Starting phenix.real_space_refine on Thu Mar 14 16:52:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7m_30608/03_2024/7d7m_30608_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1953 atoms to isotropic. 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 40 5.16 5 C 4707 2.51 5 N 1226 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D ASP 252": "OD1" <-> "OD2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D ASP 310": "OD1" <-> "OD2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 381": "OD1" <-> "OD2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2097 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 272} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2276 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 19, 'ASN:plan1': 8, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 328 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1713 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 11, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 887 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.82, per 1000 atoms: 0.66 Number of scatterers: 7326 At special positions: 0 Unit cell: (100.362, 91.026, 119.034, 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 40 16.00 O 1353 8.00 N 1226 7.00 C 4707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 170 " 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=2.02 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 44 Proline residue: A 24 - end of helix removed outlier: 3.661A pdb=" N ASN A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 Proline residue: A 74 - end of helix removed outlier: 3.731A pdb=" N THR A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 122 removed outlier: 3.615A pdb=" N LEU A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 133 through 156 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 179 through 216 removed outlier: 3.681A pdb=" N GLN A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 297 removed outlier: 4.011A pdb=" N MET A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.558A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 Proline residue: A 322 - end of helix Proline residue: A 326 - end of helix removed outlier: 3.710A pdb=" N TYR A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 removed outlier: 3.652A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.520A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 13 through 39 Processing helix chain 'D' and resid 253 through 278 removed outlier: 3.834A pdb=" N GLN D 267 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 268 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 308 through 311 No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 332 through 352 removed outlier: 3.577A pdb=" N ARG D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 391 removed outlier: 3.972A pdb=" N ASP D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 382 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.764A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.783A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 167 through 170 Processing sheet with id= D, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.648A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.257A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.781A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.793A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 41 through 43 removed outlier: 4.266A pdb=" N ASP D 223 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 246 through 249 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.727A pdb=" N GLY E 10 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 12 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 124 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 17 through 22 347 hydrogen bonds defined for protein. 