Starting phenix.real_space_refine on Wed Apr 10 16:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3o_18131/04_2024/8q3o_18131_updated.pdb" } resolution = 3.0 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= 0.006 sd= 0.046 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 12466 2.51 5 N 3530 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 19907 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'0O2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'0O2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'0O2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' MG': 1, '0O2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.60, per 1000 atoms: 0.53 Number of scatterers: 19907 At special positions: 0 Unit cell: (112.32, 130.624, 148.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 20 15.00 Mg 1 11.99 O 3788 8.00 N 3530 7.00 C 12466 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: 8.04 Conformation dependent library (CDL) restraints added in 3.6 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 13 sheets defined 43.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 11 through 21 Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.608A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 293 through 303 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 389 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.665A pdb=" N PHE B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 124 through 129 removed outlier: 4.271A pdb=" N ASN B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.577A pdb=" N THR B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 256 removed outlier: 3.585A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 293 through 303 Proline residue: B 297 - end of helix removed outlier: 3.665A pdb=" N ALA B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 392 through 405 removed outlier: 4.349A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 124 through 129 removed outlier: 4.085A pdb=" N ASN C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 154 through 165 removed outlier: 4.390A pdb=" N THR C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 236 through 256 removed outlier: 3.688A pdb=" N HIS C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.527A pdb=" N ARG C 296 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Proline residue: C 297 - end of helix removed outlier: 3.753A pdb=" N GLY C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 303 " --> pdb=" O PHE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 392 through 404 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 11 through 21 Processing helix chain 'D' and resid 31 through 43 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.753A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'D' and resid 213 through 222 removed outlier: 3.507A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 256 removed outlier: 3.656A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 293 through 303 Proline residue: D 297 - end of helix removed outlier: 3.774A pdb=" N GLY D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 303 " --> pdb=" O PHE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.654A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.737A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 11 through 21 Processing helix chain 'E' and resid 31 through 45 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.321A pdb=" N THR E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.944A pdb=" N ASN E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 222 removed outlier: 3.856A pdb=" N THR E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 255 Processing helix chain 'E' and resid 267 through 277 Processing helix chain 'E' and resid 293 through 303 Proline residue: E 297 - end of helix removed outlier: 3.920A pdb=" N ALA E 303 " --> pdb=" O ARG E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.682A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 371 No H-bonds generated for 'chain 'E' and resid 368 through 371' Processing helix chain 'E' and resid 374 through 388 Processing helix chain 'E' and resid 392 through 405 Processing helix chain 'E' and resid 409 through 416 Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 31 through 45 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 154 through 165 Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 236 through 255 Processing helix chain 'F' and resid 267 through 277 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 291 through 302 Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 326 through 338 removed outlier: 4.522A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 368 through 371 No H-bonds generated for 'chain 'F' and resid 368 through 371' Processing helix chain 'F' and resid 374 through 389 Proline residue: F 389 - end of helix Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 409 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 79 through 81 removed outlier: 4.685A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.503A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A 176 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 317 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA A 178 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 319 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A 226 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LEU A 208 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 228 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 79 through 81 removed outlier: 3.678A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS B 100 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 116 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 341 through 344 removed outlier: 8.051A pdb=" N GLY B 174 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 315 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE B 176 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 317 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA B 178 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA B 319 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU B 226 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU B 208 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 228 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASP B 210 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N SER B 230 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.828A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS C 100 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL C 116 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.635A pdb=" N MET C 341 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY C 174 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 315 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE C 176 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 317 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA C 178 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA C 319 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU C 226 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU C 208 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 228 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASP C 210 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER C 230 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.825A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 341 through 344 removed outlier: 3.658A pdb=" N MET D 341 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY D 174 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 315 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE D 176 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA D 317 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA D 178 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA D 319 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 226 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 208 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 228 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP D 210 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER D 230 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.908A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 341 through 344 removed outlier: 3.961A pdb=" N MET E 341 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY E 174 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE E 315 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE E 176 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA E 317 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA E 178 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA E 319 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU E 226 