Starting phenix.real_space_refine on Mon Apr 6 01:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wlr_66072/04_2026/9wlr_66072.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9231 2.51 5 N 2381 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14554 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2492 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 22, 'TRANS': 336} Chain breaks: 6 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 13, 'TYR:plan': 7, 'GLN:plan1': 11, 'PHE:plan': 9, 'ASN:plan1': 2, 'GLU:plan': 9, 'HIS:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 292 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2330 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 6 Unresolved non-hydrogen bonds: 478 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 15, 'ASP:plan': 12, 'TYR:plan': 10, 'GLN:plan1': 13, 'PHE:plan': 9, 'GLU:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 348 Chain: "F" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2408 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 20, 'TRANS': 329} Chain breaks: 6 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 541 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 14, 'TYR:plan': 7, 'GLN:plan1': 11, 'PHE:plan': 10, 'ASP:plan': 7, 'GLU:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 302 Chain: "G" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2448 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 20, 'TRANS': 330} Chain breaks: 6 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 10, 'TYR:plan': 6, 'PHE:plan': 9, 'GLU:plan': 7, 'ASP:plan': 7, 'HIS:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 273 Chain: "H" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2523 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 23, 'TRANS': 336} Chain breaks: 6 Unresolved non-hydrogen bonds: 399 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 9, 'TYR:plan': 6, 'PHE:plan': 9, 'GLU:plan': 8, 'ASP:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 265 Chain: "I" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2353 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 19, 'TRANS': 321} Chain breaks: 6 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 14, 'TYR:plan': 9, 'PHE:plan': 9, 'GLN:plan1': 9, 'GLU:plan': 8, 'ASP:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 291 Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14554 At special positions: 0 Unit cell: (132.16, 122.08, 164.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2872 8.00 N 2381 7.00 C 9231 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 - 3.00 Amino acid : True - 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: 1.08 Conformation dependent library (CDL) restraints added in 518.9 milliseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 39 sheets defined 13.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 388 through 399 Processing helix chain 'D' and resid 399 through 406 removed outlier: 4.102A pdb=" N LEU D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.881A pdb=" N ASP D 446 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS D 447 " --> pdb=" O PRO D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 443 through 447' Processing helix chain 'D' and resid 462 through 465 removed outlier: 4.246A pdb=" N GLN D 465 " --> pdb=" O ASP D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 466 through 476 removed outlier: 3.501A pdb=" N LYS D 471 " --> pdb=" O PRO D 467 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 473 " --> pdb=" O GLY D 469 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 475 " --> pdb=" O LYS D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 388 through 399 Processing helix chain 'E' and resid 400 through 403 Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.824A pdb=" N ASP E 446 " --> pdb=" O ASP E 443 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS E 447 " --> pdb=" O PRO E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 465 removed outlier: 3.911A pdb=" N GLN E 465 " --> pdb=" O ASP E 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 465' Processing helix chain 'E' and resid 466 through 476 removed outlier: 3.560A pdb=" N LEU E 473 " --> pdb=" O GLY E 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 227 removed outlier: 4.597A pdb=" N GLN F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 388 through 399 Processing helix chain 'F' and resid 399 through 405 removed outlier: 4.120A pdb=" N LEU F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 476 removed outlier: 3.574A pdb=" N LYS F 471 " --> pdb=" O PRO F 467 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 476 " --> pdb=" O PHE F 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 215 removed outlier: 3.788A pdb=" N GLN G 215 " --> pdb=" O PHE G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.775A pdb=" N MET G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 327 through 329 No H-bonds generated for 'chain 'G' and resid 327 through 329' Processing helix chain 'G' and resid 388 through 399 Processing helix chain 'G' and resid 400 through 406 removed outlier: 3.845A pdb=" N TRP G 406 " --> pdb=" O ILE G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 removed outlier: 3.523A pdb=" N LYS G 471 " --> pdb=" O PRO G 467 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 474 " --> pdb=" O ARG G 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 removed outlier: 3.919A pdb=" N GLY H 85 " --> pdb=" O ASN H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 240 removed outlier: 3.752A pdb=" N MET H 238 " --> pdb=" O ASP H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 327 through 329 No H-bonds generated for 'chain 'H' and resid 327 through 329' Processing helix chain 'H' and resid 388 through 399 Processing helix chain 'H' and resid 399 through 406 removed outlier: 4.151A pdb=" N LEU H 403 " --> pdb=" O ASN H 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP H 406 " --> pdb=" O ILE H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 475 removed outlier: 3.537A pdb=" N LYS H 471 " --> pdb=" O PRO H 467 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN H 475 " --> pdb=" O LYS H 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 234 through 240 removed outlier: 3.794A pdb=" N MET I 238 " --> pdb=" O ASP I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 399 Processing helix chain 'I' and resid 400 through 407 removed outlier: 4.577A pdb=" N GLU I 404 " --> pdb=" O SER I 400 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN I 405 " --> pdb=" O SER I 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP I 406 " --> pdb=" O ILE I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 475 removed outlier: 3.593A pdb=" N ARG I 470 " --> pdb=" O TYR I 466 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS I 471 " --> pdb=" O PRO I 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 30 through 38 removed outlier: 6.791A pdb=" N THR D 31 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 384 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE D 33 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 382 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN D 377 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET D 106 " --> pdb=" O GLN D 377 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 379 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 98 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET D 106 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 44 through 46 removed outlier: 3.519A pdb=" N LEU D 347 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 369 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 200 through 201 removed outlier: 4.459A pdb=" N ASP D 200 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN D 70 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP D 338 " --> pdb=" O GLN D 70 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 72 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 154 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.549A pdb=" N SER D 297 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS D 260 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER D 299 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA D 258 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 154 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 72 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP D 338 " --> pdb=" O GLN D 70 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN D 70 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'D' and resid 119 through 124 removed outlier: 5.338A pdb=" N GLY D 120 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 150 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL D 148 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.531A pdb=" N HIS D 169 " --> pdb=" O LYS D 192 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 192 " --> pdb=" O HIS D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 303 through 304 removed outlier: 3.575A pdb=" N LEU G 256 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG G 72 " --> pdb=" O VAL G 336 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL G 73 " --> pdb=" O TRP G 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 38 removed outlier: 9.098A pdb=" N SER E 29 " --> pdb=" O THR E 386 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR E 386 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR E 31 " --> pdb=" O THR E 384 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N THR E 384 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 33 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 382 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN E 377 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N MET E 106 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 379 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 106 " --> pdb=" O TYR E 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AB2, first strand: chain 'E' and resid 295 through 299 removed outlier: 4.176A pdb=" N HIS E 260 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER E 299 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA E 258 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 251 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 72 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 295 through 299 removed outlier: 4.176A pdb=" N HIS E 260 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER E 299 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA E 258 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 120 through 124 removed outlier: 5.342A pdb=" N VAL E 148 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 146 " --> pdb=" O TYR E 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'F' and resid 30 through 38 removed outlier: 6.874A pdb=" N THR F 31 " --> pdb=" O THR F 384 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR F 384 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE F 33 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP F 375 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE F 108 " --> pdb=" O ASP F 375 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN F 377 " --> pdb=" O MET F 106 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET F 106 " --> pdb=" O GLN F 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 379 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 98 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET F 106 " --> pdb=" O TYR F 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 44 through 46 Processing sheet with id=AB8, first strand: chain 'F' and resid 72 through 77 removed outlier: 3.569A pdb=" N ARG F 72 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA F 258 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER F 299 " --> pdb=" O ALA F 258 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS F 260 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER F 297 " --> pdb=" O HIS F 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 72 through 77 removed outlier: 3.569A pdb=" N ARG F 72 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 119 through 124 removed outlier: 5.115A pdb=" N GLY F 120 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL F 150 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL F 148 " --> pdb=" O PRO F 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 171 Processing sheet with id=AC3, first strand: chain 'G' and resid 29 through 38 removed outlier: 7.045A pdb=" N THR G 31 " --> pdb=" O THR G 384 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR G 384 " --> pdb=" O THR G 31 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE G 33 " --> pdb=" O LEU G 382 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU G 382 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP G 375 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE G 108 " --> pdb=" O ASP G 375 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN G 377 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET G 106 " --> pdb=" O GLN G 377 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE G 379 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G 106 " --> pdb=" O TYR G 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 44 through 46 removed outlier: 3.545A pdb=" N THR G 44 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG G 369 " --> pdb=" O LEU G 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 119 through 124 removed outlier: 5.333A pdb=" N GLY G 120 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL G 150 " --> pdb=" O GLY G 120 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL G 148 " --> pdb=" O PRO G 122 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP G 146 " --> pdb=" O TYR G 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 166 through 171 Processing sheet with id=AC7, first strand: chain 'G' and resid 201 through 202 removed outlier: 7.007A pdb=" N MET G 201 " --> pdb=" O LYS G 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 303 through 304 removed outlier: 5.861A pdb=" N ALA H 258 " --> pdb=" O SER H 299 