Starting phenix.real_space_refine on Thu Feb 15 22:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qlf_4581/02_2024/6qlf_4581.pdb" } resolution = 3.45 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= 0.003 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 76 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 53 5.16 5 C 8639 2.51 5 N 2348 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 32": "OD1" <-> "OD2" Residue "L ASP 45": "OD1" <-> "OD2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N ASP 216": "OD1" <-> "OD2" Residue "N ASP 285": "OD1" <-> "OD2" Residue "N TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N ASP 425": "OD1" <-> "OD2" Residue "O ASP 185": "OD1" <-> "OD2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O ASP 263": "OD1" <-> "OD2" Residue "O ASP 296": "OD1" <-> "OD2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "P ASP 159": "OD1" <-> "OD2" Residue "P ASP 173": "OD1" <-> "OD2" Residue "P TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 209": "OD1" <-> "OD2" Residue "P GLU 246": "OE1" <-> "OE2" Residue "Q GLU 256": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "Q GLU 270": "OE1" <-> "OE2" Residue "Q GLU 271": "OE1" <-> "OE2" Residue "Q GLU 331": "OE1" <-> "OE2" Residue "Q ASP 338": "OD1" <-> "OD2" Residue "Q ASP 345": "OD1" <-> "OD2" Residue "Q PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 187": "NH1" <-> "NH2" Residue "U ARG 212": "NH1" <-> "NH2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U GLU 242": "OE1" <-> "OE2" Residue "U ASP 285": "OD1" <-> "OD2" Residue "U ASP 300": "OD1" <-> "OD2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y GLU 111": "OE1" <-> "OE2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y GLU 183": "OE1" <-> "OE2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z GLU 118": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13501 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1939 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2923 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1795 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "Q" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1421 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 156 Chain: "U" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1229 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 7.19, per 1000 atoms: 0.53 Number of scatterers: 13501 At special positions: 0 Unit cell: (139.52, 164.59, 134.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2461 8.00 N 2348 7.00 C 8639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.96 Conformation dependent library (CDL) restraints added in 2.5 seconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3438 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 56.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 95 through 108 removed outlier: 3.573A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.596A pdb=" N LYS L 156 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.645A pdb=" N LEU L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 4.024A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.510A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 65 removed outlier: 3.630A pdb=" N ASP N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU N 61 " --> pdb=" O THR N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.655A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.784A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 126 through 138 removed outlier: 3.806A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.849A pdb=" N ARG N 222 " --> pdb=" O ASP N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 removed outlier: 3.977A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 265 removed outlier: 3.551A pdb=" N ALA N 264 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 261 through 265' Processing helix chain 'N' and resid 268 through 273 removed outlier: 4.301A pdb=" N CYS N 272 " --> pdb=" O PRO N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 removed outlier: 3.637A pdb=" N GLY N 433 " --> pdb=" O GLY N 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 172 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.890A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.761A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 349 removed outlier: 3.801A pdb=" N TRP O 344 " --> pdb=" O ASN O 340 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 360 removed outlier: 3.878A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.565A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 