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU E 208 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL E 228 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASP E 210 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER E 230 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 305 through 307 removed outlier: 3.559A pdb=" N GLY E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.758A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 54 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS F 100 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL F 116 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 227 through 229 removed outlier: 7.646A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2184 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: 6.67 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3420 1.31 - 1.44: 4694 1.44 - 1.56: 11858 1.56 - 1.69: 38 1.69 - 1.82: 198 Bond restraints: 20208 Sorted by residual: bond pdb=" C4' 0O2 E 501 " pdb=" O4' 0O2 E 501 " ideal model delta sigma weight residual 1.305 1.622 -0.317 2.00e-02 2.50e+03 2.52e+02 bond pdb=" C4' 0O2 B 501 " pdb=" O4' 0O2 B 501 " ideal model delta sigma weight residual 1.305 1.619 -0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C1' 0O2 C 501 " pdb=" O4' 0O2 C 501 " ideal model delta sigma weight residual 1.616 1.302 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C4' 0O2 D 501 " pdb=" O4' 0O2 D 501 " ideal model delta sigma weight residual 1.305 1.618 -0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C4' 0O2 C 501 " pdb=" O4' 0O2 C 501 " ideal model delta sigma weight residual 1.305 1.617 -0.312 2.00e-02 2.50e+03 2.44e+02 ... (remaining 20203 not shown) Histogram of bond angle deviations from ideal: 94.95 - 102.79: 137 102.79 - 110.63: 6103 110.63 - 118.47: 9959 118.47 - 126.31: 10873 126.31 - 134.15: 182 Bond angle restraints: 27254 Sorted by residual: angle pdb=" CA PRO F 356 " pdb=" N PRO F 356 " pdb=" CD PRO F 356 " ideal model delta sigma weight residual 111.50 103.15 8.35 1.40e+00 5.10e-01 3.56e+01 angle pdb=" N PRO F 356 " pdb=" CD PRO F 356 " pdb=" CG PRO F 356 " ideal model delta sigma weight residual 103.80 97.01 6.79 1.20e+00 6.94e-01 3.20e+01 angle pdb=" CA MET F 380 " pdb=" CB MET F 380 " pdb=" CG MET F 380 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.71e+01 angle pdb=" C GLU A 414 " pdb=" N MET A 415 " pdb=" CA MET A 415 " ideal model delta sigma weight residual 122.65 116.23 6.42 1.60e+00 3.91e-01 1.61e+01 angle pdb=" CA ARG F 299 " pdb=" CB ARG F 299 " pdb=" CG ARG F 299 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 27249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 11040 20.49 - 40.98: 1199 40.98 - 61.47: 222 61.47 - 81.96: 22 81.96 - 102.45: 7 Dihedral angle restraints: 12490 sinusoidal: 5278 harmonic: 7212 Sorted by residual: dihedral pdb=" CA MET A 415 " pdb=" C MET A 415 " pdb=" N MET A 416 " pdb=" CA MET A 416 " ideal model delta harmonic sigma weight residual 180.00 146.29 33.71 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA GLU E 134 " pdb=" C GLU E 134 " pdb=" N ASN E 135 " pdb=" CA ASN E 135 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C3' 0O2 B 501 " pdb=" O3' 0O2 B 501 " pdb=" PC 0O2 B 501 " pdb=" O2C 0O2 B 501 " ideal model delta sinusoidal sigma weight residual -45.34 57.11 -102.45 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 12487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2665 0.060 - 0.120: 398 0.120 - 0.180: 20 0.180 - 0.240: 3 0.240 - 0.300: 2 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CG LEU A 164 " pdb=" CB LEU A 164 " pdb=" CD1 LEU A 164 " pdb=" CD2 LEU A 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CG LEU E 164 " pdb=" CB LEU E 164 " pdb=" CD1 LEU E 164 " pdb=" CD2 LEU E 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C2' 0O2 E 501 " pdb=" C1' 0O2 E 501 " pdb=" C3' 0O2 E 501 " pdb=" O2' 0O2 E 501 " both_signs ideal model delta sigma weight residual False -2.39 -2.61 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3085 not shown) Planarity restraints: 3526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 299 " -0.203 9.50e-02 1.11e+02 9.12e-02 5.14e+00 pdb=" NE ARG F 299 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 299 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 299 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 299 