Starting phenix.real_space_refine on Tue Apr 9 16:00:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd2_12273/04_2024/7nd2_12273.pdb" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10670 2.51 5 N 2894 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H ASP 175": "OD1" <-> "OD2" Residue "H ASP 186": "OD1" <-> "OD2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 184": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16824 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2565 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2721 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 335} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "F" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2721 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 335} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2565 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "G" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS E 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS E 195 " occ=0.58 residue: pdb=" N AHIS F 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS F 195 " occ=0.58 residue: pdb=" N AHIS H 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS H 195 " occ=0.58 residue: pdb=" N AHIS G 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS G 195 " occ=0.58 Time building chain proxies: 11.65, per 1000 atoms: 0.69 Number of scatterers: 16824 At special positions: 0 Unit cell: (180.36, 102.6, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3168 8.00 N 2894 7.00 C 10670 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: 7.23 Conformation dependent library (CDL) restraints added in 4.0 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 15 sheets defined 55.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.905A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.936A pdb=" N LEU A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.966A pdb=" N GLN A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 4.013A pdb=" N ALA A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.997A pdb=" N GLN A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 335 through 370 removed outlier: 3.673A pdb=" N LEU A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 374 through 406 removed outlier: 3.610A pdb=" N ARG A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 455 removed outlier: 4.773A pdb=" N THR A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 436 " --> pdb=" O HIS A 432 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 499 removed outlier: 4.247A pdb=" N CYS A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 513 through 532 Processing helix chain 'A' and resid 540 through 552 removed outlier: 4.477A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 118 through 138 removed outlier: 5.041A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 4.123A pdb=" N ILE C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 296 through 314 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 328 through 339 removed outlier: 4.341A pdb=" N ALA C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 39 removed outlier: 3.775A pdb=" N THR E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.864A pdb=" N LYS E 49 " --> pdb=" O PRO E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.622A pdb=" N ARG E 85 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 3.599A pdb=" N LEU E 98 " --> pdb=" O PRO E 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 99 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.603A pdb=" N ALA E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.851A pdb=" N LEU E 156 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.688A pdb=" N LYS E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.698A pdb=" N ALA E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 209 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN E 210 " --> pdb=" O VAL E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 39 removed outlier: 3.815A pdb=" N MET F 34 " --> pdb=" O HIS F 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 35 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.647A pdb=" N LYS F 49 " --> pdb=" O PRO F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.797A pdb=" N ARG F 85 " --> pdb=" O ASP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 4.615A pdb=" N LEU F 98 " --> pdb=" O PRO F 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 99 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 103 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 126 through 134 removed outlier: 3.805A pdb=" N CYS F 133 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 158 removed outlier: 3.838A pdb=" N ARG F 158 " --> pdb=" O CYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.735A pdb=" N VAL F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 216 removed outlier: 3.802A pdb=" N ALA F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 210 " --> pdb=" O VAL F 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 118 through 138 removed outlier: 5.043A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 168 removed outlier: 4.130A pdb=" N ILE