160 removed outlier: 3.737A pdb=" N HIS P 160 " --> pdb=" O TYR P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 231 removed outlier: 4.218A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 226 through 231' Processing helix chain 'P' and resid 232 through 234 No H-bonds generated for 'chain 'P' and resid 232 through 234' Processing helix chain 'P' and resid 236 through 264 Processing helix chain 'P' and resid 333 through 348 Processing helix chain 'P' and resid 352 through 363 removed outlier: 3.726A pdb=" N GLU P 356 " --> pdb=" O THR P 352 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 184 removed outlier: 3.657A pdb=" N GLU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.809A pdb=" N ARG Q 198 " --> pdb=" O ASN Q 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 199 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 199' Processing helix chain 'Q' and resid 200 through 217 removed outlier: 3.716A pdb=" N GLU Q 204 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Q 217 " --> pdb=" O LYS Q 213 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 293 removed outlier: 3.861A pdb=" N ILE Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 291 " --> pdb=" O LEU Q 287 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE Q 292 " --> pdb=" O THR Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 323 through 333 removed outlier: 3.694A pdb=" N ASN Q 327 " --> pdb=" O VAL Q 323 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU Q 332 " --> pdb=" O ASP Q 328 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 359 through 381 Processing helix chain 'Q' and resid 382 through 391 removed outlier: 3.728A pdb=" N LYS Q 387 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU Q 388 " --> pdb=" O GLU Q 384 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL Q 391 " --> pdb=" O LYS Q 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 156 Proline residue: U 152 - end of helix Processing helix chain 'U' and resid 170 through 232 removed outlier: 4.315A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.564A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 318 removed outlier: 3.595A pdb=" N ILE U 309 " --> pdb=" O LEU U 305 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN U 315 " --> pdb=" O LYS U 311 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.911A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.078A pdb=" N ALA Y 31 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 82 removed outlier: 3.654A pdb=" N LEU Y 61 " --> pdb=" O GLY Y 57 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 103 removed outlier: 3.669A pdb=" N GLU Y 102 " --> pdb=" O ARG Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 118 Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 196 Processing helix chain 'Y' and resid 196 through 214 removed outlier: 3.543A pdb=" N VAL Y 203 " --> pdb=" O GLY Y 199 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA Y 204 " --> pdb=" O LYS Y 200 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU Y 210 " --> pdb=" O GLU Y 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Y 211 " --> pdb=" O GLU Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 236 removed outlier: 3.923A pdb=" N GLU Y 227 " --> pdb=" O PRO Y 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 13 removed outlier: 3.977A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 24 removed outlier: 3.907A pdb=" N GLN Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 50 removed outlier: 4.269A pdb=" N TYR Z 43 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 45 " --> pdb=" O HIS Z 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN Z 47 " --> pdb=" O TYR Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 57 Processing helix chain 'Z' and resid 57 through 81 removed outlier: 3.663A pdb=" N PHE Z 65 " --> pdb=" O ILE Z 61 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE Z 75 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU Z 81 " --> pdb=" O GLU Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.836A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 152 Processing sheet with id=AA1, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.553A pdb=" N GLN L 36 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 56 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR L 223 " --> pdb=" O TYR L 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 130 through 131 removed outlier: 3.605A pdb=" N GLN L 139 " --> pdb=" O HIS L 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 