Starting phenix.real_space_refine on Sat Apr 6 13:54:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xms_33303/04_2024/7xms_33303.pdb" } resolution = 2.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5336 2.51 5 N 1413 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 94": "OE1" <-> "OE2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R ARG 252": "NH1" <-> "NH2" Residue "R TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ASP 74": "OD1" <-> "OD2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ASP 201": "OD1" <-> "OD2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8370 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2021 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 264} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 6, 'GLN:plan1': 1, 'HIS:plan': 3, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "A" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1721 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 319} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 331 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1764 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 100 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 4.71, per 1000 atoms: 0.56 Number of scatterers: 8370 At special positions: 0 Unit cell: (114.95, 112.86, 107.635, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1564 8.00 N 1413 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " distance=2.04 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 32.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 47 through 76 removed outlier: 3.671A pdb=" N ALA R 55 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 56 " --> pdb=" O CYS R 52 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE R 69 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG R 74 " --> pdb=" O PHE R 70 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR R 75 " --> pdb=" O VAL R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 110 removed outlier: 3.823A pdb=" N ILE R 84 " --> pdb=" O THR R 80 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR R 85 " --> pdb=" O ALA R 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) Proline residue: R 101 - end of helix removed outlier: 3.656A pdb=" N SER R 105 " --> pdb=" O PRO R 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER R 106 " --> pdb=" O PHE R 102 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 150 removed outlier: 3.726A pdb=" N CYS R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.723A pdb=" N ALA R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 179 removed outlier: 3.637A pdb=" N LEU R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 184 removed outlier: 3.583A pdb=" N PHE R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 removed outlier: 3.777A pdb=" N SER R 208 " --> pdb=" O HIS R 204 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 209 " --> pdb=" O PRO R 205 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 211 " --> pdb=" O TRP R 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE R 216 " --> pdb=" O VAL R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 245 Processing helix chain 'R' and resid 251 through 282 removed outlier: 3.543A pdb=" N PHE R 264 " --> pdb=" O LEU R 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Proline residue: R 274 - end of helix removed outlier: 3.650A pdb=" N VAL R 278 " --> pdb=" O PRO R 274 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN R 279 " --> pdb=" O PHE R 275 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 313 removed outlier: 3.610A pdb=" N ILE R 298 " --> pdb=" O HIS R 294 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.761A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 4.199A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.585A pdb=" N CYS A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.745A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.663A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.735A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.573A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.868A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.624A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.206A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.447A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.543A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.673A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.146A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.873A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.923A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.730A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.536A pdb=" N TYR S 175 " --> pdb=" O MET S 230 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 157 333 hydrogen bonds defined for protein. 