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 178 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 179 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 355 " -0.030 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO F 356 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 356 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 356 " -0.021 5.00e-02 4.00e+02 ... (remaining 3523 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.17: 17229 3.17 - 3.75: 32985 3.75 - 4.32: 44189 4.32 - 4.90: 72349 Nonbonded interactions: 166980 Sorted by model distance: nonbonded pdb=" O1G 0O2 E 501 " pdb="MG MG E 502 " model vdw 2.014 2.170 nonbonded pdb=" O ASP C 265 " pdb=" OG1 THR C 318 " model vdw 2.085 2.440 nonbonded pdb=" O ASP D 265 " pdb=" OG1 THR D 318 " model vdw 2.105 2.440 nonbonded pdb=" O ASP A 265 " pdb=" OG1 THR A 318 " model vdw 2.138 2.440 nonbonded pdb=" O ASP E 265 " pdb=" OG1 THR E 318 " model vdw 2.141 2.440 ... (remaining 166975 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' and resid 1 through 418) selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) selection = (chain 'E' and resid 1 through 418) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 12.680 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 53.840 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.317 20208 Z= 0.634 Angle : 0.616 11.820 27254 Z= 0.307 Chirality : 0.043 0.300 3088 Planarity : 0.004 0.091 3526 Dihedral : 16.408 102.449 7822 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.33 % Allowed : 26.72 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.81 (0.17), residues: 2496 helix: 1.29 (0.16), residues: 1156 sheet: -0.02 (0.26), residues: 403 loop : -0.01 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 381 HIS 0.006 0.001 HIS B 42 PHE 0.018 0.001 PHE A 413 TYR 0.027 0.001 TYR E 80 ARG 0.009 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 2.461 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 378 GLN cc_start: 0.8748 (mm110) cc_final: 0.8474 (mm-40) REVERT: A 381 TRP cc_start: 0.7771 (m100) cc_final: 0.7369 (m100) REVERT: A 396 MET cc_start: 0.8149 (tpp) cc_final: 0.7881 (tmm) REVERT: B 21 MET cc_start: 0.7873 (ppp) cc_final: 0.7144 (ppp) REVERT: B 341 MET cc_start: 0.7351 (tmm) cc_final: 0.7088 (tmt) REVERT: D 21 MET cc_start: 0.7984 (mtt) cc_final: 0.7777 (ttp) REVERT: D 336 LYS cc_start: 0.7865 (mttp) cc_final: 0.7282 (mttp) REVERT: E 1 MET cc_start: 0.7244 (tpp) cc_final: 0.6942 (tpp) REVERT: F 55 LEU cc_start: 0.7226 (tp) cc_final: 0.6900 (tp) REVERT: F 341 MET cc_start: 0.5054 (ppp) cc_final: 0.4747 (ppp) outliers start: 7 outliers final: 1 residues processed: 242 average time/residue: 1.5374 time to fit residues: 414.5026 Evaluate side-chains 222 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20208 Z= 0.318 Angle : 0.578 10.592 27254 Z= 0.285 Chirality : 0.042 0.247 3088 Planarity : 0.004 0.072 3526 Dihedral : 5.575 105.787 2765 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.47 % Allowed : 25.37 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2496 helix: 1.30 (0.16), residues: 1152 sheet: -0.05 (0.26), residues: 400 loop : -0.04 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.008 0.001 HIS A 256 PHE 0.016 0.001 PHE A 62 TYR 0.023 0.002 TYR E 80 ARG 0.006 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 231 time to evaluate : 2.542 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7847 (mpp) REVERT: A 244 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 378 GLN cc_start: 0.8763 (mm110) cc_final: 0.8453 (mm-40) REVERT: A 381 TRP cc_start: 0.7790 (m100) cc_final: 0.7398 (m100) REVERT: A 396 MET cc_start: 0.8162 (tpp) cc_final: 0.7904 (tmm) REVERT: B 21 MET cc_start: 0.7990 (ppp) cc_final: 0.7248 (ppp) REVERT: B 114 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7289 (pt) REVERT: B 341 MET cc_start: 0.7368 (tmm) cc_final: 0.7109 (tmt) REVERT: B 416 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: D 21 MET cc_start: 0.8015 (mtt) cc_final: 0.7813 (ttp) REVERT: E 1 MET cc_start: 0.7265 (tpp) cc_final: 0.6998 (tpp) REVERT: F 55 LEU cc_start: 0.7161 (tp) cc_final: 0.6870 (tp) REVERT: F 147 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6901 (mpp) REVERT: F 341 MET cc_start: 0.4666 (ppp) cc_final: 0.3829 (pmt) REVERT: F 390 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3982 (ptt) outliers start: 96 outliers final: 34 