161 through 164 removed outlier: 6.421A pdb=" N LYS L 146 " --> pdb=" O VAL L 208 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL L 208 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR L 148 " --> pdb=" O THR L 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 117 through 118 removed outlier: 3.618A pdb=" N LYS N 117 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 141 through 146 removed outlier: 4.008A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 295 through 298 removed outlier: 3.671A pdb=" N LYS N 295 " --> pdb=" O ILE P 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 384 through 385 removed outlier: 3.622A pdb=" N VAL N 385 " --> pdb=" O PHE N 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 398 through 400 removed outlier: 3.594A pdb=" N ILE N 398 " --> pdb=" O ASN N 391 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET N 443 " --> pdb=" O ASP N 446 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 4.166A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 Processing sheet with id=AB2, first strand: chain 'O' and resid 305 through 309 removed outlier: 3.839A pdb=" N LYS O 314 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 330 " --> pdb=" O LYS O 314 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 168 through 172 removed outlier: 5.425A pdb=" N VAL P 169 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN P 186 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL P 185 " --> pdb=" O PHE P 201 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 270 through 272 removed outlier: 3.563A pdb=" N MET P 318 " --> pdb=" O THR P 303 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2334 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: 4.01 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4207 1.34 - 1.46: 2284 1.46 - 1.58: 7119 1.58 - 1.70: 1 1.70 - 1.82: 87 Bond restraints: 13698 Sorted by residual: bond pdb=" CA THR N 14 " pdb=" CB THR N 14 " ideal model delta sigma weight residual 1.529 1.591 -0.062 1.43e-02 4.89e+03 1.89e+01 bond pdb=" N MET P 274 " pdb=" CA MET P 274 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.25e-02 6.40e+03 8.10e+00 bond pdb=" N VAL L 40 " pdb=" CA VAL L 40 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.23e-02 6.61e+03 7.39e+00 bond pdb=" N LEU Q 296 " pdb=" CA LEU Q 296 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.68e+00 bond pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.08e+00 ... (remaining 13693 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 208 105.93 - 112.96: 7578 112.96 - 119.98: 4604 119.98 - 127.01: 6042 127.01 - 134.04: 101 Bond angle restraints: 18533 Sorted by residual: angle pdb=" N ILE U 283 " pdb=" CA ILE U 283 " pdb=" C ILE U 283 " ideal model delta sigma weight residual 112.96 106.94 6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" N VAL P 224 " pdb=" CA VAL P 224 " pdb=" C VAL P 224 " ideal model delta sigma weight residual 112.17 107.28 4.89 9.50e-01 1.11e+00 2.65e+01 angle pdb=" N VAL O 310 " pdb=" CA VAL O 310 " pdb=" C VAL O 310 " ideal model delta sigma weight residual 109.34 99.62 9.72 2.08e+00 2.31e-01 2.18e+01 angle pdb=" C GLU L 135 " pdb=" N ASN L 136 " pdb=" CA ASN L 136 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ILE N 393 " pdb=" N ASN N 394 " pdb=" CA ASN N 394 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 ... (remaining 18528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7366 17.67 - 35.34: 826 35.34 - 53.00: 133 53.00 - 70.67: 26 70.67 - 88.34: 11 Dihedral angle restraints: 8362 sinusoidal: 3113 harmonic: 5249 Sorted by residual: dihedral pdb=" CA TYR N 77 " pdb=" C TYR N 77 " pdb=" N VAL N 78 " pdb=" CA VAL N 78 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASP P 209 " pdb=" C ASP P 209 " pdb=" N SER P 210 " pdb=" CA SER P 210 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU P 208 " pdb=" C GLU P 208 " pdb=" N ASP P 209 " pdb=" CA ASP P 209 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 8359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1577 0.043 - 0.086: 459 0.086 - 0.129: 144 0.129 - 0.172: 33 0.172 - 0.215: 8 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA ASN N 394 " pdb=" N ASN N 394 " pdb=" C ASN N 394 " pdb=" CB ASN N 394 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA VAL O 310 " pdb=" N VAL O 310 " pdb=" C VAL O 310 " pdb=" CB VAL O 310 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL P 224 " pdb=" CA VAL P 224 " pdb=" CG1 VAL P 224 " pdb=" CG2 VAL P 