Starting phenix.real_space_refine on Mon Aug 5 20:42:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r7h_18973/08_2024/8r7h_18973.cif" } resolution = 3.29 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= 0.001 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 8994 2.51 5 N 2496 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14258 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3590 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3539 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3539 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3590 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 444} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 9.52, per 1000 atoms: 0.67 Number of scatterers: 14258 At special positions: 0 Unit cell: (132.461, 123.571, 99.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 2 15.00 O 2694 8.00 N 2496 7.00 C 8994 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: 5.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 16 sheets defined 53.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.632A pdb=" N LEU A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.797A pdb=" N ASN A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.859A pdb=" N TYR A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.527A pdb=" N GLY A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.675A pdb=" N ARG A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.898A pdb=" N GLU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.717A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.776A pdb=" N LYS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.674A pdb=" N ALA A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 440 Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 457 through 473 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.579A pdb=" N TYR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.569A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.927A pdb=" N ASN B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 71 " --> pdb=" O CYS B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.846A pdb=" N TYR B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.880A pdb=" N GLU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.593A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'B' and resid 321 through 345 removed outlier: 3.793A pdb=" N LYS B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.690A pdb=" N SER B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 440 removed outlier: 3.784A pdb=" N LYS B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 454 through 473 removed outlier: 4.350A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.990A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.681A pdb=" N TYR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.508A pdb=" N LEU C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.923A pdb=" N ASN C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.865A pdb=" N TYR C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.880A pdb=" N LEU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.897A pdb=" N GLU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 247' Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.553A pdb=" N LEU C 291 " --> pdb=" O ASN C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 Processing helix chain 'C' and resid 321 through 345 removed outlier: 3.791A pdb=" N LYS C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.989A pdb=" N GLY C 352 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.586A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 414 through 440 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.694A pdb=" N ALA C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 473 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.618A pdb=" N TYR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.743A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.893A pdb=" N TYR D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.736A pdb=" N ARG D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.941A pdb=" N GLU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.716A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 320 Processing helix chain 'D' and resid 321 through 345 removed outlier: 3.798A pdb=" N LYS D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.774A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 440 Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 454 through 473 removed outlier: 4.329A pdb=" N