residues processed: 289 average time/residue: 1.4328 time to fit residues: 464.2867 Evaluate side-chains 265 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 241 optimal weight: 0.0870 chunk 199 optimal weight: 0.8980 chunk 221 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20208 Z= 0.195 Angle : 0.552 11.129 27254 Z= 0.270 Chirality : 0.041 0.223 3088 Planarity : 0.003 0.057 3526 Dihedral : 5.478 102.294 2765 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.05 % Allowed : 25.98 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2496 helix: 1.37 (0.16), residues: 1150 sheet: -0.09 (0.26), residues: 394 loop : -0.01 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.019 0.001 HIS F 344 PHE 0.015 0.001 PHE A 62 TYR 0.019 0.001 TYR F 80 ARG 0.007 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 236 time to evaluate : 2.504 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8089 (ptm) cc_final: 0.7816 (pp-130) REVERT: A 147 MET cc_start: 0.8066 (mpp) cc_final: 0.7860 (mpp) REVERT: A 244 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 378 GLN cc_start: 0.8752 (mm110) cc_final: 0.8451 (mm-40) REVERT: A 381 TRP cc_start: 0.7790 (m100) cc_final: 0.7394 (m100) REVERT: B 21 MET cc_start: 0.7969 (ppp) cc_final: 0.7206 (ppp) REVERT: B 341 MET cc_start: 0.7308 (tmm) cc_final: 0.7044 (tmt) REVERT: D 21 MET cc_start: 0.8020 (mtt) cc_final: 0.7812 (ttp) REVERT: D 32 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7921 (mm-40) REVERT: D 329 GLU cc_start: 0.7464 (tp30) cc_final: 0.6341 (tp30) REVERT: E 245 MET cc_start: 0.7396 (mmm) cc_final: 0.7189 (tpt) REVERT: F 147 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7017 (mpp) REVERT: F 341 MET cc_start: 0.5015 (ppp) cc_final: 0.4302 (pmt) REVERT: F 345 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5711 (mm) outliers start: 87 outliers final: 37 residues processed: 297 average time/residue: 1.4097 time to fit residues: 471.7819 Evaluate side-chains 267 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 40.0000 chunk 168 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 237 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 212 optimal weight: 30.0000 chunk 64 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20208 Z= 0.177 Angle : 0.567 11.696 27254 Z= 0.273 Chirality : 0.041 0.217 3088 Planarity : 0.003 0.051 3526 Dihedral : 5.413 102.494 2765 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.05 % Allowed : 26.21 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2496 helix: 1.36 (0.16), residues: 1155 sheet: -0.07 (0.26), residues: 396 loop : -0.02 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.014 0.001 HIS F 344 PHE 0.014 0.001 PHE A 62 TYR 0.026 0.001 TYR E 80 ARG 0.007 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 237 time to evaluate : 2.415 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8059 (mpp) cc_final: 0.7855 (mpp) REVERT: A 244 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 327 MET cc_start: 0.7865 (mmm) cc_final: 0.7661 (mmp) REVERT: A 360 TYR cc_start: 0.7352 (t80) cc_final: 0.7084 (t80) REVERT: A 378 GLN cc_start: 0.8748 (mm110) cc_final: 0.8459 (mm-40) REVERT: B 21 MET cc_start: 0.7959 (ppp) cc_final: 0.7174 (ppp) REVERT: B 341 MET cc_start: 0.7311 (tmm) cc_final: 0.7043 (tmt) REVERT: B 416 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7362 (ttp) REVERT: D 21 MET cc_start: 0.8024 (mtt) cc_final: 0.7810 (ttp) REVERT: D 23 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (tt) REVERT: D 32 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: D 190 ASN cc_start: 0.7842 (t0) cc_final: 0.7641 (t0) REVERT: D 329 GLU cc_start: 0.7272 (tp30) cc_final: 0.7071 (tp30) REVERT: D 333 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6516 (mm-30) REVERT: F 147 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: F 341 MET cc_start: 0.5008 (ppp) cc_final: 0.4305 (pmt) REVERT: F 345 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5710 (mm) outliers start: 87 outliers final: 42 residues processed: 300 average time/residue: 1.3924 time to fit residues: 469.7155 Evaluate side-chains 279 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20208 Z= 0.270 Angle : 0.595 11.494 27254 Z= 0.288 Chirality : 0.042 0.251 3088 Planarity : 0.004 0.052 3526 Dihedral : 5.435 102.778 2764 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.28 % Allowed : 27.33 