1002 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: 2.09 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1521 1.33 - 1.45: 1792 1.45 - 1.57: 4122 1.57 - 1.69: 1 1.69 - 1.81: 50 Bond restraints: 7486 Sorted by residual: bond pdb=" C15 P2E A 401 " pdb=" C16 P2E A 401 " ideal model delta sigma weight residual 1.530 1.574 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C14 P2E A 401 " pdb=" C15 P2E A 401 " ideal model delta sigma weight residual 1.503 1.540 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C12 P2E A 401 " pdb=" C13 P2E A 401 " ideal model delta sigma weight residual 1.491 1.525 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C11 P2E A 401 " pdb=" C12 P2E A 401 " ideal model delta sigma weight residual 1.529 1.563 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.64: 162 106.64 - 113.54: 4229 113.54 - 120.44: 2774 120.44 - 127.34: 3014 127.34 - 134.25: 89 Bond angle restraints: 10268 Sorted by residual: angle pdb=" CB LEU B 95 " pdb=" CG LEU B 95 " pdb=" CD2 LEU B 95 " ideal model delta sigma weight residual 110.70 120.48 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C7 P2E A 401 " pdb=" C8 P2E A 401 " pdb=" C9 P2E A 401 " ideal model delta sigma weight residual 115.46 106.47 8.99 3.00e+00 1.11e-01 8.97e+00 angle pdb=" C14 P2E A 401 " pdb=" C15 P2E A 401 " pdb=" O5 P2E A 401 " ideal model delta sigma weight residual 113.16 104.24 8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" CA GLY B 144 " pdb=" C GLY B 144 " pdb=" N TYR B 145 " ideal model delta sigma weight residual 114.84 117.91 -3.07 1.06e+00 8.90e-01 8.40e+00 angle pdb=" CB LEU B 95 " pdb=" CG LEU B 95 " pdb=" CD1 LEU B 95 " ideal model delta sigma weight residual 110.70 119.25 -8.55 3.00e+00 1.11e-01 8.12e+00 ... (remaining 10263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3896 18.00 - 36.00: 350 36.00 - 53.99: 69 53.99 - 71.99: 18 71.99 - 89.99: 5 Dihedral angle restraints: 4338 sinusoidal: 1339 harmonic: 2999 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 170 " pdb=" CB CYS A 170 " ideal model delta sinusoidal sigma weight residual -86.00 -124.46 38.46 1 1.00e+01 1.00e-02 2.08e+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 57.35 35.65 1 1.00e+01 1.00e-02 1.80e+01 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 93.00 122.66 -29.66 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1252 0.299 - 0.599: 1 0.599 - 0.898: 0 0.898 - 1.198: 0 1.198 - 1.497: 1 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CG LEU B 95 " pdb=" CB LEU B 95 " pdb=" CD1 LEU B 95 " pdb=" CD2 LEU B 95 " both_signs ideal model delta sigma weight residual False -2.59 -1.09 -1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb=" C15 P2E A 401 " pdb=" C14 P2E A 401 " pdb=" C16 P2E A 401 " pdb=" O5 P2E A 401 " both_signs ideal model delta sigma weight residual False 2.23 2.57 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C8 P2E A 401 " pdb=" C12 P2E A 401 " pdb=" C7 P2E A 401 " pdb=" C9 P2E A 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.81 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1251 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 333 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ARG A 333 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG A 333 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A 334 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 321 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.82e+00 pdb=" N PRO A 322 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 236 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 918 2.75 - 3.28: 7779 3.28 - 3.82: 12078 3.82 - 4.36: 13546 4.36 - 4.90: 23939 Nonbonded interactions: 58260 Sorted by model distance: nonbonded pdb=" O ASP D 223 " pdb=" OD1 ASP D 223 " model vdw 2.208 3.040 nonbonded pdb=" O VAL E 48 " pdb=" OG1 THR E 61 " model vdw 2.237 2.440 nonbonded pdb=" O ASP A 167 " pdb=" OD1 ASP A 167 " model vdw 2.295 3.040 nonbonded pdb=" O THR D 325 " pdb=" OG1 THR D 325 " model vdw 2.319 2.440 nonbonded pdb=" O ALA D 48 " pdb=" OG SER D 51 " model vdw 2.333 2.440 ... (remaining 58255 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.830 Find NCS groups from input model: 0.250 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.004 0.044 7486 Z= 0.267 Angle : 0.637 9.779 10268 Z= 0.342 Chirality : 0.059 1.497 1254 Planarity : 0.004 0.074 1298 Dihedral : 15.090 89.988 2393 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.14 (0.26), residues: 1019 helix: 1.79 (0.26), residues: 390 sheet: -1.00 (0.36), residues: 197 loop : -0.92 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 234 HIS 0.010 0.002 HIS B 142 PHE 0.016 0.002 PHE B 241 TYR 0.014 0.002 TYR A 127 ARG 0.008 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.848 