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2218 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 273 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C LEU P 273 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU P 273 " -0.017 2.00e-02 2.50e+03 pdb=" N MET P 274 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 152 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO N 153 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO N 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO N 153 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 145 " -0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO P 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 146 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 146 " -0.031 5.00e-02 4.00e+02 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3821 2.81 - 3.33: 11635 3.33 - 3.86: 21378 3.86 - 4.38: 22977 4.38 - 4.90: 41963 Nonbonded interactions: 101774 Sorted by model distance: nonbonded pdb=" OH TYR U 302 " pdb=" OE1 GLU Y 183 " model vdw 2.290 2.440 nonbonded pdb=" O SER O 153 " pdb=" OG SER O 153 " model vdw 2.326 2.440 nonbonded pdb=" OG SER N 46 " pdb=" O VAL N 78 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR L 133 " pdb=" O ILE L 137 " model vdw 2.350 2.440 nonbonded pdb=" OG1 THR Q 364 " pdb=" OG SER U 282 " model vdw 2.351 2.440 ... (remaining 101769 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 7.590 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13698 Z= 0.305 Angle : 0.828 9.722 18533 Z= 0.481 Chirality : 0.048 0.215 2221 Planarity : 0.005 0.056 2336 Dihedral : 15.137 88.340 4924 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 0.44 % Allowed : 6.80 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.16), residues: 1733 helix: -2.03 (0.13), residues: 917 sheet: -2.94 (0.30), residues: 222 loop : -3.09 (0.20), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 236 HIS 0.006 0.001 HIS U 237 PHE 0.020 0.002 PHE L 161 TYR 0.028 0.002 TYR P 156 ARG 0.004 0.000 ARG N 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: L 32 ASP cc_start: 0.7762 (p0) cc_final: 0.7541 (p0) REVERT: L 34 ASP cc_start: 0.7090 (p0) cc_final: 0.6684 (p0) REVERT: L 160 GLN cc_start: 0.8045 (pp30) cc_final: 0.7811 (pt0) REVERT: N 97 MET cc_start: 0.8043 (ttm) cc_final: 0.7827 (ttm) REVERT: N 403 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7699 (mttp) REVERT: O 252 ASP cc_start: 0.8119 (t0) cc_final: 0.7732 (t0) REVERT: P 318 MET cc_start: 0.7701 (ptm) cc_final: 0.7487 (ptt) REVERT: Q 264 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7787 (tpp80) REVERT: Q 266 GLN cc_start: 0.8234 (tp40) cc_final: 0.7932 (mm-40) REVERT: Q 270 GLU cc_start: 0.7623 (tp30) cc_final: 0.7173 (tp30) REVERT: Q 274 LYS cc_start: 0.7262 (pptt) cc_final: 0.6921 (tppt) REVERT: U 218 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7830 (tm-30) REVERT: U 249 LYS cc_start: 0.8269 (mttt) cc_final: 0.7864 (mptt) REVERT: U 251 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8789 (mmmt) REVERT: U 254 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8074 (ttpt) REVERT: U 285 ASP cc_start: 0.8599 (t70) cc_final: 0.8365 (t0) REVERT: U 308 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8202 (mttp) REVERT: Y 64 LYS cc_start: 0.8331 (tptp) cc_final: 0.8063 (tptp) REVERT: Y 180 SER cc_start: 0.8435 (t) cc_final: 0.8224 (t) REVERT: Z 20 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6299 (mp) REVERT: Z 62 LYS cc_start: 0.8384 (tttt) cc_final: 0.7692 (mtpt) outliers start: 6 outliers final: 3 residues processed: 314 average time/residue: 0.3389 time to fit residues: 141.9373 Evaluate side-chains 235 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Z residue 20 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 ASN L 96 ASN N 165 ASN N 213 HIS N 226 GLN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 277 ASN N 435 ASN O 274 GLN O 322 ASN P 135 GLN P 297 GLN Q 245 GLN U 208 GLN U 257 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Z 113 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13698 Z= 0.181 Angle : 0.531 10.126 18533 Z= 0.279 Chirality : 0.040 0.204 2221 Planarity : 0.004 0.039 2336 Dihedral : 4.910 58.989 1896 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.60 % Favored : 94.29 % Rotamer: Outliers : 1.90 % Allowed : 13.90 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1733 helix: 0.21 (0.17), residues: 934 sheet: -2.12 (0.33), residues: 231 loop : -2.73 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 102 HIS 0.003 0.001 HIS N 213 PHE 0.014 0.001 