ALA D 460 " --> pdb=" O LYS D 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.154A pdb=" N LEU A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 252 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 227 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR A 254 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 198 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 200 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG A 137 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE A 199 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N MET A 139 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 201 " --> pdb=" O MET A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 276 removed outlier: 7.268A pdb=" N ILE A 284 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.910A pdb=" N LYS A 348 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 385 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.175A pdb=" N LEU B 225 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR B 252 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B 227 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR B 254 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 228 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG B 137 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE B 199 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET B 139 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 201 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 273 through 276 removed outlier: 7.131A pdb=" N ILE B 284 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 removed outlier: 7.050A pdb=" N LEU C 48 " --> pdb=" O ALA C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 77 removed outlier: 4.079A pdb=" N TYR C 77 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.175A pdb=" N LEU C 225 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 252 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA C 227 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR C 254 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG C 137 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 199 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET C 139 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY C 201 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.696A pdb=" N SER C 275 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 362 removed outlier: 4.354A pdb=" N ILE C 359 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 402 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 385 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 48 through 49 removed outlier: 7.339A pdb=" N LEU D 48 " --> pdb=" O ALA D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 77 removed outlier: 4.051A pdb=" N TYR D 77 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 111 through 114 removed outlier: 6.254A pdb=" N LEU D 225 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR D 252 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA D 227 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR D 254 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG D 137 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE D 199 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET D 139 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLY D 201 " --> pdb=" O MET D 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 273 through 276 removed outlier: 3.783A pdb=" N SER D 275 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 348 through 349 removed outlier: 4.172A pdb=" N LYS D 348 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 385 " --> pdb=" O ARG D 402 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4740 1.34 - 1.46: 1938 1.46 - 1.57: 7756 1.57 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 14540 Sorted by residual: bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C4 LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 1.464 1.616 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 14535 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.42: 490 107.42 - 114.06: 8195 114.06 - 120.69: 6222 120.69 - 127.33: 4637 127.33 - 133.96: 128 Bond angle restraints: 19672 Sorted by residual: angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.09 109.45 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " pdb=" C4 LLP A 257 " ideal model delta sigma weight residual 120.09 109.66 10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CE LLP D 257 " pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " ideal