Fit side-chains REVERT: A 133 LYS cc_start: 0.7671 (tmmt) cc_final: 0.7332 (tmtt) REVERT: A 261 ARG cc_start: 0.6012 (mtt-85) cc_final: 0.5677 (mmt90) REVERT: B 59 TYR cc_start: 0.8657 (t80) cc_final: 0.8396 (t80) REVERT: D 253 TYR cc_start: 0.8249 (m-10) cc_final: 0.8020 (m-80) REVERT: D 344 GLU cc_start: 0.8373 (tp30) cc_final: 0.8138 (tp30) REVERT: D 377 ASN cc_start: 0.7824 (t0) cc_final: 0.7414 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1703 time to fit residues: 41.2099 Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 311 HIS D 267 GLN D 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7486 Z= 0.236 Angle : 0.613 8.377 10268 Z= 0.312 Chirality : 0.042 0.177 1254 Planarity : 0.004 0.058 1298 Dihedral : 7.608 84.619 1121 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.27), residues: 1019 helix: 2.21 (0.26), residues: 396 sheet: -1.04 (0.34), residues: 209 loop : -0.42 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 234 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.002 PHE A 28 TYR 0.012 0.001 TYR E 80 ARG 0.003 0.001 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 0.814 Fit side-chains REVERT: A 261 ARG cc_start: 0.6060 (mtt-85) cc_final: 0.5780 (mmt90) REVERT: D 252 ASP cc_start: 0.7485 (t0) cc_final: 0.7251 (t0) REVERT: D 377 ASN cc_start: 0.7700 (t0) cc_final: 0.7341 (t0) outliers start: 16 outliers final: 12 residues processed: 164 average time/residue: 0.1568 time to fit residues: 36.1490 Evaluate side-chains 151 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 75 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.207 Angle : 0.563 8.145 10268 Z= 0.285 Chirality : 0.041 0.141 1254 Planarity : 0.004 0.050 1298 Dihedral : 6.738 80.358 1121 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.24 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.71 (0.27), residues: 1019 helix: 2.26 (0.26), residues: 397 sheet: -1.06 (0.34), residues: 210 loop : -0.39 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 234 HIS 0.004 0.001 HIS D 357 PHE 0.016 0.001 PHE A 28 TYR 0.011 0.001 TYR D 339 ARG 0.002 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.856 Fit side-chains REVERT: A 23 ILE cc_start: 0.7033 (mt) cc_final: 0.6618 (mm) REVERT: A 70 LEU cc_start: 0.8777 (tp) cc_final: 0.8485 (mm) REVERT: B 101 MET cc_start: 0.8456 (mtp) cc_final: 0.8141 (mtp) REVERT: B 146 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8237 (tp) REVERT: D 252 ASP cc_start: 0.7537 (t0) cc_final: 0.7331 (t0) REVERT: D 377 ASN cc_start: 0.7447 (t0) cc_final: 0.7098 (t0) outliers start: 22 outliers final: 17 residues processed: 159 average time/residue: 0.1666 time to fit residues: 37.6424 Evaluate side-chains 155 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 54 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN E 31 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7486 Z= 0.188 Angle : 0.534 8.321 10268 Z= 0.271 Chirality : 0.040 0.159 1254 Planarity : 0.003 0.045 1298 Dihedral : 6.246 82.043 1121 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.68 % Allowed : 20.59 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.27), residues: 1019 helix: 2.39 (0.26), residues: 397 sheet: -1.15 (0.32), residues: 221 loop : -0.43 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 169 HIS 0.011 0.001 HIS B 54 PHE 0.019 0.001 PHE A 28 TYR 0.010 0.001 TYR A 94 ARG 0.002 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.821 Fit side-chains REVERT: A 23 ILE cc_start: 0.7095 (mt) cc_final: 0.6713 (mm) REVERT: B 101 MET cc_start: 0.8499 (mtp) cc_final: 0.8198 (mtp) REVERT: B 146 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 230 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 327 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8456 (p) REVERT: D 25 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7310 (mttp) REVERT: D 253 TYR cc_start: 0.7805 (m-80) cc_final: 0.7516 (m-80) REVERT: D 377 ASN cc_start: 0.7496 (t0) cc_final: 0.7260 (m-40) outliers start: 25 outliers final: 19 residues processed: 168 average time/residue: 0.1524 time to fit residues: 36.7271 Evaluate side-chains 159 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.167 Angle : 0.512 8.350 10268 Z= 0.260 Chirality : 0.040 0.144 1254 Planarity : 0.003 0.042 1298 Dihedral : 5.887 