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER H 299 " --> pdb=" O ALA H 258 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS H 260 " --> pdb=" O SER H 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 303 through 304 removed outlier: 3.514A pdb=" N LEU H 332 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 72 " --> pdb=" O VAL H 336 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP H 451 " --> pdb=" O VAL H 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 29 through 38 removed outlier: 4.746A pdb=" N LEU H 382 " --> pdb=" O THR H 31 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 33 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE H 380 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR H 35 " --> pdb=" O PHE H 378 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE H 378 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 37 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU H 376 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 44 " --> pdb=" O GLU H 372 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 29 through 38 removed outlier: 4.746A pdb=" N LEU H 382 " --> pdb=" O THR H 31 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 33 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE H 380 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR H 35 " --> pdb=" O PHE H 378 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE H 378 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 37 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU H 376 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU H 373 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG H 110 " --> pdb=" O GLU H 373 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP H 375 " --> pdb=" O ILE H 108 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE H 108 " --> pdb=" O ASP H 375 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN H 377 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET H 106 " --> pdb=" O GLN H 377 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE H 379 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG H 98 " --> pdb=" O ILE H 385 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 119 through 124 removed outlier: 3.644A pdb=" N VAL H 148 " --> pdb=" O HIS H 121 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE H 123 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASP H 146 " --> pdb=" O PHE H 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 166 through 171 removed outlier: 3.543A pdb=" N THR H 194 " --> pdb=" O GLY H 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS H 169 " --> pdb=" O LYS H 192 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 201 through 202 removed outlier: 7.423A pdb=" N MET H 201 " --> pdb=" O LYS H 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 346 through 347 removed outlier: 3.562A pdb=" N TYR H 367 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 30 through 38 removed outlier: 6.621A pdb=" N THR I 31 " --> pdb=" O THR I 384 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR I 384 " --> pdb=" O THR I 31 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE I 33 " --> pdb=" O LEU I 382 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE I 379 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRP I 101 " --> pdb=" O CYS I 327 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.668A pdb=" N THR I 44 " --> pdb=" O GLU I 372 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 250 through 255 removed outlier: 3.618A pdb=" N LEU I 332 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL I 73 " --> pdb=" O TRP I 451 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 119 through 124 removed outlier: 3.560A pdb=" N VAL I 148 " --> pdb=" O HIS I 121 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE I 123 " --> pdb=" O ASP I 146 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP I 146 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 166 through 171 removed outlier: 3.614A pdb=" N HIS I 169 " --> pdb=" O LYS I 192 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 257 through 262 removed outlier: 6.901A pdb=" N SER I 297 " --> pdb=" O ARG I 259 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE I 261 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER I 295 " --> pdb=" O PHE I 261 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.52 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: 4773 1.34 - 1.46: 3556 1.46 - 1.58: 6477 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 14880 Sorted by residual: bond pdb=" C ALA F 77 " pdb=" N LEU F 78 " ideal model delta sigma weight residual 1.331 1.230 0.101 1.48e-02 4.57e+03 4.62e+01 bond pdb=" CA SER D 228 " pdb=" CB SER D 228 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.36e-02 5.41e+03 1.23e+01 bond pdb=" C TYR E 232 " pdb=" N PRO E 233 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.01e-02 9.80e+03 1.22e+01 bond pdb=" C ALA H 77 " pdb=" N LEU H 78 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.59e-02 3.96e+03 8.43e+00 bond pdb=" N ASP F 88 " pdb=" CA ASP F 88 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 ... (remaining 14875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 19995 2.75 - 5.50: 497 5.50 - 8.24: 46 8.24 - 10.99: 7 10.99 - 13.74: 1 Bond angle restraints: 20546 Sorted by residual: angle pdb=" N ILE D 225 " pdb=" CA ILE D 225 " pdb=" C ILE D 225 " ideal model delta sigma weight residual 112.80 105.88 6.92 1.15e+00 7.56e-01 3.62e+01 angle pdb=" C SER F 89 " pdb=" N THR F 90 " pdb=" CA THR F 90 " ideal model delta sigma weight residual 121.94 112.40 9.54 2.00e+00 2.50e-01 2.27e+01 angle pdb=" C LEU D 127 " pdb=" N ASP D 128 " pdb=" CA ASP D 128 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C LEU E 463 " pdb=" N ASP E 464 " pdb=" CA ASP E 464 " ideal model delta sigma weight residual 120.60 127.74 -7.14 1.60e+00 3.91e-01 1.99e+01 angle pdb=" C LYS E 83 " pdb=" N PHE E 84 " pdb=" CA PHE E 84 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.36: 7899 12.36 - 24.71: 518 24.71 - 37.07: 155 37.07 - 49.42: 22 49.42 - 61.78: 4 Dihedral angle restraints: 8598 sinusoidal: 2479 harmonic: 6119 Sorted by residual: dihedral pdb=" CA LYS G 458 " pdb=" C LYS G 458 " pdb=" N PHE G 459 " pdb=" CA PHE G 459 " ideal model delta harmonic sigma weight residual 180.00 125.89 54.11 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA LYS H 458 " pdb=" C LYS H 458 " pdb=" N PHE H 459 " pdb=" CA PHE H 459 " ideal model delta harmonic sigma weight residual 180.00 126.39 53.61 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ILE G 225 " pdb=" C ILE G 225 " pdb=" N CYS G 226 " pdb=" CA CYS G 226 " ideal model delta harmonic sigma weight residual 180.00 -149.88 -30.12 0 5.00e+00 4.00e-02 3.63e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1935 0.068 - 0.137: 471 0.137 - 0.205: 103 0.205 - 0.273: 8 0.273 - 0.342: 10 Chirality restraints: 2527 Sorted by residual: chirality pdb=" CB ILE G 91 " pdb=" CA ILE G 91 " pdb=" CG1 ILE G 91 " pdb=" CG2 ILE G 91 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE G 302 " pdb=" CA ILE G 302 " pdb=" CG1 ILE G 302 " pdb=" CG2 ILE G 302 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL F 163 " pdb=" CA VAL F 163 " pdb=" CG1 VAL F 163 " pdb=" CG2 VAL F 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2524 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 225 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ILE E 225 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE E 225 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS E 226 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 225 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C ILE H 225 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE H 225 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS H 226 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 47 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO G 48 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 48 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 48 " 0.036 5.00e-02 4.00e+02 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3877 2.78 - 3.31: 12938 3.31 - 3.84: 22720 3.84 - 4.37: 23878 4.37 - 4.90: 41444 Nonbonded interactions: 104857 Sorted by model distance: nonbonded pdb=" OG SER E 29 " pdb=" OG1 THR E 384 " model vdw 2.254 3.040 nonbonded pdb=" O LEU H 236 " pdb=" OG SER H 239 " model vdw 2.255 3.040 nonbonded pdb=" O LEU D 309 " pdb=" OH TYR D 314 " model vdw 2.270 3.040 nonbonded pdb=" O LEU G 236 " pdb=" OG SER G 239 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR I 31 " pdb=" O LEU I 382 " model vdw 2.276 3.040 ... (remaining 104852 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 'D' and (resid 20 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 34 or (resid 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 49 or (res \ id 50 through 51 and (name N or name CA or name C or name O or name CB )) or res \ id 52 or resid 64 through 68 or (resid 69 through 72 and (name N or name CA or n \ ame C or name O or name CB )) or resid 73 through 85 or (resid 86 and (name N or \ name CA or name C or name O or name CB )) or resid 87 or (resid 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 through 90 or (resid 91 \ through 93 and (name N or name CA or name C or name O or name CB )) or resid 94 \ through 109 or (resid 110 and (name N or name CA or name C or name O or name CB \ )) or resid 111 through 124 or (resid 125 and (name N or name CA or name C or n \ ame O or name CB )) or resid 144 through 209 or (resid 210 through 211 and (name \ N or name CA or name C or name O or name CB )) or resid 212 through 235 or (res \ id 236 through 238 and (name N or name CA or name C or name O or name CB )) or r \ esid 239 through 240 or (resid 241 and (name N or name CA or name C or name O or \ name CB )) or resid 242 or (resid 243 and (name N or name CA or name C or name \ O or name CB )) or resid 244 through 262 or (resid 263 through 264 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 308 or (resid 3 \ 09 through 310 and (name N or name CA or name C or name O or name CB )) or resid \ 311 through 321 or (resid 322 and (name N or name CA or name C or name O or nam \ e CB )) or resid 323 through 340 or (resid 341 and (name N or name CA or name C \ or name O or name CB )) or resid 342 through 346 or (resid 347 and (name N or na \ me CA or name C or name O or name CB )) or (resid 366 through 367 and (name N or \ name CA or name C or name O or name CB )) or resid 368 through 389 or (resid 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 or (resi \ d 392 and (name N or name CA or name C or name O or name CB )) or resid 393 thro \ ugh 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 447 or (resid 448 through 449 and (name N or name CA or name \ C or name O or name CB )) or resid 450 through 461 or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 through 464 or (resid 46 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 466 through \ 469 or (resid 470 through 471 and (name N or name CA or name C or name O or name \ CB )) or resid 472 through 476)) selection = (chain 'E' and (resid 20 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 42 or (resid 43 and (name N or nam \ e CA or name C or name O or name CB )) or resid 44 through 49 or (resid 50 throu \ gh 51 and (name N or name CA or name C or name O or name CB )) or resid 63 throu \ gh 68 or (resid 69 through 72 and (name N or name CA or name C or name O or name \ CB )) or resid 73 through 85 or (resid 86 and (name N or name CA or name C or n \ ame O or name CB )) or resid 87 or (resid 88 and (name N or name CA or name C or \ name O or name CB )) or resid 89 through 90 or (resid 91 through 93 and (name N \ or name CA or name C or name O or name CB )) or resid 94 through 120 or (resid \ 121 and (name N or name CA or name C or name O or name CB )) or resid 122 throug \ h 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) or \ resid 144 through 224 or (resid 225 and (name N or name CA or name C or name O o \ r name CB )) or resid 226 through 308 or (resid 309 through 310 and (name N or n \ ame CA or name C or name O or name CB )) or resid 311 through 321 or (resid 322 \ and (name N or name CA or name C or name O or name CB )) or resid 323 through 34 \ 0 or (resid 341 and (name N or name CA or name C or name O or name CB )) or resi \ d 342 through 346 or (resid 347 through 367 and (name N or name CA or name C or \ name O or name CB )) or resid 368 through 389 or (resid 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 or (resid 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 through 397 or (resid 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 44 \ 7 or (resid 448 through 449 and (name N or name CA or name C or name O or name C \ B )) or resid 450 through 461 or (resid 462 and (name N or name CA or name C or \ name O or name CB )) or resid 463 through 476)) selection = (chain 'F' and (resid 20 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 34 or (resid 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 42 or (res \ id 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 49 or (resid 50 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 or resid 64 through 68 or (resid 69 through 72 and (name N or \ name CA or name C or name O or name CB )) or resid 73 through 91 or (resid 92 t \ hrough 93 and (name N or name CA or name C or name O or name CB )) or resid 94 o \ r (resid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 \ or (resid 97 through 98 and (name N or name CA or name C or name O or name CB ) \ ) or resid 99 through 109 or (resid 110 and (name N or name CA or name C or name \ O or name CB )) or resid 111 through 120 or (resid 121 and (name N or name CA o \ r name C or name O or name CB )) or resid 122 through 125 or resid 144 through 2 \ 09 or (resid 210 through 211 and (name N or name CA or name C or name O or name \ CB )) or resid 212 through 222 or (resid 223 through 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 235 or (resid 236 through \ 238 and (name N or name CA or name C or name O or name CB )) or resid 239 