939 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: 2.24 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2702 1.34 - 1.46: 2050 1.46 - 1.58: 3715 1.58 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8546 Sorted by residual: bond pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 9.54e-01 bond pdb=" C VAL R 100 " pdb=" N PRO R 101 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.19e-02 7.06e+03 7.77e-01 bond pdb=" CA ILE B 93 " pdb=" C ILE B 93 " ideal model delta sigma weight residual 1.528 1.533 -0.006 8.10e-03 1.52e+04 5.34e-01 bond pdb=" CA VAL R 100 " pdb=" C VAL R 100 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.05e-02 9.07e+03 5.30e-01 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 226 107.25 - 113.94: 4863 113.94 - 120.62: 3341 120.62 - 127.31: 3113 127.31 - 134.00: 88 Bond angle restraints: 11631 Sorted by residual: angle pdb=" N VAL C 30 " pdb=" CA VAL C 30 " pdb=" C VAL C 30 " ideal model delta sigma weight residual 113.42 109.55 3.87 1.17e+00 7.31e-01 1.09e+01 angle pdb=" CA LEU R 179 " pdb=" CB LEU R 179 " pdb=" CG LEU R 179 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.98e+00 angle pdb=" CA VAL C 30 " pdb=" C VAL C 30 " pdb=" N SER C 31 " ideal model delta sigma weight residual 118.90 116.85 2.05 9.40e-01 1.13e+00 4.76e+00 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 121.54 125.65 -4.11 1.91e+00 2.74e-01 4.62e+00 ... (remaining 11626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 4706 15.86 - 31.72: 252 31.72 - 47.58: 51 47.58 - 63.43: 8 63.43 - 79.29: 2 Dihedral angle restraints: 5019 sinusoidal: 1793 harmonic: 3226 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual 93.00 60.93 32.07 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " pdb=" CD LYS A 330 " pdb=" CE LYS A 330 " ideal model delta sinusoidal sigma weight residual 60.00 116.21 -56.21 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " pdb=" OD1 ASP B 27 " ideal model delta sinusoidal sigma weight residual -30.00 -82.31 52.31 1 2.00e+01 2.50e-03 9.33e+00 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 840 0.028 - 0.056: 353 0.056 - 0.084: 86 0.084 - 0.112: 64 0.112 - 0.140: 13 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE S 157 " pdb=" N ILE S 157 " pdb=" C ILE S 157 " pdb=" CB ILE S 157 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1353 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO S 75 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO S 151 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO C 60 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.017 5.00e-02 4.00e+02 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1872 2.78 - 3.31: 7696 3.31 - 3.84: 13897 3.84 - 4.37: 16412 4.37 - 4.90: 27954 Nonbonded interactions: 67831 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.251 2.440 nonbonded pdb=" O PHE A 336 " pdb=" OG1 THR A 340 " model vdw 2.298 2.440 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.300 2.440 nonbonded pdb=" O TYR R 311 " pdb=" OG SER R 315 " model vdw 2.309 2.440 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.320 2.520 ... (remaining 67826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.080 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.920 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 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 : 0.002 0.024 8546 Z= 0.104 Angle : 0.455 10.217 11631 Z= 0.257 Chirality : 0.038 0.140 1356 Planarity : 0.003 0.032 1472 Dihedral : 10.087 79.292 2928 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -4.06 (0.20), residues: 1097 helix: -3.32 (0.18), residues: 313 sheet: -2.11 (0.31), residues: 226 loop : -2.52 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP S 36 HIS 0.004 0.000 HIS S 35 PHE 0.006 0.001 PHE B 199 TYR 0.007 0.001 TYR S 102 ARG 0.001 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 120 ARG cc_start: 0.5332 (ttp-170) cc_final: 0.4831 (ttp-110) REVERT: R 262 LEU cc_start: 0.7570 (tp) cc_final: 0.7156 (tp) REVERT: B 264 TYR cc_start: 0.6271 (m-80) cc_final: 0.5985 (m-80) REVERT: C 21 MET cc_start: 0.4955 (mmp) cc_final: 0.4750 (mpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.0813 time to fit residues: 265.6387 Evaluate side-chains 136 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 GLN R 129 ASN R 150 HIS ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN ** R 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 ASN A 188 HIS A 306 GLN A 333 GLN B 36 ASN B 125 ASN B 295 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN S 39 GLN S 77 ASN S 82 GLN S 113 GLN S 142 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8546 Z= 0.248 Angle : 0.630 9.095 11631 Z= 0.318 Chirality : 0.043 0.155 1356 Planarity : 0.004 0.047 1472 Dihedral : 3.691 19.847 1189 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.68 % Allowed : 15.65 % Favored : 80.67 % 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: -2.47 (0.23), residues: 1097 helix: -1.09 (0.25), residues: 339 sheet: -1.83 (0.31), residues: 245 loop : -1.82 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.006 0.002 HIS B 54 PHE 0.014 0.002 PHE R 216 TYR 0.014 0.002 TYR S 102 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: R 225 LEU cc_start: 0.8180 (tt) cc_final: 0.7813 (mp) REVERT: R 310 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5386 (tt) REVERT: B 43 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7355 (mp) REVERT: B 82 TRP cc_start: 0.7303 (OUTLIER) cc_final: 0.5333 (p90) REVERT: S 5 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7101 (t) outliers start: 32 outliers final: 8 residues processed: 174 average time/residue: 1.0857 time to fit residues: 202.0492 Evaluate side-chains 129 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 GLN R 83 ASN ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN B 125 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8546 Z= 0.227 Angle : 0.605 8.875 11631 Z= 0.299 Chirality : 0.042 0.140 1356 Planarity : 0.004 0.033 1472 Dihedral : 3.830 21.343 1189 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.14 % Allowed : 17.72 % Favored : 78.14 % 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: -1.61 (0.24), residues: 1097 helix: 0.02 (0.28), residues: 339 sheet: -1.39 (0.30), residues: 255 loop : -1.59 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 8 HIS 0.006 0.001 HIS B 62 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR S 103 ARG 0.008 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: R 244 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6694 (mtp180) REVERT: R 310 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5561 (pp) REVERT: B 82 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.6831 (p90) REVERT: S 46 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: S 76 LYS cc_start: 0.7698 (ttmm) cc_final: 0.7331 (mtmm) outliers start: 36 outliers final: 13 residues processed: 154 average time/residue: 1.0396 time to fit residues: 172.2634 Evaluate side-chains 135 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 333 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8546 Z= 0.202 Angle : 0.584 9.183 11631 Z= 0.287 Chirality : 0.041 0.150 1356 Planarity : 0.004 0.056 1472 Dihedral : 3.809 20.996 1189 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.91 % Allowed : 19.79 % Favored : 76.29 % 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: -1.21 (0.25), residues: 1097 helix: 0.50 (0.29), residues: 339 sheet: -1.32 (0.29), residues: 267 loop : -1.35 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 8 HIS 0.005 0.001 HIS B 183 PHE 0.025 0.001 PHE R 275 TYR 0.012 0.002 TYR B 59 ARG 0.007 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: R 222 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7588 (mp) REVERT: R 244 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6745 (mtp180) REVERT: R 310 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5579 (tt) REVERT: S 46 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: S 109 ASP cc_start: 0.7031 (t0) cc_final: 0.6649 (m-30) outliers start: 34 outliers final: 15 residues processed: 153 average time/residue: 1.0290 time to fit residues: 169.6703 Evaluate side-chains 139 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.8578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8546 Z= 0.221 Angle : 0.614 9.356 11631 Z= 0.301 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.039 1472 Dihedral : 3.937 22.123 1189 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.95 % Allowed : 20.60 % Favored : 74.45 % 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: -0.95 (0.25), residues: 1097 helix: 0.75 (0.29), residues: 339 sheet: -1.19 (0.31), residues: 260 loop : -1.22 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 8 HIS 0.005 0.001 HIS B 62 PHE 0.032 0.002 PHE R 275 TYR 0.014 0.002 TYR B 264 ARG 0.010 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: R 222 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7580 (mp) REVERT: R 244 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6842 (mtp180) REVERT: R 310 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5784 (tt) REVERT: B 230 ASN cc_start: 0.7615 (t0) cc_final: 0.7385 (t160) REVERT: S 109 ASP cc_start: 0.7101 (t0) cc_final: 0.6712 (m-30) REVERT: S 141 THR cc_start: 0.7760 (t) cc_final: 0.7471 (p) outliers start: 43 outliers final: 17 residues processed: 153 average time/residue: 0.9943 time to fit residues: 163.9986 Evaluate side-chains 138 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 26 optimal weight: 0.0010 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 333 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8546 Z= 0.169 Angle : 0.582 10.614 11631 Z= 0.284 Chirality : 0.040 0.139 1356 Planarity : 0.003 0.041 1472 Dihedral : 3.788 20.721 1189 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 23.25 % Favored : 73.76 % 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 (0.26), residues: 1097 helix: 0.94 (0.29), residues: 342 sheet: -1.02 (0.31), residues: 276 loop : -1.15 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 8 HIS 0.005 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR B 264 ARG 0.010 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: R 222 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7554 (mp) REVERT: R 238 MET cc_start: 0.7019 (tpt) cc_final: 0.6661 (ttm) REVERT: R 244 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6819 (mtp180) REVERT: R 310 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5805 (tt) REVERT: A 198 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6828 (mpp) REVERT: B 230 ASN cc_start: 0.7482 (t0) cc_final: 0.7257 (t160) REVERT: B 325 MET cc_start: 0.7379 (tpp) cc_final: 0.7177 (tpp) REVERT: S 109 ASP cc_start: 0.7194 (t0) cc_final: 0.6802 (m-30) REVERT: S 141 THR cc_start: 0.7689 (t) cc_final: 0.7376 (p) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 0.9723 time to fit residues: 147.2152 Evaluate side-chains 133 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8546 Z= 0.173 Angle : 0.597 11.610 11631 Z= 0.286 Chirality : 0.041 0.138 1356 Planarity : 0.003 0.044 1472 Dihedral : 3.799 20.246 1189 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.22 % Allowed : 23.59 % Favored : 73.19 % 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: -0.59 (0.26), residues: 1097 helix: 1.04 (0.29), residues: 341 sheet: -0.81 (0.31), residues: 270 loop : -1.12 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 8 HIS 0.005 0.001 HIS B 183 PHE 0.031 0.001 PHE B 199 TYR 0.016 0.001 TYR B 264 