D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 288 through 293 Processing helix chain 'D' and resid 296 through 314 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 328 through 339 removed outlier: 4.335A pdb=" N ALA D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.919A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.935A pdb=" N LEU B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.966A pdb=" N GLN B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 4.010A pdb=" N ALA B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 306 removed outlier: 3.852A pdb=" N GLN B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 325 Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 335 through 370 removed outlier: 3.677A pdb=" N LEU B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 374 through 407 removed outlier: 3.606A pdb=" N ARG B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 455 removed outlier: 4.547A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 436 " --> pdb=" O HIS B 432 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 499 removed outlier: 4.207A pdb=" N CYS B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 513 through 532 Processing helix chain 'B' and resid 540 through 552 removed outlier: 4.475A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.852A pdb=" N MET H 34 " --> pdb=" O HIS H 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA H 35 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.660A pdb=" N LYS H 49 " --> pdb=" O PRO H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.765A pdb=" N ARG H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 4.598A pdb=" N LEU H 98 " --> pdb=" O PRO H 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 99 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'H' and resid 126 through 134 removed outlier: 3.801A pdb=" N CYS H 133 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 158 removed outlier: 3.817A pdb=" N ARG H 158 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 176 removed outlier: 3.668A pdb=" N VAL H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU H 170 " --> pdb=" O PRO H 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 removed outlier: 3.855A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 39 removed outlier: 3.770A pdb=" N THR G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.886A pdb=" N LYS G 49 " --> pdb=" O PRO G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.587A pdb=" N LEU G 98 " --> pdb=" O PRO G 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 99 " --> pdb=" O GLY G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 117 Processing helix chain 'G' and resid 126 through 134 removed outlier: 3.607A pdb=" N ALA G 134 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.794A pdb=" N LEU G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 176 removed outlier: 3.775A pdb=" N LYS G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 removed outlier: 3.701A pdb=" N ALA G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 209 " --> pdb=" O THR G 205 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 210 " --> pdb=" O VAL G 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 0 through 3 Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.800A pdb=" N LYS C 34 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 67 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS C 40 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 65 " --> pdb=" O CYS C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 106 Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.779A pdb=" N VAL C 172 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 196 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 174 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER C 147 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL C 218 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY C 255 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE C 220 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 257 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 222 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 259 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR C 281 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY C 256 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA C 283 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP C 258 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR D 281 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY D 256 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA D 283 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TRP D 258 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL D 218 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY D 255 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 220 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 257 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU D 222 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 259 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 147 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 172 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE D 196 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER D 174 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.824A pdb=" N ALA E 11 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU E 90 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU E 13 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 121 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY E 199 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA E 123 " --> pdb=" O GLY E 199 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 196 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU F 89 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL F 124 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 91 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA F 11 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU F 90 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU F 13 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.121A pdb=" N VAL E 23 " --> pdb=" O VAL E 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.429A pdb=" N VAL F 23 " --> pdb=" O VAL F 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 0 through 3 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106 removed outlier: 6.803A pdb=" N LYS D 34 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 67 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS D 40 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU D 65 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 106 Processing sheet with id=AB4, first strand: chain 'H' and resid 76 through 77 removed outlier: 7.139A pdb=" N ALA H 11 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEU H 90 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU H 13 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU H 89 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL H 124 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 91 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 196 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE G 121 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY G 199 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA G 123 " --> pdb=" O GLY G 199 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA G 11 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU G 90 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU G 13 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 24 removed outlier: 5.637A pdb=" N VAL H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 23 through 24 removed outlier: 5.984A pdb=" N VAL G 23 " --> pdb=" O VAL G 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 874 hydrogen bonds defined for protein. 2505 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: 5.44 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4863 1.33 - 1.46: 3702 1.46 - 1.58: 8473 1.58 - 1.70: 4 1.70 - 1.83: 124 Bond restraints: 17166 Sorted by residual: bond pdb=" CG PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 1.503 1.212 0.291 3.40e-02 8.65e+02 7.35e+01 bond pdb=" N PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CG1 ILE B 350 " pdb=" CD1 ILE B 350 " ideal model delta sigma weight residual 1.513 1.368 0.145 3.90e-02 6.57e+02 1.38e+01 bond pdb=" CG1 ILE A 350 " pdb=" CD1 ILE A 350 " ideal model delta sigma weight residual 1.513 1.375 0.138 3.90e-02 6.57e+02 1.26e+01 bond pdb=" CB PRO G 92 " pdb=" CG PRO G 92 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.04e+01 ... (remaining 17161 not shown) Histogram of bond angle deviations from ideal: 87.80 - 97.67: 12 97.67 - 107.54: 963 107.54 - 117.42: 11796 117.42 - 127.29: 10300 127.29 - 137.16: 241 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N PRO G 92 " pdb=" CD PRO G 92 " pdb=" CG PRO G 92 " ideal model delta sigma weight residual 103.20 87.80 15.40 1.50e+00 4.44e-01 1.05e+02 angle pdb=" CA GLU E 21 " pdb=" CB GLU E 21 " pdb=" CG GLU E 21 " ideal model delta sigma weight residual 114.10 131.62 -17.52 2.00e+00 2.50e-01 7.67e+01 angle pdb=" CA PRO G 92 " pdb=" N PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 112.00 100.04 11.96 1.40e+00 5.10e-01 7.30e+01 angle pdb=" CA GLU G 21 " pdb=" CB GLU G 21 " pdb=" CG GLU G 21 " ideal model delta sigma weight residual 114.10 130.06 -15.96 2.00e+00 2.50e-01 6.37e+01 angle pdb=" CA ARG F 164 " pdb=" CB ARG F 164 " pdb=" CG ARG F 164 " ideal model delta sigma weight residual 114.10 129.25 -15.15 2.00e+00 2.50e-01 5.74e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9367 17.87 - 35.75: 833 35.75 - 53.62: 111 53.62 - 71.50: 27 71.50 - 89.37: 10 Dihedral angle restraints: 10348 sinusoidal: 3922 harmonic: 6426 Sorted by residual: dihedral pdb=" CA LYS H 70 " pdb=" C LYS H 70 " pdb=" N ALA H 71 " pdb=" CA ALA H 71 " ideal model delta harmonic sigma weight residual 180.00 -148.47 -31.53 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA LYS F 70 " pdb=" C LYS F 70 " pdb=" N ALA F 71 " pdb=" CA ALA F 71 " ideal model delta harmonic sigma weight residual -180.00 -149.41 -30.59 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA PRO H 151 " pdb=" C PRO H 151 " pdb=" N SER H 152 " pdb=" CA SER H 152 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1991 