 (tttp) cc_final: 0.7409 (ttmt) REVERT: C 263 THR cc_start: 0.8061 (m) cc_final: 0.7684 (p) REVERT: E 3 GLN cc_start: 0.6095 (mp10) cc_final: 0.5341 (mp10) REVERT: E 50 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.7905 (p0) REVERT: E 80 TYR cc_start: 0.7479 (m-80) cc_final: 0.7017 (m-80) REVERT: E 115 TYR cc_start: 0.8060 (t80) cc_final: 0.7797 (t80) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 0.1838 time to fit residues: 40.9637 Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7693 Z= 0.181 Angle : 0.563 11.674 10503 Z= 0.292 Chirality : 0.042 0.171 1223 Planarity : 0.004 0.068 1324 Dihedral : 5.194 54.278 1149 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 17.09 % Favored : 80.48 % 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: 988 helix: 2.53 (0.27), residues: 381 sheet: 0.16 (0.33), residues: 220 loop : -0.61 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.014 0.001 PHE B 212 TYR 0.020 0.001 TYR C 85 ARG 0.002 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8474 (m) cc_final: 0.8108 (p) REVERT: A 327 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.6803 (m-10) REVERT: B 266 LEU cc_start: 0.8291 (tp) cc_final: 0.7885 (tp) REVERT: B 274 LYS cc_start: 0.7610 (tttp) cc_final: 0.7399 (ttmt) REVERT: E 3 GLN cc_start: 0.6182 (mp10) cc_final: 0.5360 (mp10) REVERT: E 50 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7843 (p0) REVERT: E 60 TYR cc_start: 0.7663 (m-80) cc_final: 0.7438 (m-80) REVERT: E 80 TYR cc_start: 0.7503 (m-80) cc_final: 0.7075 (m-80) REVERT: E 115 TYR cc_start: 0.8029 (t80) cc_final: 0.7731 (t80) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.1988 time to fit residues: 42.7535 Evaluate side-chains 164 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 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** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7693 Z= 0.191 Angle : 0.567 11.963 10503 Z= 0.295 Chirality : 0.042 0.168 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.125 54.201 1149 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.29 % Allowed : 17.23 % Favored : 80.48 % 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: 1.20 (0.27), residues: 988 helix: 2.55 (0.27), residues: 381 sheet: 0.08 (0.33), residues: 222 loop : -0.55 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 220 PHE 0.014 0.001 PHE B 212 TYR 0.020 0.002 TYR C 85 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.5732 (t-100) cc_final: 0.5101 (t-100) REVERT: A 134 VAL cc_start: 0.8477 (m) cc_final: 0.8114 (p) REVERT: A 205 LEU cc_start: 0.7888 (tp) cc_final: 0.7508 (tp) REVERT: A 327 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: B 38 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7118 (ttp80) REVERT: B 266 LEU cc_start: 0.8409 (tp) cc_final: 0.8057 (tp) REVERT: B 274 LYS cc_start: 0.7617 (tttp) cc_final: 0.7407 (ttmt) REVERT: E 50 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.7896 (p0) REVERT: E 60 TYR cc_start: 0.7673 (m-80) cc_final: 0.7445 (m-80) REVERT: E 80 TYR cc_start: 0.7452 (m-80) cc_final: 0.7063 (m-80) REVERT: E 115 TYR cc_start: 0.8025 (t80) cc_final: 0.7750 (t80) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.1815 time to fit residues: 40.3529 Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7693 Z= 0.239 Angle : 0.598 12.357 10503 Z= 0.314 Chirality : 0.044 0.179 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.212 54.235 1149 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 17.63 % Favored : 79.95 % 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: 1.11 (0.27), residues: 988 helix: 2.47 (0.27), residues: 381 sheet: 0.02 (0.33), residues: 217 loop : -0.58 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.006 0.001 HIS B 220 PHE 0.015 0.002 PHE E 108 TYR 0.022 0.002 TYR C 85 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8545 (m) cc_final: 0.8175 (p) REVERT: A 327 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: B 38 ARG cc_start: 0.7615 (ttp80) cc_final: 0.6969 (ttp80) REVERT: B 266 LEU cc_start: 0.8526 (tp) cc_final: 0.8174 (tp) REVERT: B 274 LYS cc_start: 0.7632 (tttp) cc_final: 0.7414 (ttmt) REVERT: E 3 GLN cc_start: 0.6066 (mp10) cc_final: 0.5391 (mp10) REVERT: E 50 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7913 (p0) REVERT: E 60 TYR cc_start: 0.7725 (m-80) cc_final: 0.7501 (m-80) REVERT: E 80 TYR cc_start: 0.7482 (m-80) cc_final: 0.7025 (m-80) REVERT: E 115 TYR cc_start: 0.8089 (t80) cc_final: 0.7798 (t80) outliers start: 18 outliers final: 15 residues processed: 159 average time/residue: 0.1844 time to fit residues: 40.0633 Evaluate side-chains 163 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.0170 chunk 96 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7693 Z= 0.187 Angle : 0.572 12.204 10503 Z= 0.299 Chirality : 0.043 0.171 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.096 53.831 1149 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.42 % Allowed : 17.77 % Favored : 79.81 % 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: 988 helix: 2.50 (0.27), residues: 381 sheet: 0.08 (0.33), residues: 220 loop : -0.51 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.014 0.001 PHE B 212 TYR 0.015 0.001 TYR C 85 ARG 0.005 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8474 (m) cc_final: 0.8112 (p) REVERT: A 327 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.6690 (m-10) REVERT: B 38 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7057 (ttp80) REVERT: B 266 LEU cc_start: 0.8493 (tp) cc_final: 0.8126 (tp) REVERT: B 274 LYS cc_start: 0.7607 (tttp) cc_final: 0.7403 (ttmt) REVERT: C 59 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: C 75 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7377 (mt0) REVERT: E 3 GLN cc_start: 0.6077 (mp10) cc_final: 0.5366 (mp10) REVERT: E 50 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7859 (p0) REVERT: E 60 TYR cc_start: 0.7660 (m-80) cc_final: 0.7453 (m-80) REVERT: E 80 TYR cc_start: 0.7491 (m-80) cc_final: 0.7063 (m-80) REVERT: E 115 TYR cc_start: 0.8086 (t80) cc_final: 0.7807 (t80) outliers start: 18 outliers final: 15 residues processed: 152 average time/residue: 0.1836 time to fit residues: 38.3964 Evaluate side-chains 156 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159732 restraints weight = 24299.697| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 5.92 r_work: 0.3591 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7693 Z= 0.205 Angle : 0.580 12.260 10503 Z= 0.304 Chirality : 0.043 0.174 1223 Planarity : 0.005 0.068 1324 Dihedral : 5.079 53.817 1149 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 18.03 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 988 helix: 2.49 (0.27), residues: 381 sheet: 0.05 (0.33), residues: 217 loop : -0.54 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.005 0.001 HIS B 220 PHE 0.014 0.001 PHE B 212 TYR 0.016 0.002 TYR C 85 ARG 0.006 0.000 ARG E 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.06 seconds wall clock time: 34 minutes 38.74 seconds (2078.74 seconds total)