model delta sigma weight residual 119.26 109.39 9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CE LLP A 257 " pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 119.26 109.48 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C HIS C 256 " pdb=" N LYS C 257 " pdb=" CA LYS C 257 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.74e+00 ... (remaining 19667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 8339 16.93 - 33.87: 356 33.87 - 50.80: 49 50.80 - 67.74: 10 67.74 - 84.67: 12 Dihedral angle restraints: 8766 sinusoidal: 3458 harmonic: 5308 Sorted by residual: dihedral pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N HIS C 135 " pdb=" CA HIS C 135 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N HIS B 135 " pdb=" CA HIS B 135 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PRO D 134 " pdb=" C PRO D 134 " pdb=" N HIS D 135 " pdb=" CA HIS D 135 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1433 0.028 - 0.055: 511 0.055 - 0.083: 140 0.083 - 0.110: 81 0.110 - 0.138: 25 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA PRO A 134 " pdb=" N PRO A 134 " pdb=" C PRO A 134 " pdb=" CB PRO A 134 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA PRO B 134 " pdb=" N PRO B 134 " pdb=" C PRO B 134 " pdb=" CB PRO B 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2187 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.164 2.00e-02 2.50e+03 2.93e-01 8.56e+02 pdb=" NZ LLP A 257 " 0.400 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.81e-01 7.89e+02 pdb=" NZ LLP D 257 " -0.381 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 116 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 117 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.021 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3548 2.79 - 3.32: 13342 3.32 - 3.84: 23072 3.84 - 4.37: 27388 4.37 - 4.90: 46349 Nonbonded interactions: 113699 Sorted by model distance: nonbonded pdb=" OG SER B 233 " pdb=" OG1 THR B 258 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 119 " pdb=" OP1 LLP A 257 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 368 " pdb=" OE1 GLN C 436 " model vdw 2.295 3.040 nonbonded pdb=" O ILE A 429 " pdb=" OG1 THR A 432 " model vdw 2.310 3.040 ... (remaining 113694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 146 or resid 153 through 256 or resid 258 throu \ gh 480)) selection = (chain 'B' and (resid 16 through 256 or resid 258 through 480)) selection = (chain 'C' and (resid 16 through 256 or resid 258 through 480)) selection = (chain 'D' and (resid 16 through 146 or resid 153 through 256 or resid 258 throu \ gh 480)) } 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: 2.640 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.650 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14540 Z= 0.285 Angle : 0.501 10.642 19672 Z= 0.260 Chirality : 0.036 0.138 2190 Planarity : 0.009 0.293 2566 Dihedral : 9.961 84.671 5378 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.86 % Allowed : 4.43 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.80 (0.17), residues: 1832 helix: -0.15 (0.16), residues: 886 sheet: -1.38 (0.33), residues: 222 loop : -2.42 (0.19), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 111 HIS 0.003 0.000 HIS C 256 PHE 0.005 0.001 PHE D 268 TYR 0.005 0.000 TYR D 205 ARG 0.001 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 263 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8751 (tp30) cc_final: 0.8501 (tp30) REVERT: A 160 ILE cc_start: 0.9290 (mt) cc_final: 0.9053 (mm) REVERT: A 229 MET cc_start: 0.8435 (ptm) cc_final: 0.7881 (ptm) REVERT: A 449 LYS cc_start: 0.8429 (tppt) cc_final: 0.8092 (tppt) REVERT: B 63 GLU cc_start: 0.8725 (tt0) cc_final: 0.8357 (tm-30) REVERT: B 173 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8297 (mmmm) REVERT: C 198 ILE cc_start: 0.8966 (mt) cc_final: 0.8701 (mp) REVERT: C 465 ARG cc_start: 0.9197 (ttm170) cc_final: 0.8949 (mtp-110) REVERT: D 159 LYS cc_start: 0.8952 (mttp) cc_final: 0.8734 (mttm) outliers start: 13 outliers final: 9 residues processed: 276 average time/residue: 0.3332 time to fit residues: 125.4806 Evaluate side-chains 153 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 102 GLN A 109 GLN A 231 HIS A 318 GLN A 357 HIS A 458 GLN B 102 GLN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN C 97 GLN C 102 GLN C 109 GLN C 330 GLN C 458 GLN D 102 GLN D 318 GLN D 458 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14540 Z= 0.174 Angle : 0.522 9.611 19672 Z= 0.261 Chirality : 0.038 0.144 2190 Planarity : 0.004 0.065 2566 Dihedral : 5.289 87.678 2042 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.79 % Allowed : 10.25 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.24 (0.19), residues: 1832 helix: 1.27 (0.17), residues: 902 sheet: -1.10 (0.33), residues: 220 loop : -1.74 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 111 HIS 0.003 0.001 HIS D 194 PHE 0.014 0.001 PHE A 418 TYR 0.020 0.001 TYR D 457 ARG 0.005 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9261 (mt) cc_final: 0.9025 (mm) REVERT: A 229 MET cc_start: 0.8673 (ptm) cc_final: 0.8010 (ptm) REVERT: A 384 CYS cc_start: 0.8445 (t) cc_final: 0.7855 (t) REVERT: A 449 LYS cc_start: 0.8539 (tppt) cc_final: 0.8264 (tppt) REVERT: B 21 MET cc_start: 0.8912 (ttp) cc_final: 0.8632 (ttt) REVERT: B 63 GLU cc_start: 0.8609 (tt0) cc_final: 0.8204 (tm-30) REVERT: B 133 GLU cc_start: 0.8289 (tp30) cc_final: 0.8063 (tp30) REVERT: B 173 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8392 (mmmm) REVERT: C 54 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8257 (mm-30) REVERT: C 198 ILE cc_start: 0.9202 (mt) cc_final: 0.8982 (mp) REVERT: C 356 ASN cc_start: 0.6870 (OUTLIER) cc_final: 0.6658 (p0) REVERT: C 465 ARG cc_start: 0.9184 (ttm170) cc_final: 0.8969 (mtp-110) REVERT: D 159 LYS cc_start: 0.9037 (mttp) cc_final: 0.8768 (mttm) REVERT: D 229 MET cc_start: 0.8996 (ptm) cc_final: 0.8613 (ptt) outliers start: 27 outliers final: 17 residues processed: 162 average time/residue: 0.2889 time to fit residues: 68.5383 Evaluate side-chains 143 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 139 optimal weight: 0.0270 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN A 334 ASN B 24 GLN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14540 Z= 0.162 Angle : 0.497 10.468 19672 Z= 0.248 Chirality : 0.038 0.202 2190 Planarity : 0.004 0.058 2566 Dihedral : 5.262 88.128 2041 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 11.90 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.26 (0.19), residues: 1832 helix: 1.73 (0.18), residues: 902 sheet: -0.91 (0.33), residues: 220 loop : -1.55 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS B 194 PHE 0.009 0.001 PHE D 418 TYR 0.006 0.001 TYR C 286 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9298 (mt) cc_final: 0.9063 (mm) REVERT: A 229 MET cc_start: 0.8740 (ptm) cc_final: 0.7979 (ptm) REVERT: A 232 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8821 (pt) REVERT: A 384 CYS cc_start: 0.8495 (t) cc_final: 0.7937 (t) REVERT: B 63 GLU cc_start: 0.8579 (tt0) cc_final: 0.8186 (tm-30) REVERT: B 133 GLU cc_start: 0.8405 (tp30) cc_final: 0.8118 (tp30) REVERT: B 173 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8417 (mmmm) REVERT: C 54 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8247 (mm-30) REVERT: C 133 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8194 (mp0) REVERT: C 198 ILE cc_start: 0.9286 (mt) cc_final: 0.9068 (mp) REVERT: C 465 ARG cc_start: 0.9173 (ttm170) cc_final: 0.8934 (mtp-110) REVERT: D 374 GLU cc_start: 0.8921 (tt0) cc_final: 0.8375 (tp30) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.2646 time to fit residues: 59.9453 Evaluate side-chains 130 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14540 Z= 0.219 Angle : 0.536 7.983 19672 Z= 0.271 Chirality : 0.039 0.138 2190 Planarity : 0.004 0.061 2566 Dihedral : 5.437 87.724 2041 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 12.96 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.55 (0.20), residues: 1832 helix: 1.99 (0.18), residues: 902 sheet: -0.76 (0.34), residues: 220 loop : -1.46 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 111 HIS 0.004 0.001 HIS D 148 PHE 0.015 0.001 PHE D 418 TYR 0.010 0.001 TYR C 224 ARG 0.005 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.9324 (mt) cc_final: 0.9094 (mm) REVERT: A 229 MET cc_start: 0.8900 (ptm) cc_final: 0.8002 (ptm) REVERT: A 232 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8851 (pt) REVERT: B 21 MET cc_start: 0.8979 (ttp) cc_final: 0.8726 (ttt) REVERT: B 63 GLU cc_start: 0.8562 (tt0) cc_final: 0.8161 (tm-30) REVERT: B 133 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: B 173 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8597 (mmmm) REVERT: C 54 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8299 (mm-30) REVERT: C 465 ARG cc_start: 0.9176 (ttm170) cc_final: 0.8918 (mtp-110) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.2626 time to fit residues: 53.3124 Evaluate side-chains 128 