0.081 - 0.163: 538 0.163 - 0.244: 155 0.244 - 0.326: 25 0.326 - 0.407: 11 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CB VAL E 173 " pdb=" CA VAL E 173 " pdb=" CG1 VAL E 173 " pdb=" CG2 VAL E 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CG LEU E 167 " pdb=" CB LEU E 167 " pdb=" CD1 LEU E 167 " pdb=" CD2 LEU E 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CG LEU H 98 " pdb=" CB LEU H 98 " pdb=" CD1 LEU H 98 " pdb=" CD2 LEU H 98 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 2717 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 91 " -0.121 5.00e-02 4.00e+02 1.72e-01 4.71e+01 pdb=" N PRO G 92 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO G 92 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO G 92 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 159 " 0.100 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO G 160 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 141 " -0.033 2.00e-02 2.50e+03 3.19e-02 2.55e+01 pdb=" CG TRP H 141 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP H 141 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP H 141 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP H 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 141 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 141 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 141 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 141 " -0.012 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1088 2.72 - 3.26: 18236 3.26 - 3.81: 28737 3.81 - 4.35: 35152 4.35 - 4.90: 56634 Nonbonded interactions: 139847 Sorted by model distance: nonbonded pdb=" O LEU B 333 " pdb=" OG1 THR B 336 " model vdw 2.172 2.440 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 336 " model vdw 2.176 2.440 nonbonded pdb=" O LYS B 340 " pdb=" OG SER B 343 " model vdw 2.216 2.440 nonbonded pdb=" O LYS A 340 " pdb=" OG SER A 343 " model vdw 2.217 2.440 nonbonded pdb=" O TYR B 493 " pdb=" OG SER B 497 " model vdw 2.224 2.440 ... (remaining 139842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'F' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'G' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'H' and (resid 8 through 194 or resid 196 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.670 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 50.570 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.150 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.011 0.291 17166 Z= 0.751 Angle : 1.654 20.859 23312 Z= 0.890 Chirality : 0.085 0.407 2720 Planarity : 0.011 0.172 3004 Dihedral : 13.917 89.373 6176 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.99 % Favored : 94.69 % Rotamer: Outliers : 0.22 % Allowed : 0.60 % Favored : 99.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2196 helix: 0.09 (0.14), residues: 1024 sheet: 0.28 (0.34), residues: 210 loop : -1.60 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.008 TRP H 141 HIS 0.030 0.004 HIS E 30 PHE 0.044 0.005 PHE B 395 TYR 0.058 0.006 TYR B 233 ARG 0.055 0.003 ARG F 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 ASP cc_start: 0.8544 (m-30) cc_final: 0.8182 (t0) REVERT: A 545 LEU cc_start: 0.7806 (pp) cc_final: 0.7147 (tp) REVERT: C 92 LEU cc_start: 0.8809 (tp) cc_final: 0.8573 (tp) REVERT: E 29 LEU cc_start: 0.7957 (tt) cc_final: 0.7081 (mm) REVERT: E 34 MET cc_start: 0.8319 (ptt) cc_final: 0.7494 (ptp) REVERT: E 155 GLU cc_start: 0.8401 (pt0) cc_final: 0.8092 (pt0) REVERT: F 34 MET cc_start: 0.6024 (tmm) cc_final: 0.5661 (ptt) REVERT: F 138 ASP cc_start: 0.8610 (p0) cc_final: 0.8156 (p0) REVERT: F 139 ARG cc_start: 0.7392 (ttp80) cc_final: 0.5967 (mmm160) REVERT: F 143 PHE cc_start: 0.8552 (m-80) cc_final: 0.7987 (m-80) REVERT: F 164 ARG cc_start: 0.8421 (tpt170) cc_final: 0.8148 (mpp-170) REVERT: D 92 LEU cc_start: 0.8824 (tp) cc_final: 0.8564 (tp) REVERT: D 265 LEU cc_start: 0.8882 (tp) cc_final: 0.8666 (tt) REVERT: B 439 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8429 (tptp) REVERT: B 440 ASP cc_start: 0.8355 (m-30) cc_final: 0.7996 (t0) REVERT: B 545 LEU cc_start: 0.7926 (pp) cc_final: 0.7348 (tp) REVERT: H 34 MET cc_start: 0.5952 (tmm) cc_final: 0.5580 (ptt) REVERT: H 138 ASP cc_start: 0.8638 (p0) cc_final: 0.8153 (p0) REVERT: H 139 ARG cc_start: 0.7418 (ttp80) cc_final: 0.5987 (mmm160) REVERT: H 143 PHE cc_start: 0.8582 (m-80) cc_final: 0.8053 (m-80) REVERT: G 34 MET cc_start: 0.8331 (ptm) cc_final: 0.7767 (ptp) REVERT: G 94 CYS cc_start: 0.7779 (p) cc_final: 0.7576 (p) REVERT: G 155 GLU cc_start: 0.8428 (pt0) cc_final: 0.7876 (pt0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3479 time to fit residues: 117.2372 Evaluate side-chains 157 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17166 Z= 0.236 Angle : 0.782 12.749 23312 Z= 0.401 Chirality : 0.044 0.177 2720 Planarity : 0.006 0.087 3004 Dihedral : 5.693 30.353 2336 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Rotamer: Outliers : 1.04 % Allowed : 9.48 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.51 (0.17), residues: 2196 helix: 0.45 (0.15), residues: 1058 sheet: 0.39 (0.31), residues: 240 loop : -1.48 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 