PHE O 178 TYR 0.015 0.001 TYR Q 363 ARG 0.007 0.000 ARG P 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 1.762 Fit side-chains REVERT: L 34 ASP cc_start: 0.7038 (p0) cc_final: 0.6577 (p0) REVERT: L 160 GLN cc_start: 0.8079 (pp30) cc_final: 0.7816 (pt0) REVERT: N 403 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7616 (mttp) REVERT: O 252 ASP cc_start: 0.8112 (t0) cc_final: 0.7744 (t0) REVERT: O 360 ASN cc_start: 0.8591 (m-40) cc_final: 0.8391 (m-40) REVERT: P 348 TYR cc_start: 0.8057 (m-10) cc_final: 0.7820 (m-10) REVERT: Q 264 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7782 (tpp80) REVERT: U 251 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8754 (mmmt) REVERT: U 285 ASP cc_start: 0.8666 (t70) cc_final: 0.8419 (t0) REVERT: Y 15 GLU cc_start: 0.8192 (tp30) cc_final: 0.7923 (tp30) REVERT: Y 119 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7840 (ttmm) REVERT: Y 122 GLN cc_start: 0.8511 (pt0) cc_final: 0.8284 (pt0) REVERT: Y 183 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6407 (tm-30) REVERT: Z 52 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7196 (ptm160) REVERT: Z 62 LYS cc_start: 0.8138 (tttt) cc_final: 0.7484 (mtmt) REVERT: Z 103 GLN cc_start: 0.8029 (mt0) cc_final: 0.7815 (tt0) outliers start: 26 outliers final: 16 residues processed: 263 average time/residue: 0.3215 time to fit residues: 117.8278 Evaluate side-chains 239 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 252 HIS O 274 GLN O 322 ASN U 208 GLN Y 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.064 13698 Z= 0.625 Angle : 0.745 12.310 18533 Z= 0.385 Chirality : 0.047 0.176 2221 Planarity : 0.005 0.064 2336 Dihedral : 5.377 58.205 1894 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 3.95 % Allowed : 18.58 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1733 helix: 0.71 (0.17), residues: 934 sheet: -1.99 (0.33), residues: 233 loop : -2.61 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 112 HIS 0.006 0.001 HIS N 213 PHE 0.031 0.003 PHE O 178 TYR 0.018 0.002 TYR Z 43 ARG 0.006 0.001 ARG N 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 1.437 Fit side-chains REVERT: L 32 ASP cc_start: 0.7582 (p0) cc_final: 0.7310 (p0) REVERT: L 34 ASP cc_start: 0.7133 (p0) cc_final: 0.6689 (p0) REVERT: L 111 MET cc_start: 0.8502 (mtt) cc_final: 0.8180 (mtt) REVERT: N 97 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8101 (ttm) REVERT: N 255 MET cc_start: 0.8873 (mmm) cc_final: 0.8663 (mmm) REVERT: O 360 ASN cc_start: 0.8613 (m-40) cc_final: 0.8412 (m-40) REVERT: Q 274 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7218 (tptt) REVERT: U 176 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6640 (mmt-90) REVERT: U 251 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8687 (mmmt) REVERT: U 299 MET cc_start: 0.8281 (mmm) cc_final: 0.7996 (mmm) REVERT: Y 120 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7832 (pp) REVERT: Y 183 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6623 (tm-30) REVERT: Z 52 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7324 (ttp-170) REVERT: Z 58 GLU cc_start: 0.7831 (tt0) cc_final: 0.7602 (mm-30) REVERT: Z 62 LYS cc_start: 0.8268 (tttt) cc_final: 0.7626 (mtmt) outliers start: 54 outliers final: 33 residues processed: 253 average time/residue: 0.3013 time to fit residues: 104.7562 Evaluate side-chains 244 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 146 MET Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 170 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 322 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13698 Z= 0.264 Angle : 0.553 11.005 18533 Z= 0.289 Chirality : 0.041 0.163 2221 Planarity : 0.003 0.043 2336 Dihedral : 4.817 51.069 1894 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.93 % Allowed : 21.36 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1733 helix: 1.29 (0.18), residues: 927 sheet: -1.73 (0.34), residues: 229 loop : -2.37 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 102 HIS 0.003 0.001 HIS N 213 PHE 0.017 0.002 PHE O 178 TYR 0.017 0.001 TYR Y 193 ARG 0.005 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.594 Fit side-chains REVERT: L 111 MET cc_start: 0.8446 (mtt) cc_final: 0.8152 (mtt) REVERT: L 160 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7761 (pp30) REVERT: N 84 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7580 (mt) REVERT: N 330 MET cc_start: 0.8969 (tpp) cc_final: 0.8560 (tpt) REVERT: P 304 MET cc_start: 0.8628 (mmm) cc_final: 0.8422 (mmm) REVERT: P 348 TYR cc_start: 0.7928 (m-10) cc_final: 