83.827 1121 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.85 % Allowed : 19.56 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.27), residues: 1019 helix: 2.48 (0.26), residues: 396 sheet: -1.26 (0.32), residues: 227 loop : -0.41 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.010 0.001 HIS B 54 PHE 0.022 0.001 PHE A 28 TYR 0.011 0.001 TYR A 94 ARG 0.002 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 0.841 Fit side-chains REVERT: A 23 ILE cc_start: 0.6878 (mt) cc_final: 0.6486 (mm) REVERT: A 91 LEU cc_start: 0.5935 (tt) cc_final: 0.5638 (tt) REVERT: B 101 MET cc_start: 0.8528 (mtt) cc_final: 0.8298 (mtp) REVERT: B 146 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 230 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7933 (p0) REVERT: B 327 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8434 (p) REVERT: D 25 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7283 (mttp) REVERT: D 253 TYR cc_start: 0.7967 (m-80) cc_final: 0.7628 (m-80) outliers start: 33 outliers final: 22 residues processed: 164 average time/residue: 0.1518 time to fit residues: 35.8409 Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7486 Z= 0.217 Angle : 0.529 8.472 10268 Z= 0.269 Chirality : 0.040 0.138 1254 Planarity : 0.003 0.043 1298 Dihedral : 5.847 84.543 1121 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.56 % Allowed : 21.03 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.70 (0.27), residues: 1019 helix: 2.43 (0.26), residues: 396 sheet: -1.26 (0.31), residues: 225 loop : -0.43 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.012 0.001 HIS B 54 PHE 0.023 0.001 PHE A 28 TYR 0.012 0.001 TYR E 95 ARG 0.002 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.799 Fit side-chains REVERT: A 91 LEU cc_start: 0.5958 (tt) cc_final: 0.5721 (tt) REVERT: B 101 MET cc_start: 0.8523 (mtt) cc_final: 0.8283 (mtp) REVERT: B 146 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 230 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8012 (p0) REVERT: B 327 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 25 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7410 (mttp) REVERT: D 253 TYR cc_start: 0.8062 (m-80) cc_final: 0.7733 (m-80) REVERT: E 80 TYR cc_start: 0.7699 (m-80) cc_final: 0.7393 (m-80) outliers start: 31 outliers final: 22 residues processed: 158 average time/residue: 0.1595 time to fit residues: 35.5246 Evaluate side-chains 153 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS D 239 ASN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7486 Z= 0.301 Angle : 0.574 8.731 10268 Z= 0.293 Chirality : 0.042 0.154 1254 Planarity : 0.004 0.044 1298 Dihedral : 6.039 81.750 1121 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.26 % Allowed : 21.76 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.57 (0.26), residues: 1019 helix: 2.28 (0.26), residues: 396 sheet: -1.31 (0.31), residues: 223 loop : -0.47 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.017 0.002 HIS B 54 PHE 0.027 0.002 PHE A 28 TYR 0.018 0.002 TYR E 95 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.842 Fit side-chains REVERT: A 91 LEU cc_start: 0.5961 (tt) cc_final: 0.5749 (tt) REVERT: B 101 MET cc_start: 0.8501 (mtt) cc_final: 0.8272 (mtp) REVERT: B 146 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 230 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7950 (p0) REVERT: D 25 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7362 (mttp) REVERT: D 253 TYR cc_start: 0.8207 (m-80) cc_final: 0.7885 (m-80) REVERT: E 80 TYR cc_start: 0.7728 (m-80) cc_final: 0.7441 (m-80) outliers start: 29 outliers final: 23 residues processed: 152 average time/residue: 0.1485 time to fit residues: 32.5273 Evaluate side-chains 152 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.196 Angle : 0.530 8.571 10268 Z= 0.267 Chirality : 0.040 0.136 1254 Planarity : 0.003 0.042 1298 Dihedral : 5.840 83.550 1121 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.12 % Allowed : 22.50 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.27), residues: 1019 helix: 2.49 (0.26), residues: 390 sheet: -1.21 (0.32), residues: 224 loop : -0.41 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.005 0.001 HIS B 54 PHE 0.023 0.001 PHE A 28 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.918 Fit side-chains