63 HIS 0.017 0.001 HIS F 113 PHE 0.029 0.002 PHE F 114 TYR 0.019 0.002 TYR D 229 ARG 0.013 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.018 Fit side-chains revert: symmetry clash REVERT: A 440 ASP cc_start: 0.8453 (m-30) cc_final: 0.8219 (t0) REVERT: A 444 HIS cc_start: 0.8432 (t-170) cc_final: 0.8148 (t-170) REVERT: A 545 LEU cc_start: 0.7930 (pp) cc_final: 0.7222 (tp) REVERT: C 92 LEU cc_start: 0.8677 (tp) cc_final: 0.8467 (tp) REVERT: E 29 LEU cc_start: 0.8209 (tt) cc_final: 0.7409 (mm) REVERT: E 34 MET cc_start: 0.8247 (ptt) cc_final: 0.7606 (ptp) REVERT: E 155 GLU cc_start: 0.8111 (pt0) cc_final: 0.7180 (pm20) REVERT: F 34 MET cc_start: 0.6125 (tmm) cc_final: 0.5825 (ptp) REVERT: F 51 MET cc_start: 0.4616 (mtt) cc_final: 0.4070 (mtt) REVERT: F 138 ASP cc_start: 0.8596 (p0) cc_final: 0.8044 (p0) REVERT: F 139 ARG cc_start: 0.7624 (ttp80) cc_final: 0.5625 (mmm160) REVERT: F 143 PHE cc_start: 0.8470 (m-80) cc_final: 0.7902 (m-80) REVERT: D 92 LEU cc_start: 0.8698 (tp) cc_final: 0.8471 (tp) REVERT: B 439 LYS cc_start: 0.8897 (mmtp) cc_final: 0.8531 (mmtp) REVERT: B 545 LEU cc_start: 0.7973 (pp) cc_final: 0.7310 (tp) REVERT: H 34 MET cc_start: 0.5660 (tmm) cc_final: 0.5187 (ptp) REVERT: H 51 MET cc_start: 0.5134 (mtt) cc_final: 0.4583 (mtt) REVERT: H 138 ASP cc_start: 0.8642 (p0) cc_final: 0.8156 (p0) REVERT: H 139 ARG cc_start: 0.7605 (ttp80) cc_final: 0.5986 (mmm160) REVERT: H 143 PHE cc_start: 0.8620 (m-80) cc_final: 0.7921 (m-80) REVERT: G 34 MET cc_start: 0.8335 (ptm) cc_final: 0.7741 (mtt) REVERT: G 146 TYR cc_start: 0.6915 (m-80) cc_final: 0.6598 (m-80) outliers start: 17 outliers final: 8 residues processed: 216 average time/residue: 0.3158 time to fit residues: 100.7525 Evaluate side-chains 161 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain G residue 115 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 189 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN B 249 GLN B 419 ASN H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17166 Z= 0.245 Angle : 0.727 11.748 23312 Z= 0.375 Chirality : 0.044 0.185 2720 Planarity : 0.005 0.069 3004 Dihedral : 5.388 36.381 2336 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.30 % Favored : 95.42 % Rotamer: Outliers : 2.08 % Allowed : 11.68 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.40 (0.17), residues: 2196 helix: 0.49 (0.15), residues: 1056 sheet: 0.40 (0.32), residues: 240 loop : -1.32 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 63 HIS 0.018 0.001 HIS H 113 PHE 0.038 0.002 PHE H 114 TYR 0.022 0.002 TYR B 303 ARG 0.006 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8491 (tptp) REVERT: A 444 HIS cc_start: 0.8528 (t-170) cc_final: 0.8173 (t-170) REVERT: A 545 LEU cc_start: 0.8052 (pp) cc_final: 0.7244 (tp) REVERT: C 92 LEU cc_start: 0.8738 (tp) cc_final: 0.8464 (tp) REVERT: E 29 LEU cc_start: 0.8168 (tt) cc_final: 0.7399 (mm) REVERT: E 34 MET cc_start: 0.8300 (ptt) cc_final: 0.7699 (mtt) REVERT: E 155 GLU cc_start: 0.8147 (pt0) cc_final: 0.7158 (pm20) REVERT: F 34 MET cc_start: 0.6398 (tmm) cc_final: 0.6141 (ptp) REVERT: F 143 PHE cc_start: 0.8550 (m-80) cc_final: 0.7999 (m-80) REVERT: D 92 LEU cc_start: 0.8759 (tp) cc_final: 0.8465 (tp) REVERT: B 325 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 396 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: B 439 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8573 (mmtp) REVERT: B 545 LEU cc_start: 0.7934 (pp) cc_final: 0.7148 (tp) REVERT: H 34 MET cc_start: 0.5820 (tmm) cc_final: 0.5433 (ptp) REVERT: H 143 PHE cc_start: 0.8692 (m-80) cc_final: 0.8027 (m-80) REVERT: H 194 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8107 (tpp-160) REVERT: G 34 MET cc_start: 0.8343 (ptm) cc_final: 0.7875 (mtt) outliers start: 37 outliers final: 18 residues processed: 192 average time/residue: 0.3157 time to fit residues: 89.8406 Evaluate side-chains 172 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 134 optimal weight: 0.1980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 104 optimal weight: 0.0030 chunk 190 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 345 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 345 GLN H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17166 Z= 0.199 Angle : 0.675 11.227 23312 Z= 0.347 Chirality : 0.042 0.174 2720 Planarity : 0.005 0.061 3004 Dihedral : 5.178 35.887 2336 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.38 % Rotamer: Outliers : 2.03 % Allowed : 13.54 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.27 (0.17), residues: 2196 helix: 0.60 (0.15), residues: 1058 sheet: 0.36 (0.32), residues: 240 loop : -1.23 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 63 HIS 0.018 0.001 HIS H 113 PHE 0.027 0.002 PHE H 114 TYR 0.021 0.002 TYR A 303 ARG 0.004 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.9239 (tpp) cc_final: 0.8871 (tpp) REVERT: A 439 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8692 (mmtp) REVERT: A 444 HIS cc_start: 0.8588 (t-170) cc_final: 0.8128 (t-170) REVERT: A 447 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: A 545 LEU cc_start: 0.8095 (pp) cc_final: 0.7234 (tp) REVERT: C 92 LEU cc_start: 0.8729 (tp) cc_final: 0.8505 (tp) REVERT: E 29 LEU cc_start: 0.8050 (tt) cc_final: 0.7399 (mm) REVERT: E 34 MET cc_start: 0.8186 (ptt) cc_final: 0.7641 (mtt) REVERT: E 155 GLU cc_start: 0.8089 (pt0) cc_final: 0.7140 (pm20) REVERT: F 34 MET cc_start: 0.6421 (tmm) cc_final: 0.6201 (ptp) REVERT: F 51 MET cc_start: 0.4683 (mtt) cc_final: 0.4167 (mtt) REVERT: F 143 PHE cc_start: 0.8503 (m-80) cc_final: 0.8003 (m-80) REVERT: F 164 ARG cc_start: 0.8603 (mpp-170) cc_final: 0.8379 (tmt170) REVERT: D 92 LEU cc_start: 0.8712 (tp) cc_final: 0.8467 (tp) REVERT: B 439 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8546 (mmtp) REVERT: B 545 LEU cc_start: 0.8047 (pp) cc_final: 0.7212 (tp) REVERT: H 34 MET cc_start: 0.5787 (tmm) cc_final: 0.5437 (ptp) REVERT: H 143 PHE cc_start: 0.8680 (m-80) cc_final: 0.8062 (m-80) REVERT: H 194 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8126 (tpp-160) REVERT: G 29 LEU cc_start: 0.8271 (tt) cc_final: 0.7342 (mm) REVERT: G 34 MET cc_start: 0.8236 (ptm) cc_final: 0.7884 (mtt) outliers start: 36 outliers final: 17 residues processed: 200 average time/residue: 0.2990 time to fit residues: 90.0505 Evaluate side-chains 174 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17166 Z= 0.228 Angle : 0.675 10.906 23312 Z= 0.346 Chirality : 0.042 0.193 2720 Planarity : 0.005 0.057 3004 Dihedral : 5.110 35.233 2336 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 2.25 % Allowed : 15.35 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.19 (0.18), residues: 2196 helix: 0.69 (0.16), residues: 1056 sheet: 0.28 (0.33), residues: 240 loop : -1.19 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 63 HIS 0.021 0.001 HIS H 113 PHE 0.033 0.002 PHE E 172 TYR 0.021 0.002 TYR F 146 ARG 0.003 0.000 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8725 (mmtp) REVERT: A 444 HIS cc_start: 0.8636 (t-170) cc_final: 0.8144 (t-170) REVERT: A 447 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: A 545 LEU cc_start: 0.7859 (pp) cc_final: 0.6969 (tp) REVERT: C 92 LEU cc_start: 0.8747 (tp) cc_final: 0.8514 (tp) REVERT: E 29 LEU cc_start: 0.7989 (tt) cc_final: 0.7371 (mm) REVERT: E 34 MET cc_start: 0.8196 (ptt) cc_final: 0.7665 (mtt) REVERT: E 144 ASP cc_start: 0.7618 (p0) cc_final: 0.7417 (m-30) REVERT: E 155 GLU cc_start: 0.8138 (pt0) cc_final: 0.7154 (pm20) REVERT: F 34 MET cc_start: 0.6465 (tmm) cc_final: 0.6222 (ptp) REVERT: F 51 MET cc_start: 0.5051 (mtt) cc_final: 0.4533 (mtt) REVERT: F 143 PHE cc_start: 0.8790 (m-80) cc_final: 0.8048 (m-80) REVERT: D 92 LEU cc_start: 0.8754 (tp) cc_final: 0.8500 (tp) REVERT: B 439 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8577 (mmtp) REVERT: B 447 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: B 545 LEU cc_start: 0.8081 (pp) cc_final: 0.7192 (tp) REVERT: H 34 MET cc_start: 0.5689 (tmm) cc_final: 0.5317 (ptp) REVERT: H 143 PHE cc_start: 0.8732 (m-80) cc_final: 0.8105 (m-80) REVERT: H 194 ARG cc_start: 0.8530 (tpp-160) cc_final: 0.8277 (tpp-160) REVERT: G 29 LEU cc_start: 0.8249 (tt) cc_final: 0.7325 (mm) REVERT: G 34 MET cc_start: 0.8233 (ptm) cc_final: 0.7907 (mtt) REVERT: G 112 GLN cc_start: 0.8263 (mt0) cc_final: 0.8047 (mt0) outliers start: 40 outliers final: 22 residues processed: 193 average time/residue: 0.3142 time to fit residues: 90.4268 Evaluate side-chains 180 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17166 Z= 0.178 Angle : 0.645 10.945 23312 Z= 0.327 Chirality : 0.042 0.179 2720 Planarity : 0.004 0.053 3004 Dihedral : 4.904 35.263 2336 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 2.36 % Allowed : 15.68 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.18), residues: 2196 helix: 0.82 (0.16), residues: 1060 sheet: 0.21 (0.33), residues: 240 loop : -1.18 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 141 HIS 0.020 0.001 HIS H 113 PHE 0.025 0.002 PHE H 114 TYR 0.017 0.002 TYR D 327 ARG 0.007 0.001 ARG G 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 178 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.9247 (tpp) cc_final: 0.8876 (tpp) REVERT: A 439 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8716 (mmtp) REVERT: A 444 HIS cc_start: 0.8533 (t-170) cc_final: 0.8200 (t-170) REVERT: A 447 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: A 545 LEU cc_start: 0.7690 (pp) cc_final: 0.6886 (tp) REVERT: C 92 LEU cc_start: 0.8690 (tp) cc_final: 0.8474 (tp) REVERT: E 29 LEU cc_start: 0.7984 (tt) cc_final: 0.7358 (mm) REVERT: E 34 MET cc_start: 0.8106 (ptt) cc_final: 0.7588 (mtt) REVERT: E 144 ASP cc_start: 0.7574 (p0) cc_final: 0.7336 (m-30) REVERT: E 155 GLU cc_start: 0.8030 (pt0) cc_final: 0.7052 (pm20) REVERT: F 51 MET cc_start: 0.5076 (mtt) cc_final: 0.4584 (mtt) REVERT: F 143 PHE cc_start: 0.8781 (m-80) cc_final: 0.8183 (m-80) REVERT: F 164 ARG cc_start: 0.8599 (mpp-170) cc_final: 0.8374 (tmt170) REVERT: D 92 LEU cc_start: 0.8762 (tp) cc_final: 0.8515 (tp) REVERT: B 439 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8549 (mmtp) REVERT: B 447 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: B 545 LEU cc_start: 0.7744 (pp) cc_final: 0.6909 (tp) REVERT: H 34 MET cc_start: 0.5597 (tmm) cc_final: 0.5277 (ptp) REVERT: H 51 MET