throu \ gh 240 or (resid 241 and (name N or name CA or name C or name O or name CB )) or \ resid 242 or (resid 243 and (name N or name CA or name C or name O or name CB ) \ ) or resid 244 through 262 or (resid 263 through 264 and (name N or name CA or n \ ame C or name O or name CB )) or resid 291 through 308 or (resid 309 through 310 \ and (name N or name CA or name C or name O or name CB )) or resid 311 through 3 \ 46 or (resid 347 and (name N or name CA or name C or name O or name CB )) or (re \ sid 366 through 367 and (name N or name CA or name C or name O or name CB )) or \ resid 368 through 371 or (resid 372 through 373 and (name N or name CA or name C \ or name O or name CB )) or resid 374 through 447 or (resid 448 through 449 and \ (name N or name CA or name C or name O or name CB )) or resid 450 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 464 or (resid 465 and (name N or name CA or name C or name O or name C \ B )) or resid 466 through 476)) selection = (chain 'G' and (resid 20 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 34 or (resid 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 42 or (res \ id 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 68 or (resid 69 through 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 through 87 or (resid 88 \ and (name N or name CA or name C or name O or name CB )) or resid 89 through 90 \ or (resid 91 through 93 and (name N or name CA or name C or name O or name CB ) \ ) or resid 94 or (resid 95 and (name N or name CA or name C or name O or name CB \ )) or resid 96 or (resid 97 through 98 and (name N or name CA or name C or name \ O or name CB )) or resid 99 through 109 or (resid 110 and (name N or name CA or \ name C or name O or name CB )) or resid 111 through 120 or (resid 121 and (name \ N or name CA or name C or name O or name CB )) or resid 122 through 124 or (res \ id 125 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 209 or (resid 210 through 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 224 or (resid 225 and (name N or name CA or nam \ e C or name O or name CB )) or resid 226 through 235 or (resid 236 through 238 a \ nd (name N or name CA or name C or name O or name CB )) or resid 239 through 240 \ or (resid 241 and (name N or name CA or name C or name O or name CB )) or resid \ 242 or (resid 243 and (name N or name CA or name C or name O or name CB )) or r \ esid 244 through 262 or (resid 263 through 264 and (name N or name CA or name C \ or name O or name CB )) or resid 291 through 308 or (resid 309 through 310 and ( \ name N or name CA or name C or name O or name CB )) or resid 311 through 340 or \ (resid 341 and (name N or name CA or name C or name O or name CB )) or resid 342 \ through 347 or (resid 366 through 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 through 371 or (resid 372 through 373 and (name N o \ r name CA or name C or name O or name CB )) or resid 374 through 376 or (resid 3 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 378 through \ 389 or (resid 390 and (name N or name CA or name C or name O or name CB )) or r \ esid 391 through 447 or (resid 448 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 470 or (resid 471 and (name N or na \ me CA or name C or name O or name CB )) or resid 472 through 476)) selection = (chain 'H' and (resid 20 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 34 or (resid 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 42 or (res \ id 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 68 or (resid 69 through 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 through 87 or (resid 88 \ and (name N or name CA or name C or name O or name CB )) or resid 89 through 90 \ or (resid 91 through 93 and (name N or name CA or name C or name O or name CB ) \ ) or resid 94 through 96 or (resid 97 through 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 109 or (resid 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 120 or (resid 121 \ and (name N or name CA or name C or name O or name CB )) or resid 122 through 12 \ 4 or (resid 125 and (name N or name CA or name C or name O or name CB )) or resi \ d 144 through 209 or (resid 210 through 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 through 224 or (resid 225 and (name N or name \ CA or name C or name O or name CB )) or resid 226 through 235 or (resid 236 thro \ ugh 238 and (name N or name CA or name C or name O or name CB )) or resid 239 th \ rough 240 or (resid 241 and (name N or name CA or name C or name O or name CB )) \ or resid 242 or (resid 243 and (name N or name CA or name C or name O or name C \ B )) or resid 244 through 262 or (resid 263 through 264 and (name N or name CA o \ r name C or name O or name CB )) or resid 291 through 308 or (resid 309 through \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throug \ h 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 340 or (resid 341 and (name N or name CA or name C or name O o \ r name CB )) or resid 342 through 346 or (resid 347 and (name N or name CA or na \ me C or name O or name CB )) or (resid 366 through 367 and (name N or name CA or \ name C or name O or name CB )) or resid 368 through 371 or (resid 372 through 3 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 374 through \ 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or r \ esid 378 through 389 or (resid 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 through 447 or (resid 448 through 449 and (name N or na \ me CA or name C or name O or name CB )) or resid 450 through 461 or (resid 462 a \ nd (name N or name CA or name C or name O or name CB )) or resid 463 through 464 \ or (resid 465 and (name N or name CA or name C or name O or name CB )) or resid \ 466 through 476)) selection = (chain 'I' and (resid 20 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 42 or (resid 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 52 or resi \ d 64 through 85 or (resid 86 and (name N or name CA or name C or name O or name \ CB )) or resid 87 or (resid 88 and (name N or name CA or name C or name O or nam \ e CB )) or resid 89 through 90 or (resid 91 through 93 and (name N or name CA or \ name C or name O or name CB )) or resid 94 or (resid 95 and (name N or name CA \ or name C or name O or name CB )) or resid 96 or (resid 97 through 98 and (name \ N or name CA or name C or name O or name CB )) or resid 99 through 109 or (resid \ 110 and (name N or name CA or name C or name O or name CB )) or resid 111 throu \ gh 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) or \ resid 122 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 144 through 209 or (resid 210 through 211 and (name N or \ name CA or name C or name O or name CB )) or resid 212 through 222 or (resid 223 \ through 225 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 26 through 235 or (resid 236 through 238 and (name N or name CA or name C or nam \ e O or name CB )) or resid 239 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 262 or (resid 263 thr \ ough 264 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 321 or (resid 322 and (name N or name CA or name C or name O or name CB ) \ ) or resid 323 through 340 or (resid 341 and (name N or name CA or name C or nam \ e O or name CB )) or resid 342 through 346 or (resid 347 and (name N or name CA \ or name C or name O or name CB )) or (resid 366 through 367 and (name N or name \ CA or name C or name O or name CB )) or resid 368 through 371 or (resid 372 thro \ ugh 373 and (name N or name CA or name C or name O or name CB )) or resid 374 th \ rough 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) \ or resid 378 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 464 or (resid 465 and (name N or name CA o \ r name C or name O or name CB )) or resid 466 through 470 or (resid 471 and (nam \ e N or name CA or name C or name O or name CB )) or resid 472 through 476)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 38.