ARG 0.011 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 222 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7560 (mp) REVERT: R 244 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6820 (mtp180) REVERT: R 310 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5937 (tt) REVERT: A 198 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6787 (mpp) REVERT: A 257 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7903 (pttm) REVERT: B 230 ASN cc_start: 0.7469 (t0) cc_final: 0.7267 (t160) outliers start: 28 outliers final: 11 residues processed: 139 average time/residue: 1.0083 time to fit residues: 151.3822 Evaluate side-chains 134 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 0.0000 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8546 Z= 0.187 Angle : 0.612 12.061 11631 Z= 0.293 Chirality : 0.041 0.148 1356 Planarity : 0.004 0.046 1472 Dihedral : 3.884 20.198 1189 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 24.28 % Favored : 72.50 % 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: -0.50 (0.26), residues: 1097 helix: 1.08 (0.29), residues: 342 sheet: -0.85 (0.32), residues: 264 loop : -0.98 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 8 HIS 0.005 0.001 HIS B 183 PHE 0.023 0.001 PHE B 199 TYR 0.012 0.001 TYR B 264 ARG 0.012 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 222 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7569 (mp) REVERT: R 238 MET cc_start: 0.7064 (tpt) cc_final: 0.6790 (ttm) REVERT: R 244 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6840 (mtp180) REVERT: R 310 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5992 (tt) REVERT: A 198 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6751 (mpp) REVERT: B 230 ASN cc_start: 0.7527 (t0) cc_final: 0.7321 (t160) REVERT: C 21 MET cc_start: 0.5287 (mpt) cc_final: 0.4265 (tmm) REVERT: S 17 SER cc_start: 0.7421 (t) cc_final: 0.7022 (m) outliers start: 28 outliers final: 14 residues processed: 142 average time/residue: 1.0021 time to fit residues: 153.8941 Evaluate side-chains 132 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8546 Z= 0.305 Angle : 0.691 12.176 11631 Z= 0.337 Chirality : 0.044 0.170 1356 Planarity : 0.004 0.055 1472 Dihedral : 4.401 20.734 1189 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.34 % Allowed : 24.63 % Favored : 72.04 % 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: -0.44 (0.26), residues: 1097 helix: 1.04 (0.29), residues: 336 sheet: -0.88 (0.33), residues: 252 loop : -0.81 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 171 HIS 0.009 0.002 HIS B 62 PHE 0.027 0.002 PHE R 275 TYR 0.026 0.002 TYR B 264 ARG 0.011 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6814 (mtp180) REVERT: A 257 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8035 (ptpt) REVERT: B 230 ASN cc_start: 0.7843 (t0) cc_final: 0.7591 (t160) REVERT: B 336 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7873 (tt) REVERT: C 21 MET cc_start: 0.5405 (mpt) cc_final: 0.4493 (tmm) REVERT: S 17 SER cc_start: 0.7584 (t) cc_final: 0.7244 (m) REVERT: S 46 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7071 (pm20) outliers start: 29 outliers final: 15 residues processed: 137 average time/residue: 0.9416 time to fit residues: 139.9430 Evaluate side-chains 125 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0040 chunk 71 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8546 Z= 0.163 Angle : 0.621 13.313 11631 Z= 0.297 Chirality : 0.041 0.164 1356 Planarity : 0.004 0.052 1472 Dihedral : 4.007 21.059 1189 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.30 % Allowed : 26.35 % Favored : 71.35 % 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: -0.39 (0.26), residues: 1097 helix: 1.11 (0.29), residues: 340 sheet: -0.81 (0.32), residues: 260 loop : -0.85 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 8 HIS 0.003 0.001 HIS B 183 PHE 0.028 0.001 PHE R 275 TYR 0.015 0.001 TYR B 264 ARG 0.012 0.001 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 135 PHE cc_start: 0.7045 (m-80) cc_final: 0.6243 (m-80) REVERT: R 310 LEU cc_start: 0.6225 (tt) cc_final: 0.5688 (tp) REVERT: A 257 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (pttm) REVERT: C 21 MET cc_start: 0.5304 (mpt) cc_final: 0.4436 (tmm) REVERT: S 46 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: S 109 ASP cc_start: 0.7651 (t0) cc_final: 0.7213 (m-30) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.9133 time to fit residues: 133.8237 Evaluate side-chains 127 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.193854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.154237 restraints weight = 9242.521| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.91 r_work: 0.3870 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8546 Z= 0.203 Angle : 0.640 13.130 11631 Z= 0.307 Chirality : 0.042 0.182 1356 Planarity : 0.004 0.050 1472 Dihedral : 4.074 20.140 1189 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.96 % Allowed : 27.85 % Favored : 70.20 % 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: -0.36 (0.26), residues: 1097 helix: 1.18 (0.29), residues: 339 sheet: -0.81 (0.32), residues: 260 loop : -0.84 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 8 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE R 275 TYR 0.019 0.002 TYR B 264 ARG 0.012 0.001 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.16 seconds wall clock time: 69 minutes 46.19 seconds (4186.19 seconds total)