cc_start: 0.5313 (mtt) cc_final: 0.2581 (pmm) REVERT: H 143 PHE cc_start: 0.8716 (m-80) cc_final: 0.8085 (m-80) REVERT: G 29 LEU cc_start: 0.8225 (tt) cc_final: 0.7323 (mm) REVERT: G 34 MET cc_start: 0.8161 (ptm) cc_final: 0.7859 (mtt) outliers start: 43 outliers final: 19 residues processed: 209 average time/residue: 0.2939 time to fit residues: 93.1993 Evaluate side-chains 181 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 121 optimal weight: 0.0870 chunk 155 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 0.2980 chunk 212 optimal weight: 0.0010 chunk 132 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 97 optimal weight: 20.0000 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 195 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17166 Z= 0.166 Angle : 0.655 10.895 23312 Z= 0.327 Chirality : 0.042 0.190 2720 Planarity : 0.004 0.052 3004 Dihedral : 4.797 35.135 2336 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Rotamer: Outliers : 2.30 % Allowed : 16.61 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2196 helix: 0.80 (0.16), residues: 1062 sheet: 0.40 (0.35), residues: 202 loop : -1.15 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 141 HIS 0.023 0.001 HIS F 113 PHE 0.040 0.002 PHE B 228 TYR 0.017 0.002 TYR C 327 ARG 0.015 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.9267 (tpp) cc_final: 0.8903 (tpp) REVERT: A 439 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8711 (mmtp) REVERT: A 444 HIS cc_start: 0.8541 (t-170) cc_final: 0.8226 (t-170) REVERT: A 447 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: A 528 MET cc_start: 0.8766 (mtm) cc_final: 0.8538 (ttm) REVERT: A 545 LEU cc_start: 0.7676 (pp) cc_final: 0.6851 (tp) REVERT: C 19 PHE cc_start: 0.7517 (p90) cc_final: 0.7233 (p90) REVERT: C 92 LEU cc_start: 0.8712 (tp) cc_final: 0.8498 (tp) REVERT: E 29 LEU cc_start: 0.8009 (tt) cc_final: 0.7372 (mm) REVERT: E 34 MET cc_start: 0.8097 (ptt) cc_final: 0.7571 (mtt) REVERT: E 144 ASP cc_start: 0.7545 (p0) cc_final: 0.7261 (m-30) REVERT: E 155 GLU cc_start: 0.8048 (pt0) cc_final: 0.7101 (pm20) REVERT: F 51 MET cc_start: 0.5164 (mtt) cc_final: 0.4651 (mtt) REVERT: F 143 PHE cc_start: 0.8808 (m-80) cc_final: 0.8098 (m-80) REVERT: D 19 PHE cc_start: 0.7457 (p90) cc_final: 0.7176 (p90) REVERT: D 92 LEU cc_start: 0.8710 (tp) cc_final: 0.8469 (tp) REVERT: D 333 MET cc_start: 0.7422 (tpp) cc_final: 0.7028 (tpp) REVERT: B 545 LEU cc_start: 0.7797 (pp) cc_final: 0.7005 (tp) REVERT: H 34 MET cc_start: 0.5572 (tmm) cc_final: 0.5272 (ptp) REVERT: H 143 PHE cc_start: 0.8703 (m-80) cc_final: 0.8098 (m-80) REVERT: G 29 LEU cc_start: 0.8035 (tt) cc_final: 0.7259 (mm) REVERT: G 34 MET cc_start: 0.8179 (ptm) cc_final: 0.7822 (mtt) outliers start: 42 outliers final: 22 residues processed: 218 average time/residue: 0.3012 time to fit residues: 97.9434 Evaluate side-chains 196 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 0.0060 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 195 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17166 Z= 0.165 Angle : 0.648 10.648 23312 Z= 0.324 Chirality : 0.042 0.197 2720 Planarity : 0.004 0.051 3004 Dihedral : 4.709 34.856 2336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 2.30 % Allowed : 16.89 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.18), residues: 2196 helix: 0.79 (0.16), residues: 1070 sheet: 0.38 (0.36), residues: 202 loop : -1.14 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 141 HIS 0.026 0.001 HIS F 113 PHE 0.041 0.002 PHE A 228 TYR 0.019 0.002 TYR C 327 ARG 0.010 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8736 (mmtp) REVERT: A 444 HIS cc_start: 0.8458 (t-170) cc_final: 0.8196 (t-170) REVERT: A 447 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: A 545 LEU cc_start: 0.7564 (pp) cc_final: 0.6734 (tp) REVERT: C 19 PHE cc_start: 0.7543 (p90) cc_final: 0.7241 (p90) REVERT: C 92 LEU cc_start: 0.8718 (tp) cc_final: 0.8500 (tp) REVERT: C 333 MET cc_start: 0.7531 (tpp) cc_final: 0.7182 (tpp) REVERT: E 29 LEU cc_start: 0.7914 (tt) cc_final: 0.7322 (mm) REVERT: E 34 MET cc_start: 0.8086 (ptt) cc_final: 0.7586 (mtt) REVERT: E 144 ASP cc_start: 0.7479 (p0) cc_final: 0.7115 (m-30) REVERT: E 155 GLU cc_start: 0.8028 (pt0) cc_final: 0.7068 (pm20) REVERT: F 51 MET cc_start: 0.5165 (mtt) cc_final: 0.4640 (mtt) REVERT: F 143 PHE cc_start: 0.8789 (m-80) cc_final: 0.8101 (m-80) REVERT: D 19 PHE cc_start: 0.7437 (p90) cc_final: 0.7136 (p90) REVERT: D 92 LEU cc_start: 0.8715 (tp) cc_final: 0.8470 (tp) REVERT: D 333 MET cc_start: 0.7494 (tpp) cc_final: 0.7139 (tpp) REVERT: B 439 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8647 (mmtp) REVERT: B 447 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: B 545 LEU cc_start: 0.7673 (pp) cc_final: 0.6840 (tp) REVERT: H 34 MET cc_start: 0.5576 (tmm) cc_final: 0.5267 (ptp) REVERT: H 143 PHE cc_start: 0.8719 (m-80) cc_final: 0.8126 (m-80) REVERT: G 29 LEU cc_start: 0.8039 (tt) cc_final: 0.7272 (mm) REVERT: G 34 MET cc_start: 0.8155 (ptm) cc_final: 0.7763 (mtt) outliers start: 42 outliers final: 25 residues processed: 212 average time/residue: 0.2849 time to fit residues: 93.3033 Evaluate side-chains 200 