0.7684 (m-10) REVERT: Q 266 GLN cc_start: 0.8231 (tp40) cc_final: 0.7904 (mm-40) REVERT: Q 274 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7193 (tptt) REVERT: U 176 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6586 (mmt-90) REVERT: U 251 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8558 (mmmt) REVERT: U 299 MET cc_start: 0.8186 (mmm) cc_final: 0.7970 (mmm) REVERT: Y 158 GLN cc_start: 0.7911 (mt0) cc_final: 0.7679 (mt0) REVERT: Z 52 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7326 (ttp-170) REVERT: Z 62 LYS cc_start: 0.8206 (tttt) cc_final: 0.7643 (mtmt) outliers start: 40 outliers final: 28 residues processed: 248 average time/residue: 0.3033 time to fit residues: 104.1290 Evaluate side-chains 240 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN Q 254 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13698 Z= 0.184 Angle : 0.510 10.853 18533 Z= 0.265 Chirality : 0.040 0.171 2221 Planarity : 0.003 0.037 2336 Dihedral : 4.398 41.608 1894 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 3.00 % Allowed : 22.60 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1733 helix: 1.73 (0.18), residues: 928 sheet: -1.54 (0.34), residues: 228 loop : -2.25 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 102 HIS 0.002 0.001 HIS N 143 PHE 0.013 0.001 PHE P 197 TYR 0.013 0.001 TYR Y 193 ARG 0.006 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 233 time to evaluate : 1.579 Fit side-chains REVERT: L 29 LEU cc_start: 0.8497 (mp) cc_final: 0.8022 (mp) REVERT: L 95 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7486 (mtm-85) REVERT: L 111 MET cc_start: 0.8386 (mtt) cc_final: 0.8150 (mtt) REVERT: L 115 LYS cc_start: 0.8004 (tttp) cc_final: 0.7783 (mtpp) REVERT: L 160 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7729 (pp30) REVERT: L 238 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7825 (mm-40) REVERT: N 100 LYS cc_start: 0.8343 (pttt) cc_final: 0.8044 (ptpt) REVERT: O 252 ASP cc_start: 0.8269 (t0) cc_final: 0.8007 (t0) REVERT: O 323 GLU cc_start: 0.7917 (pt0) cc_final: 0.7645 (pt0) REVERT: P 348 TYR cc_start: 0.7869 (m-10) cc_final: 0.7655 (m-10) REVERT: Q 266 GLN cc_start: 0.8245 (tp40) cc_final: 0.7909 (mm-40) REVERT: U 176 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6498 (mmt-90) REVERT: U 218 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7995 (tm-30) REVERT: U 251 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8593 (mmmt) REVERT: Y 119 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7947 (ttmm) REVERT: Y 120 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7519 (pp) REVERT: Y 158 GLN cc_start: 0.7863 (mt0) cc_final: 0.7531 (mt0) REVERT: Z 43 TYR cc_start: 0.6326 (p90) cc_final: 0.4883 (t80) REVERT: Z 62 LYS cc_start: 0.8253 (tttt) cc_final: 0.7593 (mtmt) outliers start: 41 outliers final: 29 residues processed: 264 average time/residue: 0.2925 time to fit residues: 107.3336 Evaluate side-chains 253 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 201 LEU Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 141 optimal weight: 0.0670 chunk 78 optimal weight: 0.0170 chunk 14 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN O 360 ASN U 208 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Z 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13698 Z= 0.137 Angle : 0.481 9.027 18533 Z= 0.250 Chirality : 0.039 0.152 2221 Planarity : 0.003 0.036 2336 Dihedral : 4.003 26.363 1892 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 2.41 % Allowed : 22.82 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1733 helix: 2.13 (0.18), residues: 927 sheet: -1.28 (0.34), residues: 230 loop : -2.15 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 102 HIS 0.002 0.000 HIS U 294 PHE 0.012 0.001 PHE P 197 TYR 0.012 0.001 TYR Y 91 ARG 0.006 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: L 29 LEU cc_start: 0.8456 (mp) cc_final: 0.7957 (mp) REVERT: L 111 MET cc_start: 0.8431 (mtt) cc_final: 0.8221 (mtt) REVERT: O 252 ASP cc_start: 0.8175 (t0) cc_final: 0.7871 (t0) REVERT: O 326 SER cc_start: 0.8866 (t) cc_final: 0.8476 (m) REVERT: P 150 MET cc_start: 0.8420 (mmt) cc_final: 0.7990 (mmm) REVERT: P 235 ARG cc_start: 0.6586 (mmm160) cc_final: 0.6333 (mmp-170) REVERT: Q 266 GLN cc_start: 0.8236 (tp40) cc_final: 0.7904 (mm-40) REVERT: U 176 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6461 (mmt-90) REVERT: U 251 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8747 (mmmt) REVERT: U 308 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7490 (tttt) REVERT: Y 119 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7791 (ttmm) REVERT: Y 120 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7483 (pp) REVERT: Z 43 TYR cc_start: 0.6150 (p90) cc_final: 0.4414 (m-80) REVERT: Z 62 LYS cc_start: 0.8192 (tttt) cc_final: 0.7539 (mtmt) outliers start: 33 outliers final: 29 residues processed: 264 average time/residue: 0.2931 time to fit residues: 107.3499 Evaluate side-chains 254 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 108 THR Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN U 208 GLN U 310 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 13698 Z= 0.588 Angle : 0.731 10.833 18533 Z= 0.375 Chirality : 0.047 0.170 2221 Planarity : 0.005 0.061 2336 Dihedral : 4.869 27.476 1890 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 3.29 % Allowed : 22.82 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1733 helix: 1.51 (0.17), residues: 931 sheet: -1.35 (0.34), residues: 239 loop : -2.23 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 112 HIS 0.006 0.001 HIS N 213 PHE 0.034 0.003 PHE O 178 TYR 0.018 0.002 TYR Z 43 ARG 0.011 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 1.658 Fit side-chains REVERT: L 95 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: L 160 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7771 (pp30) REVERT: L 238 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8041 (mm-40) REVERT: N 255 MET cc_start: 0.8756 (mmm) cc_final: 0.8354 (mmm) REVERT: P 347 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7797 (pp20) REVERT: Q 266 GLN cc_start: 0.8370 (tp40) cc_final: 0.7988 (mm-40) REVERT: Q 274 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7280 (tptt) REVERT: U 176 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6716 (mmt-90) REVERT: U 251 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8731 (mmmt) REVERT: U 299 MET cc_start: 0.8584 (mmm) cc_final: 0.8143 (mmm) REVERT: Y 120 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7821 (pp) REVERT: Z 43 TYR cc_start: 0.6023 (p90) cc_final: 0.4251 (m-80) REVERT: Z 62 LYS cc_start: 0.8286 (tttt) cc_final: 0.7695 (mtmt) outliers start: 45 outliers final: 30 residues processed: 256 average time/residue: 0.2929 time to fit residues: 104.2391 Evaluate side-chains 249 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN O 360 ASN U 310 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13698 Z= 0.215 Angle : 0.551 11.542 18533 Z= 0.286 Chirality : 0.041 0.163 2221 Planarity : 0.003 0.041 2336 Dihedral : 4.379 24.504 1890 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 2.41 % Allowed : 23.56 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1733 helix: 1.92 (0.18), residues: 928 sheet: -1.22 (0.35), residues: 229 loop : -2.06 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 102 HIS 0.002 0.001 HIS N 213 PHE 0.016 0.001 PHE L 149 TYR 0.020 0.001 TYR N 33 ARG 0.004 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: L 160 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7709 (pp30) REVERT: N 255 MET cc_start: 0.8556 (mmm) cc_final: 0.8207 (mmm) REVERT: N 330 MET cc_start: 0.8957 (tpp) cc_final: 0.8520 (tpt) REVERT: O 252 ASP cc_start: 0.8260 (t0) cc_final: 0.8010 (t0) REVERT: P 347 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7854 (pp20) REVERT: Q 266 GLN cc_start: 0.8290 (tp40) cc_final: 0.7930 (mm-40) REVERT: Q 274 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7196 (tptt) REVERT: U 176 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6573 (mmt-90) REVERT: U 251 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8722 (mmmt) REVERT: U 299 MET cc_start: 0.8615 (mmm) cc_final: 0.8130 (mmm) REVERT: Y 119 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8017 (ttmm) REVERT: Y 120 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7497 (pp) REVERT: Z 43 TYR cc_start: 0.6309 (p90) cc_final: 0.4389 (m-80) REVERT: Z 62 LYS cc_start: 0.8264 (tttt) cc_final: 0.7646 (mtmt) outliers start: 33 outliers final: 26 residues processed: 257 average time/residue: 0.3128 time to fit residues: 110.4104 Evaluate side-chains 253 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 376 GLN Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Z residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 0.0170 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 149 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 435 ASN O 220 HIS O 322 ASN O 360 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13698 Z= 0.175 Angle : 0.533 11.147 18533 Z= 0.277 Chirality : 