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14540 Z= 0.186 Angle : 0.513 9.579 19672 Z= 0.257 Chirality : 0.039 0.266 2190 Planarity : 0.004 0.057 2566 Dihedral : 5.344 87.558 2040 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.46 % Allowed : 13.56 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.70 (0.20), residues: 1832 helix: 2.09 (0.18), residues: 914 sheet: -0.61 (0.34), residues: 220 loop : -1.44 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 111 HIS 0.002 0.001 HIS D 148 PHE 0.011 0.001 PHE D 418 TYR 0.009 0.001 TYR A 172 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.7802 (t) cc_final: 0.7477 (t) REVERT: A 93 GLU cc_start: 0.8956 (tt0) cc_final: 0.8732 (pp20) REVERT: A 160 ILE cc_start: 0.9323 (mt) cc_final: 0.9094 (mm) REVERT: A 229 MET cc_start: 0.8870 (ptm) cc_final: 0.8006 (ptm) REVERT: A 232 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (pt) REVERT: B 21 MET cc_start: 0.8978 (ttp) cc_final: 0.8693 (ttt) REVERT: B 63 GLU cc_start: 0.8566 (tt0) cc_final: 0.8155 (tm-30) REVERT: B 133 GLU cc_start: 0.8459 (tp30) cc_final: 0.8161 (tp30) REVERT: B 173 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8614 (mmmm) REVERT: C 54 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 210 GLU cc_start: 0.8515 (mp0) cc_final: 0.8290 (mp0) REVERT: C 465 ARG cc_start: 0.9178 (ttm170) cc_final: 0.8912 (mtp-110) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.2532 time to fit residues: 51.4190 Evaluate side-chains 124 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 0.0670 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS D 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14540 Z= 0.187 Angle : 0.515 10.355 19672 Z= 0.258 Chirality : 0.039 0.234 2190 Planarity : 0.004 0.056 2566 Dihedral : 5.237 87.623 2038 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.18 % Allowed : 13.03 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.86 (0.20), residues: 1832 helix: 2.20 (0.18), residues: 914 sheet: -0.55 (0.34), residues: 228 loop : -1.33 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 148 PHE 0.012 0.001 PHE D 418 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.7943 (t) cc_final: 0.7614 (t) REVERT: A 160 ILE cc_start: 0.9313 (mt) cc_final: 0.9097 (mm) REVERT: A 229 MET cc_start: 0.8889 (ptm) cc_final: 0.8022 (ptm) REVERT: A 232 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8871 (pt) REVERT: B 21 MET cc_start: 0.8966 (ttp) cc_final: 0.8691 (ttt) REVERT: B 63 GLU cc_start: 0.8558 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 173 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8655 (mmmm) REVERT: C 210 GLU cc_start: 0.8508 (mp0) cc_final: 0.8261 (mp0) REVERT: C 465 ARG cc_start: 0.9175 (ttm170) cc_final: 0.8908 (mtp-110) outliers start: 33 outliers final: 19 residues processed: 134 average time/residue: 0.2585 time to fit residues: 51.8870 Evaluate side-chains 125 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14540 Z= 0.167 Angle : 0.514 10.362 19672 Z= 0.256 Chirality : 0.038 0.173 2190 Planarity : 0.004 0.054 2566 Dihedral : 5.221 87.745 2038 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.59 % Allowed : 13.89 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.98 (0.20), residues: 1832 helix: 2.30 (0.18), residues: 910 sheet: -0.47 (0.35), residues: 228 loop : -1.26 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 148 PHE 0.010 0.001 PHE D 418 TYR 0.009 0.001 TYR A 172 ARG 0.002 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.7954 (t) cc_final: 0.7620 (t) REVERT: A 160 ILE cc_start: 0.9306 (mt) cc_final: 0.9087 (mm) REVERT: A 229 MET cc_start: 0.8873 (ptm) cc_final: 0.8248 (ptm) REVERT: A 232 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8827 (pt) REVERT: A 389 CYS cc_start: 0.8050 (m) cc_final: 0.7502 (m) REVERT: B 21 MET cc_start: 0.8991 (ttp) cc_final: 0.8707 (ttt) REVERT: B 63 GLU cc_start: 0.8542 (tt0) cc_final: 0.8139 (tm-30) REVERT: B 142 ASP cc_start: 0.6589 (t0) cc_final: 0.5417 (t70) REVERT: B 173 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8786 (mmmt) REVERT: C 210 GLU cc_start: 0.8491 (mp0) cc_final: 0.8230 (mp0) REVERT: C 432 THR cc_start: 0.8891 (m) cc_final: 0.8587 (p) REVERT: C 465 ARG cc_start: 0.9169 (ttm170) cc_final: 0.8911 (mtp-110) outliers start: 24 outliers final: 20 residues processed: 133 average time/residue: 0.2667 time to fit residues: 53.1187 Evaluate side-chains 130 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN D 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14540 Z= 0.254 