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 300 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN H 113 HIS ** H 195 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17166 Z= 0.308 Angle : 0.722 10.344 23312 Z= 0.372 Chirality : 0.044 0.216 2720 Planarity : 0.005 0.052 3004 Dihedral : 4.962 32.927 2336 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 2.08 % Allowed : 17.16 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.21 (0.18), residues: 2196 helix: 0.72 (0.16), residues: 1068 sheet: -0.01 (0.32), residues: 246 loop : -1.20 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 63 HIS 0.026 0.002 HIS H 113 PHE 0.030 0.002 PHE A 228 TYR 0.020 0.003 TYR B 420 ARG 0.008 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.9253 (tpp) cc_final: 0.8836 (tpp) REVERT: A 439 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8713 (mmtp) REVERT: A 444 HIS cc_start: 0.8598 (t-170) cc_final: 0.8288 (t-170) REVERT: C 92 LEU cc_start: 0.8775 (tp) cc_final: 0.8501 (tp) REVERT: C 128 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7700 (p0) REVERT: C 333 MET cc_start: 0.7760 (tpp) cc_final: 0.7330 (tpp) REVERT: E 29 LEU cc_start: 0.7831 (tt) cc_final: 0.7266 (mp) REVERT: E 34 MET cc_start: 0.8134 (ptt) cc_final: 0.7631 (mtt) REVERT: E 144 ASP cc_start: 0.7565 (p0) cc_final: 0.7156 (m-30) REVERT: E 155 GLU cc_start: 0.8169 (pt0) cc_final: 0.7090 (pm20) REVERT: F 51 MET cc_start: 0.5314 (mtt) cc_final: 0.4778 (mtt) REVERT: F 143 PHE cc_start: 0.8954 (m-80) cc_final: 0.8307 (m-80) REVERT: D 92 LEU cc_start: 0.8777 (tp) cc_final: 0.8475 (tp) REVERT: D 333 MET cc_start: 0.7717 (tpp) cc_final: 0.7373 (tpp) REVERT: B 439 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8626 (mmtp) REVERT: H 34 MET cc_start: 0.5714 (tmm) cc_final: 0.5400 (ptp) REVERT: H 51 MET cc_start: 0.5753 (mtt) cc_final: 0.5345 (mtt) REVERT: H 143 PHE cc_start: 0.8891 (m-80) cc_final: 0.8306 (m-80) REVERT: G 34 MET cc_start: 0.8194 (ptm) cc_final: 0.7843 (mtt) outliers start: 38 outliers final: 27 residues processed: 180 average time/residue: 0.2875 time to fit residues: 80.7781 Evaluate side-chains 175 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 300 TYR Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 447 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17166 Z= 0.183 Angle : 0.663 10.857 23312 Z= 0.336 Chirality : 0.043 0.190 2720 Planarity : 0.005 0.054 3004 Dihedral : 4.843 33.562 2336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 17.82 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.18 (0.18), residues: 2196 helix: 0.80 (0.16), residues: 1062 sheet: -0.33 (0.31), residues: 260 loop : -1.14 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 141 HIS 0.027 0.001 HIS H 113 PHE 0.033 0.002 PHE E 172 TYR 0.024 0.002 TYR H 86 ARG 0.008 0.001 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8725 (mmtp) REVERT: C 92 LEU cc_start: 0.8735 (tp) cc_final: 0.8520 (tp) REVERT: C 333 MET cc_start: 0.7580 (tpp) cc_final: 0.7174 (tpp) REVERT: E 29 LEU cc_start: 0.7834 (tt) cc_final: 0.7291 (mp) REVERT: E 34 MET cc_start: 0.8060 (ptt) cc_final: 0.7556 (mtt) REVERT: E 155 GLU cc_start: 0.8051 (pt0) cc_final: 0.7026 (pm20) REVERT: F 51 MET cc_start: 0.5318 (mtt) cc_final: 0.4901 (mtt) REVERT: F 143 PHE cc_start: 0.8933 (m-80) cc_final: 0.8268 (m-80) REVERT: F 164 ARG cc_start: 0.8653 (mpp-170) cc_final: 0.8352 (tmt170) REVERT: D 92 LEU cc_start: 0.8729 (tp) cc_final: 0.8485 (tp) REVERT: D 333 MET cc_start: 0.7465 (tpp) cc_final: 0.7117 (tpp) REVERT: B 439 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8629 (mmtp) REVERT: H 34 MET cc_start: 0.5622 (tmm) cc_final: 0.5359 (ptp) REVERT: H 143 PHE cc_start: 0.8857 (m-80) cc_final: 0.8271 (m-80) REVERT: G 34 MET cc_start: 0.8150 (ptm) cc_final: 0.7769 (mtt) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.2879 time to fit residues: 83.5155 Evaluate side-chains 184 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 300 TYR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 179 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** 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 = 0.4267 r_free = 0.4267 target = 0.115015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.091737 restraints weight = 181613.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.095218 restraints weight = 118573.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.095745 restraints weight = 74683.654| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17166 Z= 0.189 Angle : 0.656 10.663 23312 Z= 0.336 Chirality : 0.042 0.193 2720 Planarity : 0.005 0.053 3004 Dihedral : 4.812 33.463 2336 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer: Outliers : 1.59 % Allowed : 17.71 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.22 (0.18), residues: 2196 helix: 0.78 (0.16), residues: 1062 sheet: -0.26 (0.31), residues: 256 loop : -1.21 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 63 HIS 0.033 0.002 HIS F 113 PHE 0.035 0.002 PHE E 172 TYR 0.046 0.002 TYR H 86 ARG 0.006 0.001 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.38 seconds wall clock time: 58 minutes 13.08 seconds (3493.08 seconds total)