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.007 0.101 14880 Z= 0.394 Angle : 1.020 13.739 20546 Z= 0.570 Chirality : 0.064 0.342 2527 Planarity : 0.007 0.066 2658 Dihedral : 10.024 61.778 4614 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.79 % Favored : 89.76 % Rotamer: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.16), residues: 2022 helix: -3.91 (0.18), residues: 183 sheet: -2.31 (0.21), residues: 515 loop : -2.86 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 341 TYR 0.042 0.003 TYR E 69 PHE 0.026 0.003 PHE E 50 TRP 0.025 0.003 TRP I 406 HIS 0.009 0.002 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00712 (14880) covalent geometry : angle 1.01986 (20546) hydrogen bonds : bond 0.30232 ( 351) hydrogen bonds : angle 9.84893 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 796 time to evaluate : 0.498 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: D 50 PHE cc_start: 0.8219 (p90) cc_final: 0.7757 (p90) REVERT: D 127 LEU cc_start: 0.8072 (pp) cc_final: 0.7830 (pp) REVERT: D 147 ASN cc_start: 0.8568 (t0) cc_final: 0.8187 (t0) REVERT: D 169 HIS cc_start: 0.8595 (p-80) cc_final: 0.8296 (p-80) REVERT: D 237 GLN cc_start: 0.7792 (pm20) cc_final: 0.7414 (pm20) REVERT: D 241 ASP cc_start: 0.8100 (t0) cc_final: 0.7787 (t0) REVERT: D 243 TYR cc_start: 0.7971 (m-10) cc_final: 0.7647 (m-80) REVERT: D 263 ASN cc_start: 0.7102 (t0) cc_final: 0.6803 (t0) REVERT: D 316 LEU cc_start: 0.8552 (mm) cc_final: 0.8272 (mm) REVERT: D 339 THR cc_start: 0.8888 (p) cc_final: 0.8657 (t) REVERT: D 376 LEU cc_start: 0.8138 (mm) cc_final: 0.7827 (tt) REVERT: D 378 PHE cc_start: 0.8184 (m-10) cc_final: 0.7365 (m-10) REVERT: D 392 MET cc_start: 0.7756 (mpp) cc_final: 0.7495 (mpp) REVERT: D 465 GLN cc_start: 0.8011 (mp10) cc_final: 0.7370 (mp10) REVERT: D 473 LEU cc_start: 0.8655 (mm) cc_final: 0.8446 (mm) REVERT: E 50 PHE cc_start: 0.7759 (p90) cc_final: 0.7400 (p90) REVERT: E 80 ASP cc_start: 0.8458 (t0) cc_final: 0.8137 (t0) REVERT: E 93 ASN cc_start: 0.8743 (t0) cc_final: 0.8245 (t0) REVERT: E 151 ASP cc_start: 0.7907 (t0) cc_final: 0.7672 (p0) REVERT: E 163 VAL cc_start: 0.9000 (m) cc_final: 0.8475 (m) REVERT: E 196 ILE cc_start: 0.8941 (mm) cc_final: 0.8509 (mm) REVERT: E 198 ASP cc_start: 0.8674 (t0) cc_final: 0.7968 (t0) REVERT: E 217 THR cc_start: 0.8696 (m) cc_final: 0.8456 (p) REVERT: E 245 ASP cc_start: 0.7379 (p0) cc_final: 0.6984 (p0) REVERT: E 303 ILE cc_start: 0.8926 (mp) cc_final: 0.8584 (mp) REVERT: E 311 ASN cc_start: 0.8636 (m-40) cc_final: 0.8334 (m110) REVERT: E 323 ASN cc_start: 0.8405 (p0) cc_final: 0.8174 (p0) REVERT: E 324 ASN cc_start: 0.8104 (t0) cc_final: 0.7734 (t0) REVERT: E 330 ASN cc_start: 0.8849 (m-40) cc_final: 0.8564 (m110) REVERT: E 332 LEU cc_start: 0.7964 (tt) cc_final: 0.7680 (tt) REVERT: E 335 THR cc_start: 0.8600 (t) cc_final: 0.8326 (p) REVERT: E 341 ARG cc_start: 0.8193 (mpt-90) cc_final: 0.7557 (mpt-90) REVERT: E 375 ASP cc_start: 0.8047 (t0) cc_final: 0.7810 (t70) REVERT: E 378 PHE cc_start: 0.8124 (m-10) cc_final: 0.7890 (m-80) REVERT: E 399 ASN cc_start: 0.8304 (t0) cc_final: 0.7446 (t0) REVERT: E 468 LEU cc_start: 0.8850 (tp) cc_final: 0.8604 (tp) REVERT: F 35 TYR cc_start: 0.8068 (m-10) cc_final: 0.7785 (m-10) REVERT: F 73 VAL cc_start: 0.9004 (t) cc_final: 0.8792 (p) REVERT: F 80 ASP cc_start: 0.8613 (t0) cc_final: 0.8174 (t0) REVERT: F 97 GLN cc_start: 0.5877 (mp-120) cc_final: 0.5328 (mp-120) REVERT: F 110 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: F 114 LEU cc_start: 0.8381 (mm) cc_final: 0.8169 (mp) REVERT: F 121 HIS cc_start: 0.7961 (t-90) cc_final: 0.7474 (t-90) REVERT: F 147 ASN cc_start: 0.8167 (t0) cc_final: 0.7953 (t0) REVERT: F 169 HIS cc_start: 0.8884 (p90) cc_final: 0.8321 (p-80) REVERT: F 204 THR cc_start: 0.8712 (p) cc_final: 0.8408 (t) REVERT: F 210 ASP cc_start: 0.8278 (t70) cc_final: 0.7689 (t70) REVERT: F 232 TYR cc_start: 0.8502 (t80) cc_final: 0.8278 (t80) REVERT: F 248 PHE cc_start: 0.8620 (m-10) cc_final: 0.7954 (m-80) REVERT: F 309 LEU cc_start: 0.8221 (mt) cc_final: 0.7990 (mt) REVERT: F 316 LEU cc_start: 0.9141 (mm) cc_final: 0.8893 (mp) REVERT: F 334 VAL cc_start: 0.8996 (t) cc_final: 0.8752 (p) REVERT: F 339 THR cc_start: 0.8679 (p) cc_final: 0.8417 (t) REVERT: F 399 ASN cc_start: 0.8962 (t0) cc_final: 0.8628 (t0) REVERT: F 401 SER cc_start: 0.8685 (m) cc_final: 0.8107 (p) REVERT: F 406 TRP cc_start: 0.8711 (m-10) cc_final: 0.8473 (m-10) REVERT: F 466 TYR cc_start: 0.7866 (m-80) cc_final: 0.7538 (m-80) REVERT: G 21 VAL cc_start: 0.8973 (t) cc_final: 0.8569 (m) REVERT: G 47 ASN cc_start: 0.8799 (t0) cc_final: 0.8398 (t0) REVERT: G 73 VAL cc_start: 0.8800 (t) cc_final: 0.8487 (t) REVERT: G 93 ASN cc_start: 0.7412 (t0) cc_final: 0.5809 (t0) REVERT: G 97 GLN cc_start: 0.7305 (mp-120) cc_final: 0.6832 (mp-120) REVERT: G 99 LEU cc_start: 0.8120 (mt) cc_final: 0.7451 (mt) REVERT: G 112 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7864 (mm-40) REVERT: G 121 HIS cc_start: 0.8512 (t-90) cc_final: 0.7874 (t-90) REVERT: G 196 ILE cc_start: 0.8438 (mm) cc_final: 0.8225 (mm) REVERT: G 210 ASP cc_start: 0.7865 (t70) cc_final: 0.7241 (t70) REVERT: G 245 ASP cc_start: 0.7543 (p0) cc_final: 0.7269 (p0) REVERT: G 260 HIS cc_start: 0.8380 (m90) cc_final: 0.8126 (m90) REVERT: G 334 VAL cc_start: 0.8739 (t) cc_final: 0.8414 (m) REVERT: G 336 VAL cc_start: 0.8677 (t) cc_final: 0.8189 (m) REVERT: G 372 GLU cc_start: 0.6715 (mp0) cc_final: 0.6084 (mp0) REVERT: G 378 PHE cc_start: 0.8116 (m-10) cc_final: 0.7860 (m-80) REVERT: G 402 ILE cc_start: 0.8403 (tp) cc_final: 0.8155 (tp) REVERT: G 405 ASN cc_start: 0.8288 (m110) cc_final: 0.8011 (m110) REVERT: G 471 LYS cc_start: 0.9168 (mttt) cc_final: 0.8742 (mtpp) REVERT: G 472 PHE cc_start: 0.8103 (t80) cc_final: 0.7811 (t80) REVERT: G 473 LEU cc_start: 0.8339 (mm) cc_final: 0.8089 (mm) REVERT: G 475 GLN cc_start: 0.8843 (pp30) cc_final: 0.8619 (pp30) REVERT: H 42 LEU cc_start: 0.8746 (mt) cc_final: 0.8463 (mp) REVERT: H 44 THR cc_start: 0.8573 (t) cc_final: 0.8246 (p) REVERT: H 78 LEU cc_start: 0.9050 (mp) cc_final: 0.8689 (mp) REVERT: H 93 ASN cc_start: 0.8216 (t0) cc_final: 0.7744 (t0) REVERT: H 97 GLN cc_start: 0.8065 (pm20) cc_final: 0.7251 (pm20) REVERT: H 147 ASN cc_start: 0.8172 (t0) cc_final: 0.7886 (t0) REVERT: H 169 HIS cc_start: 0.8524 (p90) cc_final: 0.8185 (p-80) REVERT: H 213 THR cc_start: 0.8912 (p) cc_final: 0.8691 (p) REVERT: H 232 TYR cc_start: 0.8556 (t80) cc_final: 0.8356 (t80) REVERT: H 245 ASP cc_start: 0.7294 (p0) cc_final: 0.6768 (p0) REVERT: H 320 GLN cc_start: 0.8517 (pp30) cc_final: 0.8193 (pp30) REVERT: H 322 HIS cc_start: 0.7672 (m-70) cc_final: 0.7466 (m-70) REVERT: H 330 ASN cc_start: 0.7985 (t0) cc_final: 0.7431 (t0) REVERT: H 344 ASN cc_start: 0.8701 (p0) cc_final: 0.8381 (p0) REVERT: H 367 TYR cc_start: 0.8212 (m-10) cc_final: 0.7970 (m-10) REVERT: H 401 SER cc_start: 0.9094 (m) cc_final: 0.7872 (p) REVERT: H 446 ASP cc_start: 0.8276 (p0) cc_final: 0.8034 (p0) REVERT: H 465 GLN cc_start: 0.8115 (mp10) cc_final: 0.7825 (mp10) REVERT: H 473 LEU cc_start: 0.8558 (mm) cc_final: 0.8299 (mm) REVERT: H 475 GLN cc_start: 0.8449 (pp30) cc_final: 0.7732 (pp30) REVERT: I 93 ASN cc_start: 0.8175 (t0) cc_final: 0.6927 (t0) REVERT: I 97 GLN cc_start: 0.6601 (mp10) cc_final: 0.6174 (mp10) REVERT: I 108 ILE cc_start: 0.8242 (mm) cc_final: 0.7999 (mm) REVERT: I 114 LEU cc_start: 0.8724 (mm) cc_final: 0.8220 (mm) REVERT: I 159 ILE cc_start: 0.8498 (mt) cc_final: 0.8154 (mt) REVERT: I 229 ILE cc_start: 0.8770 (mt) cc_final: 0.8438 (tp) REVERT: I 232 TYR cc_start: 0.8882 (t80) cc_final: 0.8637 (t80) REVERT: I 248 PHE cc_start: 0.8901 (m-10) cc_final: 0.8613 (m-80) REVERT: I 333 PHE cc_start: 0.8245 (m-10) cc_final: 0.7902 (m-10) REVERT: I 370 HIS cc_start: 0.7977 (t-90) cc_final: 0.7264 (t-90) REVERT: I 374 TYR cc_start: 0.8213 (m-10) cc_final: 0.7632 (m-10) REVERT: I 375 ASP cc_start: 0.7742 (t0) cc_final: 0.7521 (t0) REVERT: I 377 GLN cc_start: 0.7441 (mp10) cc_final: 0.6681 (mp10) REVERT: I 399 ASN cc_start: 0.8327 (t0) cc_final: 0.8042 (t0) REVERT: I 405 ASN cc_start: 0.8478 (m-40) cc_final: 0.8160 (m-40) REVERT: I 465 GLN cc_start: 0.8321 (mp10) cc_final: 0.8058 (mp10) REVERT: I 466 TYR cc_start: 0.8043 (m-10) cc_final: 0.7653 (m-80) REVERT: I 468 LEU cc_start: 0.8504 (mm) cc_final: 0.8296 (mm) REVERT: I 473 LEU cc_start: 0.8665 (mt) cc_final: 0.8437 (mt) outliers start: 5 outliers final: 2 residues processed: 799 average time/residue: 0.0852 time to fit residues: 111.5175 Evaluate side-chains 738 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 736 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 370 HIS E 47 ASN E 193 ASN E 344 ASN F 47 ASN F 82 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN F 323 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 ASN H 323 ASN H 370 HIS I 263 ASN I 323 ASN I 330 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.076752 restraints weight = 32348.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.079481 restraints weight = 16549.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.081278 restraints weight = 10323.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082463 restraints weight = 7384.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083253 restraints weight = 5829.519| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 14880 Z= 0.344 Angle : 0.753 9.031 20546 Z= 0.397 Chirality : 0.050 0.178 2527 Planarity : 0.005 0.049 2658 Dihedral : 5.932 47.091 2152 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.80 % Favored : 90.95 % Rotamer: Outliers : 4.28 % Allowed : 17.65 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.17), residues: 2022 helix: -2.03 (0.30), residues: 205 sheet: -1.96 (0.22), residues: 484 loop : -2.58 (0.15), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 341 TYR 0.023 0.002 TYR G 69 PHE 0.027 0.003 PHE H 249 TRP 0.041 0.003 TRP I 406 HIS 0.012 0.002 HIS D 370 Details of bonding type rmsd covalent geometry : bond 0.00649 (14880) covalent geometry : angle 0.75294 (20546) hydrogen bonds : bond 0.05096 ( 351) hydrogen bonds : angle 6.49207 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 738 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 LEU cc_start: 0.8788 (mm) cc_final: 0.8578 (mm) REVERT: D 50 PHE cc_start: 0.8485 (p90) cc_final: 0.8178 (p90) REVERT: D 127 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7643 (pp) REVERT: D 147 ASN cc_start: 0.8400 (t0) cc_final: 0.7935 (t0) REVERT: D 155 THR cc_start: 0.8378 (t) cc_final: 0.8120 (p) REVERT: D 241 ASP cc_start: 0.8419 (t0) cc_final: 0.8058 (t0) REVERT: D 256 LEU cc_start: 0.8857 (tp) cc_final: 0.8577 (tp) REVERT: D 316 LEU cc_start: 0.8582 (mm) cc_final: 0.8231 (mm) REVERT: D 320 GLN cc_start: 0.8776 (pp30) cc_final: 0.8519 (pp30) REVERT: D 324 ASN cc_start: 0.7689 (t0) cc_final: 0.7468 (t0) REVERT: D 339 THR cc_start: 0.8907 (p) cc_final: 0.8589 (t) REVERT: D 378 PHE cc_start: 0.8018 (m-10) cc_final: 0.7784 (m-80) REVERT: D 465 GLN cc_start: 0.7964 (mp10) cc_final: 0.7276 (mp10) REVERT: E 69 TYR cc_start: 0.8129 (m-80) cc_final: 0.7741 (m-10) REVERT: E 80 ASP cc_start: 0.8527 (t0) cc_final: 0.8297 (t0) REVERT: E 82 ASN cc_start: 0.8688 (m-40) cc_final: 0.8440 (m110) REVERT: E 93 ASN cc_start: 0.8818 (t0) cc_final: 0.8597 (t0) REVERT: E 112 GLN cc_start: 0.8156 (tp40) cc_final: 0.7756 (mm110) REVERT: E 163 VAL cc_start: 0.8918 (m) cc_final: 0.8474 (m) REVERT: E 196 ILE cc_start: 0.8880 (mm) cc_final: 0.8503 (mm) REVERT: E 198 ASP cc_start: 0.8674 (t0) cc_final: 0.8118 (t0) REVERT: E 217 THR cc_start: 0.8720 (m) cc_final: 0.8503 (p) REVERT: E 245 ASP cc_start: 0.7407 (p0) cc_final: 0.6976 (p0) REVERT: E 303 ILE cc_start: 0.8917 (mp) cc_final: 0.8684 (mp) REVERT: E 324 ASN cc_start: 0.8125 (t0) cc_final: 0.7780 (t0) REVERT: E 335 THR cc_start: 0.8788 (t) cc_final: 0.8497 (p) REVERT: E 341 ARG cc_start: 0.8155 (mpt-90) cc_final: 0.7824 (tpp80) REVERT: E 399 ASN cc_start: 0.8442 (t0) cc_final: 0.8142 (t0) REVERT: F 80 ASP cc_start: 0.8697 (t0) cc_final: 0.8389 (t0) REVERT: F 97 GLN cc_start: 0.5794 (mp-120) cc_final: 0.5345 (mp10) REVERT: F 99 LEU cc_start: 0.8352 (mp) cc_final: 0.8087 (mp) REVERT: F 114 LEU cc_start: 0.8393 (mm) cc_final: 0.8155 (mp) REVERT: F 121 HIS cc_start: 0.8177 (t-90) cc_final: 0.7702 (t-90) REVERT: F 169 HIS cc_start: 0.8848 (p90) cc_final: 0.8272 (p-80) REVERT: F 232 TYR cc_start: 0.8551 (t80) cc_final: 0.8279 (t80) REVERT: F 248 PHE cc_start: 0.8674 (m-10) cc_final: 0.7947 (m-80) REVERT: F 309 LEU cc_start: 0.8372 (mt) cc_final: 0.8161 (mt) REVERT: F 339 THR cc_start: 0.8769 (p) cc_final: 0.8415 (t) REVERT: F 399 ASN cc_start: 0.9133 (t0) cc_final: 0.8528 (t0) REVERT: F 406 TRP cc_start: 0.8690 (m-10) cc_final: 0.8408 (m-10) REVERT: G 44 THR cc_start: 0.7561 (p) cc_final: 0.6228 (t) REVERT: G 45 VAL cc_start: 0.8741 (t) cc_final: 0.8429 (p) REVERT: G 47 ASN cc_start: 0.8990 (t0) cc_final: 0.8639 (t0) REVERT: G 73 VAL cc_start: 0.8993 (t) cc_final: 0.8766 (p) REVERT: G 93 ASN cc_start: 0.7413 (t0) cc_final: 0.5719 (t0) REVERT: G 97 GLN cc_start: 0.7380 (mp-120) cc_final: 0.6891 (mp-120) REVERT: G 121 HIS cc_start: 0.8576 (t-90) cc_final: 0.8025 (t-90) REVERT: G 170 TRP cc_start: 0.8362 (m100) cc_final: 0.8067 (m100) REVERT: G 191 LEU cc_start: 0.8850 (tt) cc_final: 0.8337 (tt) REVERT: G 