Angle : 0.559 8.075 19672 Z= 0.281 Chirality : 0.040 0.141 2190 Planarity : 0.004 0.057 2566 Dihedral : 5.350 87.277 2038 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.18 % Allowed : 13.69 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.97 (0.20), residues: 1832 helix: 2.30 (0.18), residues: 914 sheet: -0.52 (0.33), residues: 246 loop : -1.28 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 111 HIS 0.003 0.001 HIS D 148 PHE 0.014 0.001 PHE D 418 TYR 0.010 0.001 TYR A 172 ARG 0.002 0.000 ARG D 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 74 SER cc_start: 0.8127 (t) cc_final: 0.7798 (t) REVERT: A 160 ILE cc_start: 0.9323 (mt) cc_final: 0.9121 (mm) REVERT: A 389 CYS cc_start: 0.8030 (m) cc_final: 0.7515 (m) REVERT: B 21 MET cc_start: 0.8997 (ttp) cc_final: 0.8714 (ttt) REVERT: B 63 GLU cc_start: 0.8579 (tt0) cc_final: 0.8160 (tm-30) REVERT: C 210 GLU cc_start: 0.8485 (mp0) cc_final: 0.8188 (mp0) REVERT: C 432 THR cc_start: 0.8929 (m) cc_final: 0.8626 (p) REVERT: C 465 ARG cc_start: 0.9164 (ttm170) cc_final: 0.8942 (mtp-110) outliers start: 33 outliers final: 25 residues processed: 130 average time/residue: 0.2530 time to fit residues: 49.9162 Evaluate side-chains 132 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14540 Z= 0.184 Angle : 0.544 11.833 19672 Z= 0.270 Chirality : 0.039 0.291 2190 Planarity : 0.004 0.054 2566 Dihedral : 5.326 87.570 2038 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 14.02 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.08 (0.20), residues: 1832 helix: 2.36 (0.17), residues: 912 sheet: -0.46 (0.33), residues: 246 loop : -1.18 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 148 PHE 0.011 0.001 PHE D 418 TYR 0.009 0.001 TYR A 172 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 74 SER cc_start: 0.8135 (t) cc_final: 0.7820 (t) REVERT: A 389 CYS cc_start: 0.7993 (m) cc_final: 0.7593 (m) REVERT: B 21 MET cc_start: 0.8992 (ttp) cc_final: 0.8708 (ttt) REVERT: B 63 GLU cc_start: 0.8557 (tt0) cc_final: 0.8142 (tm-30) REVERT: C 210 GLU cc_start: 0.8434 (mp0) cc_final: 0.8145 (mp0) REVERT: C 432 THR cc_start: 0.8894 (m) cc_final: 0.8595 (p) REVERT: C 465 ARG cc_start: 0.9157 (ttm170) cc_final: 0.8937 (mtp-110) outliers start: 28 outliers final: 24 residues processed: 129 average time/residue: 0.2476 time to fit residues: 48.5091 Evaluate side-chains 131 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14540 Z= 0.188 Angle : 0.546 11.570 19672 Z= 0.272 Chirality : 0.039 0.284 2190 Planarity : 0.004 0.055 2566 Dihedral : 5.331 87.939 2038 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.59 % Allowed : 14.42 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.07 (0.20), residues: 1832 helix: 2.37 (0.18), residues: 910 sheet: -0.54 (0.34), residues: 224 loop : -1.15 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 148 PHE 0.012 0.001 PHE D 418 TYR 0.010 0.001 TYR A 172 ARG 0.002 0.000 ARG A 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 SER cc_start: 0.8132 (t) cc_final: 0.7814 (t) REVERT: A 389 CYS cc_start: 0.8062 (m) cc_final: 0.7694 (m) REVERT: B 21 MET cc_start: 0.8994 (ttp) cc_final: 0.8705 (ttt) REVERT: B 63 GLU cc_start: 0.8558 (tt0) cc_final: 0.8140 (tm-30) REVERT: B 384 CYS cc_start: 0.8005 (p) cc_final: 0.7669 (p) REVERT: C 210 GLU cc_start: 0.8450 (mp0) cc_final: 0.8172 (mp0) REVERT: C 432 THR cc_start: 0.8888 (m) cc_final: 0.8592 (p) REVERT: C 465 ARG cc_start: 0.9171 (ttm170) cc_final: 0.8954 (mtp-110) outliers start: 24 outliers final: 23 residues processed: 126 average time/residue: 0.2600 time to fit residues: 50.1705 Evaluate side-chains 129 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 457 TYR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.051777 restraints weight = 51555.376| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.06 r_work: 0.2671 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14540 Z= 0.175 Angle : 0.541 11.314 19672 Z= 0.269 Chirality : 0.039 0.273 2190 Planarity : 0.004 0.054 2566 Dihedral : 5.331 88.452 2038 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.59 % Allowed : 14.42 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.12 (0.20), residues: 1832 helix: 2.38 (0.18), residues: 910 sheet: -0.51 (0.35), residues: 224 loop : -1.09 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 148 PHE 0.012 0.001 PHE C 193 TYR 0.010 0.001 TYR A 172 ARG 0.001 0.000 ARG D 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.29 seconds wall clock time: 53 minutes 32.34 seconds (3212.34 seconds total)