REVERT: A 23 ILE cc_start: 0.7144 (mt) cc_final: 0.6650 (mm) REVERT: A 91 LEU cc_start: 0.5911 (tt) cc_final: 0.5673 (tt) REVERT: A 316 ARG cc_start: 0.5862 (ttm110) cc_final: 0.5612 (ttp-170) REVERT: B 101 MET cc_start: 0.8473 (mtt) cc_final: 0.8257 (mtp) REVERT: B 146 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8129 (tp) REVERT: B 230 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 297 TRP cc_start: 0.8368 (m100) cc_final: 0.7911 (m100) REVERT: B 327 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (p) REVERT: D 25 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7237 (mttp) REVERT: D 253 TYR cc_start: 0.8249 (m-80) cc_final: 0.7929 (m-80) REVERT: E 80 TYR cc_start: 0.7716 (m-80) cc_final: 0.7443 (m-80) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.1537 time to fit residues: 33.4692 Evaluate side-chains 154 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.0060 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7486 Z= 0.164 Angle : 0.514 8.488 10268 Z= 0.258 Chirality : 0.039 0.136 1254 Planarity : 0.003 0.042 1298 Dihedral : 5.646 83.925 1121 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.82 % Allowed : 22.79 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1019 helix: 2.48 (0.26), residues: 396 sheet: -0.99 (0.32), residues: 228 loop : -0.41 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 169 HIS 0.005 0.001 HIS B 54 PHE 0.031 0.001 PHE A 28 TYR 0.012 0.001 TYR A 94 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.904 Fit side-chains REVERT: A 23 ILE cc_start: 0.7124 (mt) cc_final: 0.6730 (mm) REVERT: B 146 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 230 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 327 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8446 (p) REVERT: D 25 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7278 (mttp) REVERT: D 253 TYR cc_start: 0.8176 (m-80) cc_final: 0.7889 (m-80) REVERT: E 80 TYR cc_start: 0.7700 (m-80) cc_final: 0.7439 (m-80) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.1442 time to fit residues: 31.4669 Evaluate side-chains 149 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.194 Angle : 0.526 9.192 10268 Z= 0.264 Chirality : 0.040 0.137 1254 Planarity : 0.003 0.042 1298 Dihedral : 5.635 83.559 1121 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.12 % Allowed : 22.50 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1019 helix: 2.47 (0.26), residues: 396 sheet: -0.98 (0.32), residues: 228 loop : -0.40 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 169 HIS 0.005 0.001 HIS B 183 PHE 0.034 0.001 PHE A 28 TYR 0.012 0.001 TYR A 94 ARG 0.005 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.840 Fit side-chains REVERT: A 23 ILE cc_start: 0.7123 (mt) cc_final: 0.6726 (mm) REVERT: A 91 LEU cc_start: 0.5863 (tt) cc_final: 0.5560 (tt) REVERT: B 146 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 230 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7944 (p0) REVERT: B 297 TRP cc_start: 0.8412 (m100) cc_final: 0.8136 (m100) REVERT: B 327 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8455 (p) REVERT: D 25 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7287 (mttp) REVERT: D 253 TYR cc_start: 0.8274 (m-80) cc_final: 0.8000 (m-80) REVERT: E 80 TYR cc_start: 0.7711 (m-80) cc_final: 0.7449 (m-80) outliers start: 28 outliers final: 21 residues processed: 147 average time/residue: 0.1485 time to fit residues: 31.4214 Evaluate side-chains 150 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147587 restraints weight = 8138.509| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.38 r_work: 0.3353 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.172 Angle : 0.517 9.085 10268 Z= 0.259 Chirality : 0.039 0.140 1254 Planarity : 0.003 0.041 1298 Dihedral : 5.545 83.228 1121 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.82 % Allowed : 22.94 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.87 (0.27), residues: 1019 helix: 2.51 (0.26), residues: 396 sheet: -0.96 (0.32), residues: 228 loop : -0.41 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.003 0.001 HIS B 183 PHE 0.027 0.001 PHE A 28 TYR 0.012 0.001 TYR A 94 ARG 0.005 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.67 seconds wall clock time: 35 minutes 45.05 seconds (2145.05 seconds total)