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.80 (0.17), residues: 2496 helix: 1.34 (0.16), residues: 1152 sheet: -0.08 (0.26), residues: 392 loop : -0.06 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 381 HIS 0.012 0.001 HIS F 344 PHE 0.014 0.001 PHE A 62 TYR 0.020 0.002 TYR E 80 ARG 0.014 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 229 time to evaluate : 2.305 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: symmetry clash revert: symmetry clash REVERT: A 381 TRP cc_start: 0.8094 (m100) cc_final: 0.7712 (m100) REVERT: A 396 MET cc_start: 0.8162 (tpp) cc_final: 0.7907 (tmm) REVERT: B 21 MET cc_start: 0.7998 (ppp) cc_final: 0.7192 (ppp) REVERT: B 341 MET cc_start: 0.7349 (tmm) cc_final: 0.7100 (tmt) REVERT: B 416 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7385 (ttp) REVERT: D 21 MET cc_start: 0.8031 (mtt) cc_final: 0.7808 (ttp) REVERT: D 23 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8109 (tt) REVERT: F 147 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7084 (mpp) REVERT: F 299 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7402 (ppt170) REVERT: F 321 ILE cc_start: 0.1520 (OUTLIER) cc_final: 0.0984 (tp) REVERT: F 341 MET cc_start: 0.5017 (ppp) cc_final: 0.4391 (pmt) outliers start: 92 outliers final: 55 residues processed: 299 average time/residue: 1.3432 time to fit residues: 453.8118 Evaluate side-chains 282 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS F 42 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20208 Z= 0.188 Angle : 0.608 15.012 27254 Z= 0.291 Chirality : 0.042 0.245 3088 Planarity : 0.003 0.050 3526 Dihedral : 5.378 102.028 2764 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.96 % Allowed : 28.21 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2496 helix: 1.36 (0.16), residues: 1153 sheet: -0.06 (0.26), residues: 396 loop : -0.03 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 381 HIS 0.018 0.001 HIS A 388 PHE 0.014 0.001 PHE A 62 TYR 0.021 0.001 TYR F 80 ARG 0.010 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 225 time to evaluate : 2.333 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 92 ARG cc_start: 0.6987 (pmt170) cc_final: 0.6709 (pmt170) REVERT: A 269 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7828 (mmm160) REVERT: A 381 TRP cc_start: 0.8245 (m100) cc_final: 0.7658 (m100) REVERT: B 21 MET cc_start: 0.7956 (ppp) cc_final: 0.7168 (ppp) REVERT: B 341 MET cc_start: 0.7312 (tmm) cc_final: 0.7064 (tmt) REVERT: B 416 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7286 (ttp) REVERT: D 21 MET cc_start: 0.8029 (mtt) cc_final: 0.7817 (ttp) REVERT: D 32 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: D 329 GLU cc_start: 0.7436 (tp30) cc_final: 0.6857 (tp30) REVERT: F 111 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6527 (t80) REVERT: F 143 SER cc_start: 0.6893 (OUTLIER) cc_final: 0.6612 (t) REVERT: F 147 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7092 (mpp) REVERT: F 299 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7380 (ppt170) REVERT: F 321 ILE cc_start: 0.1470 (OUTLIER) cc_final: 0.0943 (tp) REVERT: F 341 MET cc_start: 0.4887 (ppp) cc_final: 0.4226 (pmt) REVERT: F 343 LEU cc_start: 0.8366 (pp) cc_final: 0.7686 (mm) REVERT: F 345 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5336 (mm) outliers start: 85 outliers final: 55 residues processed: 293 average time/residue: 1.3419 time to fit residues: 444.4770 Evaluate side-chains 283 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20208 Z= 0.171 Angle : 0.607 12.404 27254 Z= 0.290 Chirality : 0.041 0.245 3088 Planarity : 0.003 0.059 3526 Dihedral : 5.340 102.115 2764 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.91 % Allowed : 28.54 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2496 helix: 1.37 (0.16), residues: 1152 sheet: -0.02 (0.26), residues: 384 loop : -0.02 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 381 HIS 0.015 0.001 HIS A 388 PHE 0.014 0.001 PHE A 413 TYR 0.018 0.001 TYR A 360 ARG 0.013 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 229 time to evaluate : 2.444 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: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.6934 (pmt170) cc_final: 0.6697 (pmt170) REVERT: A 269 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7814 (mmm160) REVERT: A 381 TRP cc_start: 0.8265 (m100) cc_final: 0.7651 (m100) REVERT: B 21 MET cc_start: 0.7932 (ppp) cc_final: 0.7150 (ppp) REVERT: B 341 MET cc_start: 0.7303 (tmm) cc_final: 0.7044 (tmt) REVERT: B 416 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7436 (ttp) REVERT: D 21 MET cc_start: 0.8055 (mtt) cc_final: 0.7824 (ttp) REVERT: D 32 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7936 (mm-40) REVERT: F 111 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6419 (t80) REVERT: F 143 SER cc_start: 0.6890 (OUTLIER) cc_final: 0.6618 (t) REVERT: F 147 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7027 (mpp) REVERT: F 299 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7351 (ppt170) REVERT: F 321 ILE cc_start: 0.1381 (OUTLIER) cc_final: 0.0890 (tp) REVERT: F 341 MET cc_start: 0.4823 (ppp) cc_final: 0.4176 (pmt) REVERT: F 343 LEU cc_start: 0.8241 (pp) cc_final: 0.7507 (mm) REVERT: F 345 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.5394 (mm) outliers start: 84 outliers final: 52 residues processed: 294 average time/residue: 1.3850 time to fit residues: 460.7017 Evaluate side-chains 286 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20208 Z= 0.198 Angle : 0.631 12.015 27254 Z= 0.302 Chirality : 0.042 0.247 3088 Planarity : 0.004 0.083 3526 Dihedral : 5.355 102.191 2764 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.77 % Allowed : 28.77 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.85 (0.17), residues: 2496 helix: 1.34 (0.16), residues: 1151 sheet: -0.01 (0.26), residues: 384 loop : -0.01 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 381 HIS 0.012 0.001 HIS A 388 PHE 0.015 0.001 PHE E 412 TYR 0.016 0.001 TYR E 80 ARG 0.016 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 233 time to evaluate : 2.583 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: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.6948 (pmt170) cc_final: 0.6686 (pmt170) REVERT: A 147 MET cc_start: 0.8198 (mpp) cc_final: 0.7906 (mpp) REVERT: A 269 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7821 (mmm160) REVERT: A 381 TRP cc_start: 0.8306 (m100) cc_final: 0.7691 (m100) REVERT: B 21 MET cc_start: 0.7955 (ppp) cc_final: 0.7166 (ppp) REVERT: B 341 MET cc_start: 0.7321 (tmm) cc_final: 0.7069 (tmt) REVERT: D 21 MET cc_start: 0.8059 (mtt) cc_final: 0.7834 (ttp) REVERT: D 32 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: D 329 GLU cc_start: 0.7297 (tp30) cc_final: 0.6327 (tp30) REVERT: E 265 ASP cc_start: 0.6530 (t70) cc_final: 0.6256 (t70) REVERT: F 111 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6369 (t80) REVERT: F 143 SER cc_start: 0.6903 (OUTLIER) cc_final: 0.6618 (t) REVERT: F 147 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7044 (mpp) REVERT: F 175 LEU cc_start: 0.7880 (tm) cc_final: 0.6871 (pt) REVERT: F 299 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7342 (ppt170) REVERT: F 321 ILE cc_start: 0.1302 (OUTLIER) cc_final: 0.0794 (tp) REVERT: F 343 LEU cc_start: 0.8147 (pp) cc_final: 0.7693 (mm) REVERT: F 345 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5311 (mm) outliers start: 81 outliers final: 58 residues processed: 295 average time/residue: 1.3782 time to fit residues: 458.1828 Evaluate side-chains 287 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 222 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 145 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20208 Z= 0.248 Angle : 0.658 12.347 27254 Z= 0.313 Chirality : 0.042 0.246 3088 Planarity : 0.004 0.069 3526 Dihedral : 5.402 102.288 2764 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.49 % Allowed : 29.24 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.80 (0.17), residues: 2496 helix: 1.28 (0.16), residues: 1152 sheet: -0.01 (0.26), residues: 384 loop : -0.00 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.014 0.001 HIS A 388 PHE 0.017 0.001 PHE A 413 TYR 0.020 0.001 TYR A 360 ARG 0.013 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 2.490 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 1 MET cc_start: 0.7859 (pp-130) cc_final: 0.7459 (ppp) REVERT: A 92 ARG cc_start: 0.6963 (pmt170) cc_final: 0.6724 (pmt170) REVERT: A 147 MET cc_start: 0.8235 (mpp) cc_final: 0.7957 (mpp) REVERT: A 269 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: A 334 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 381 TRP cc_start: 0.8339 (m100) cc_final: 0.7699 (m100) REVERT: B 21 MET cc_start: 0.8008 (ppp) cc_final: 0.7123 (ppp) REVERT: B 341 MET cc_start: 0.7361 (tmm) cc_final: 0.7111 (tmt) REVERT: B 416 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7411 (ttp) REVERT: D 21 MET cc_start: 0.8062 (mtt) cc_final: 0.7830 (ttp) REVERT: D 32 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: D 333 GLU cc_start: 0.6913 (mp0) cc_final: 0.6692 (mm-30) REVERT: F 111 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6373 (t80) REVERT: F 143 SER cc_start: 0.6858 (OUTLIER) cc_final: 0.6577 (t) REVERT: F 147 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7140 (mpp) REVERT: F 175 LEU cc_start: 0.8006 (tm) cc_final: 0.7202 (pt) REVERT: F 299 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7359 (ppt170) REVERT: F 321 ILE cc_start: 0.1346 (OUTLIER) cc_final: 0.0880 (tp) REVERT: F 343 LEU cc_start: 0.8401 (pp) cc_final: 0.7513 (mm) REVERT: F 345 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5871 (mp) outliers start: 75 outliers final: 54 residues processed: 285 average time/residue: 1.3452 time to fit residues: 433.3088 Evaluate side-chains 285 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 223 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 358 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 50.0000 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS F 172 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20208 Z= 0.200 Angle : 0.693 17.227 27254 Z= 0.331 Chirality : 0.042 0.224 3088 Planarity : 0.004 0.120 3526 Dihedral : 5.524 101.656 2764 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 29.66 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.75 (0.17), residues: 2496 helix: 1.22 (0.16), residues: 1151 sheet: -0.03 (0.26), residues: 390 loop : -0.01 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.015 0.001 HIS A 388 PHE 0.026 0.001 PHE E 412 TYR 0.016 0.001 TYR E 80 ARG 0.019 0.000 ARG E 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 2.497 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 1 MET cc_start: 0.7822 (pp-130) cc_final: 0.7423 (ppp) REVERT: A 92 ARG cc_start: 0.6943 (pmt170) cc_final: 0.6688 (pmt170) REVERT: A 147 MET cc_start: 0.8200 (mpp) cc_final: 0.7817 (mpm) REVERT: A 244 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 269 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7662 (mmm-85) REVERT: A 334 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 381 TRP cc_start: 0.8320 (m100) cc_final: 0.7705 (m100) REVERT: B 21 MET cc_start: 0.8030 (ppp) cc_final: 0.7150 (ppp) REVERT: B 341 MET cc_start: 0.7325 (tmm) cc_final: 0.7073 (tmt) REVERT: D 21 MET cc_start: 0.8051 (mtt) cc_final: 0.7824 (ttp) REVERT: D 32 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7971 (mm-40) REVERT: F 143 SER cc_start: 0.6857 (OUTLIER) cc_final: 0.6572 (t) REVERT: F 147 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: F 175 LEU cc_start: 0.7916 (tm) cc_final: 0.7088 (pt) REVERT: F 205 MET cc_start: 0.2014 (ppp) cc_final: 0.1695 (ppp) REVERT: F 299 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7389 (ppt170) REVERT: F 321 ILE cc_start: 0.1254 (OUTLIER) cc_final: 0.0846 (tp) REVERT: F 343 LEU cc_start: 0.8323 (pp) cc_final: 0.7401 (mm) REVERT: F 345 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5662 (mp) REVERT: F 348 LYS cc_start: 0.8424 (tppt) cc_final: 0.8055 (mmmm) outliers start: 64 outliers final: 52 residues processed: 283 average time/residue: 1.3637 time to fit residues: 437.6254 Evaluate side-chains 277 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.124965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084638 restraints weight = 50804.908| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.89 r_work: 0.3126 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20208 Z= 0.200 Angle : 0.678 12.782 27254 Z= 0.323 Chirality : 0.042 0.209 3088 Planarity : 0.003 0.049 3526 Dihedral : 5.470 101.944 2764 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.07 % Allowed : 29.89 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.75 (0.17), residues: 2496 helix: 1.23 (0.16), residues: 1150 sheet: -0.05 (0.26), residues: 390 loop : -0.00 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.015 0.001 HIS A 388 PHE 0.015 0.001 PHE A 413 TYR 0.019 0.001 TYR A 360 ARG 0.011 0.000 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7869.51 seconds wall clock time: 141 minutes 33.44 seconds (8493.44 seconds total)