0.040 0.154 2221 Planarity : 0.003 0.037 2336 Dihedral : 4.104 24.058 1890 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.34 % Allowed : 23.92 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1733 helix: 2.17 (0.18), residues: 928 sheet: -1.11 (0.35), residues: 229 loop : -1.96 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 102 HIS 0.002 0.001 HIS N 213 PHE 0.013 0.001 PHE P 197 TYR 0.017 0.001 TYR Y 193 ARG 0.015 0.000 ARG Y 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 160 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7601 (pp30) REVERT: N 219 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8035 (tp) REVERT: N 255 MET cc_start: 0.8509 (mmm) cc_final: 0.8249 (mmm) REVERT: O 252 ASP cc_start: 0.8235 (t0) cc_final: 0.7973 (t0) REVERT: P 347 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7814 (pp20) REVERT: Q 266 GLN cc_start: 0.8283 (tp40) cc_final: 0.7928 (mm-40) REVERT: U 176 ARG cc_start: 0.7359 (mtt180) cc_final: 0.6511 (mmt-90) REVERT: U 251 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8714 (mmmt) REVERT: U 299 MET cc_start: 0.8520 (mmm) cc_final: 0.8104 (mmm) REVERT: Y 119 LYS cc_start: 0.8423 (mtpp) cc_final: 0.7959 (ttmm) REVERT: Y 120 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7529 (pp) REVERT: Y 197 TYR cc_start: 0.8524 (t80) cc_final: 0.8284 (t80) REVERT: Z 43 TYR cc_start: 0.6088 (p90) cc_final: 0.4318 (m-80) REVERT: Z 62 LYS cc_start: 0.8313 (tttt) cc_final: 0.7667 (mtmt) outliers start: 32 outliers final: 26 residues processed: 256 average time/residue: 0.2915 time to fit residues: 103.6063 Evaluate side-chains 252 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN O 360 ASN U 310 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 13698 Z= 0.484 Angle : 0.678 11.023 18533 Z= 0.350 Chirality : 0.046 0.163 2221 Planarity : 0.004 0.058 2336 Dihedral : 4.714 28.196 1890 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.77 % Rotamer: Outliers : 2.63 % Allowed : 23.85 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1733 helix: 1.78 (0.17), residues: 934 sheet: -1.15 (0.35), residues: 238 loop : -2.07 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 112 HIS 0.005 0.001 HIS N 213 PHE 0.028 0.002 PHE O 178 TYR 0.017 0.002 TYR L 177 ARG 0.014 0.001 ARG Y 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: L 111 MET cc_start: 0.8846 (mmm) cc_final: 0.8641 (mmm) REVERT: L 160 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7705 (pp30) REVERT: N 219 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8297 (tp) REVERT: P 347 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7773 (pp20) REVERT: Q 266 GLN cc_start: 0.8357 (tp40) cc_final: 0.7940 (mm-40) REVERT: Q 274 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7257 (tptt) REVERT: U 176 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6662 (mmt-90) REVERT: U 251 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8706 (mmmt) REVERT: U 299 MET cc_start: 0.8563 (mmm) cc_final: 0.8132 (mmm) REVERT: Y 119 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8117 (ttmm) REVERT: Y 120 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7704 (pp) REVERT: Z 43 TYR cc_start: 0.6090 (p90) cc_final: 0.4231 (m-80) REVERT: Z 62 LYS cc_start: 0.8243 (tttt) cc_final: 0.7631 (mtmt) outliers start: 36 outliers final: 26 residues processed: 250 average time/residue: 0.3024 time to fit residues: 105.1182 Evaluate side-chains 252 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 376 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 139 optimal weight: 0.0050 chunk 58 optimal weight: 0.2980 chunk 143 optimal weight: 0.0010 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN Y 99 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113765 restraints weight = 18766.425| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.13 r_work: 0.3144 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13698 Z= 0.155 Angle : 0.536 11.350 18533 Z= 0.279 Chirality : 0.040 0.154 2221 Planarity : 0.003 0.054 2336 Dihedral : 4.122 24.358 1890 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.34 % Allowed : 24.21 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1733 helix: 2.20 (0.18), residues: 932 sheet: -1.08 (0.35), residues: 228 loop : -1.92 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 102 HIS 0.002 0.000 HIS N 414 PHE 0.014 0.001 PHE Q 325 TYR 0.019 0.001 TYR Y 193 ARG 0.014 0.001 ARG Y 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.76 seconds wall clock time: 62 minutes 4.89 seconds (3724.89 seconds total)