196 ILE cc_start: 0.8541 (mm) cc_final: 0.8298 (mm) REVERT: G 210 ASP cc_start: 0.7633 (t70) cc_final: 0.7090 (t70) REVERT: G 232 TYR cc_start: 0.8582 (t80) cc_final: 0.8301 (t80) REVERT: G 248 PHE cc_start: 0.8788 (m-80) cc_final: 0.8482 (m-80) REVERT: G 324 ASN cc_start: 0.8336 (t0) cc_final: 0.8119 (t0) REVERT: G 372 GLU cc_start: 0.7008 (mp0) cc_final: 0.6328 (mp0) REVERT: G 378 PHE cc_start: 0.8289 (m-10) cc_final: 0.8009 (m-80) REVERT: G 402 ILE cc_start: 0.8337 (tp) cc_final: 0.7820 (tp) REVERT: G 405 ASN cc_start: 0.8182 (m110) cc_final: 0.7805 (m110) REVERT: G 406 TRP cc_start: 0.7738 (m-10) cc_final: 0.7045 (m-10) REVERT: G 463 LEU cc_start: 0.8517 (mt) cc_final: 0.8317 (mt) REVERT: G 471 LYS cc_start: 0.9214 (mttt) cc_final: 0.8856 (mttm) REVERT: G 473 LEU cc_start: 0.8582 (mm) cc_final: 0.8294 (mm) REVERT: G 475 GLN cc_start: 0.8913 (pp30) cc_final: 0.8654 (pp30) REVERT: H 78 LEU cc_start: 0.8972 (mp) cc_final: 0.8596 (mp) REVERT: H 92 TYR cc_start: 0.7206 (t80) cc_final: 0.6803 (t80) REVERT: H 93 ASN cc_start: 0.8168 (t0) cc_final: 0.7087 (t0) REVERT: H 97 GLN cc_start: 0.8146 (pm20) cc_final: 0.7549 (pm20) REVERT: H 121 HIS cc_start: 0.7866 (t-90) cc_final: 0.7604 (t-90) REVERT: H 169 HIS cc_start: 0.8443 (p90) cc_final: 0.7884 (p90) REVERT: H 204 THR cc_start: 0.8075 (p) cc_final: 0.7813 (m) REVERT: H 232 TYR cc_start: 0.8597 (t80) cc_final: 0.8381 (t80) REVERT: H 245 ASP cc_start: 0.7333 (p0) cc_final: 0.6851 (p0) REVERT: H 263 ASN cc_start: 0.7906 (t0) cc_final: 0.7631 (t0) REVERT: H 320 GLN cc_start: 0.8574 (pp30) cc_final: 0.8230 (pp30) REVERT: H 330 ASN cc_start: 0.8074 (t0) cc_final: 0.7600 (t0) REVERT: H 333 PHE cc_start: 0.7956 (m-80) cc_final: 0.7677 (m-80) REVERT: H 338 ASP cc_start: 0.8353 (t0) cc_final: 0.8135 (t0) REVERT: H 339 THR cc_start: 0.8745 (p) cc_final: 0.8412 (t) REVERT: H 344 ASN cc_start: 0.8664 (p0) cc_final: 0.8332 (p0) REVERT: H 367 TYR cc_start: 0.8211 (m-10) cc_final: 0.7961 (m-10) REVERT: H 372 GLU cc_start: 0.7316 (mp0) cc_final: 0.6937 (mp0) REVERT: H 446 ASP cc_start: 0.8138 (p0) cc_final: 0.7821 (p0) REVERT: H 473 LEU cc_start: 0.8649 (mm) cc_final: 0.8324 (mm) REVERT: H 475 GLN cc_start: 0.8595 (pp30) cc_final: 0.7859 (pp30) REVERT: I 93 ASN cc_start: 0.8099 (t0) cc_final: 0.6696 (t0) REVERT: I 97 GLN cc_start: 0.6324 (mp10) cc_final: 0.5836 (mp10) REVERT: I 114 LEU cc_start: 0.8572 (mm) cc_final: 0.8355 (mm) REVERT: I 163 VAL cc_start: 0.8962 (t) cc_final: 0.8746 (m) REVERT: I 229 ILE cc_start: 0.8778 (mt) cc_final: 0.8418 (tp) REVERT: I 232 TYR cc_start: 0.8958 (t80) cc_final: 0.8749 (t80) REVERT: I 237 GLN cc_start: 0.8012 (pm20) cc_final: 0.7766 (pm20) REVERT: I 248 PHE cc_start: 0.8829 (m-10) cc_final: 0.8603 (m-80) REVERT: I 333 PHE cc_start: 0.8148 (m-10) cc_final: 0.7833 (m-10) REVERT: I 377 GLN cc_start: 0.7530 (mp10) cc_final: 0.6655 (mp10) REVERT: I 399 ASN cc_start: 0.8515 (t0) cc_final: 0.8142 (t0) outliers start: 59 outliers final: 44 residues processed: 755 average time/residue: 0.0866 time to fit residues: 106.4782 Evaluate side-chains 765 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 720 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 395 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 0.0970 chunk 205 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN E 47 ASN E 311 ASN E 323 ASN F 97 GLN F 193 ASN F 323 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 GLN H 323 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079431 restraints weight = 32126.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082147 restraints weight = 16641.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.083913 restraints weight = 10402.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085044 restraints weight = 7455.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085880 restraints weight = 5928.118| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14880 Z= 0.137 Angle : 0.659 10.071 20546 Z= 0.330 Chirality : 0.047 0.189 2527 Planarity : 0.004 0.042 2658 Dihedral : 5.091 45.494 2151 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 4.14 % Allowed : 22.88 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.17), residues: 2022 helix: -0.99 (0.36), residues: 201 sheet: -1.72 (0.21), residues: 513 loop : -2.22 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 110 TYR 0.018 0.001 TYR G 69 PHE 0.033 0.002 PHE F 249 TRP 0.022 0.001 TRP E 406 HIS 0.006 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00278 (14880) covalent geometry : angle 0.65934 (20546) hydrogen bonds : bond 0.03401 ( 351) hydrogen bonds : angle 5.57905 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 730 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7669 (pp) REVERT: D 147 ASN cc_start: 0.8420 (t0) cc_final: 0.8005 (t0) REVERT: D 210 ASP cc_start: 0.8573 (t0) cc_final: 0.8243 (t70) REVERT: D 241 ASP cc_start: 0.8368 (t0) cc_final: 0.8008 (t0) REVERT: D 256 LEU cc_start: 0.8842 (tp) cc_final: 0.8577 (tp) REVERT: D 316 LEU cc_start: 0.8592 (mm) cc_final: 0.8219 (mm) REVERT: D 320 GLN cc_start: 0.8867 (pp30) cc_final: 0.8603 (pp30) REVERT: D 324 ASN cc_start: 0.7604 (t0) cc_final: 0.7383 (t0) REVERT: D 380 PHE cc_start: 0.8423 (m-80) cc_final: 0.8032 (m-80) REVERT: D 465 GLN cc_start: 0.7815 (mp10) cc_final: 0.7237 (mp10) REVERT: E 50 PHE cc_start: 0.7654 (p90) cc_final: 0.7420 (p90) REVERT: E 80 ASP cc_start: 0.8444 (t0) cc_final: 0.8039 (t0) REVERT: E 93 ASN cc_start: 0.8434 (t0) cc_final: 0.8169 (t0) REVERT: E 163 VAL cc_start: 0.8917 (m) cc_final: 0.8427 (m) REVERT: E 196 ILE cc_start: 0.8901 (mm) cc_final: 0.8560 (mm) REVERT: E 198 ASP cc_start: 0.8619 (t0) cc_final: 0.8050 (t0) REVERT: E 217 THR cc_start: 0.8720 (m) cc_final: 0.8433 (p) REVERT: E 245 ASP cc_start: 0.7366 (p0) cc_final: 0.6880 (p0) REVERT: E 324 ASN cc_start: 0.7972 (t0) cc_final: 0.7549 (t0) REVERT: E 335 THR cc_start: 0.8771 (t) cc_final: 0.8431 (p) REVERT: E 399 ASN cc_start: 0.8486 (t0) cc_final: 0.8097 (t0) REVERT: F 80 ASP cc_start: 0.8696 (t0) cc_final: 0.8382 (t0) REVERT: F 97 GLN cc_start: 0.5848 (mp10) cc_final: 0.5344 (mp10) REVERT: F 114 LEU cc_start: 0.8349 (mm) cc_final: 0.8062 (mp) REVERT: F 121 HIS cc_start: 0.8141 (t-90) cc_final: 0.7608 (t-90) REVERT: F 169 HIS cc_start: 0.8738 (p90) cc_final: 0.8068 (p-80) REVERT: F 210 ASP cc_start: 0.8355 (t0) cc_final: 0.8067 (t0) REVERT: F 217 THR cc_start: 0.8313 (p) cc_final: 0.8009 (t) REVERT: F 232 TYR cc_start: 0.8484 (t80) cc_final: 0.8229 (t80) REVERT: F 248 PHE cc_start: 0.8603 (m-10) cc_final: 0.8000 (m-80) REVERT: F 339 THR cc_start: 0.8721 (p) cc_final: 0.8381 (t) REVERT: F 399 ASN cc_start: 0.9126 (t0) cc_final: 0.8524 (t0) REVERT: F 405 ASN cc_start: 0.8726 (m110) cc_final: 0.8459 (m-40) REVERT: G 36 HIS cc_start: 0.8707 (t-90) cc_final: 0.8505 (t70) REVERT: G 44 THR cc_start: 0.7552 (p) cc_final: 0.6427 (t) REVERT: G 45 VAL cc_start: 0.8720 (t) cc_final: 0.8397 (p) REVERT: G 47 ASN cc_start: 0.8999 (t0) cc_final: 0.8701 (t0) REVERT: G 93 ASN cc_start: 0.7589 (t0) cc_final: 0.5902 (t0) REVERT: G 97 GLN cc_start: 0.7355 (mp-120) cc_final: 0.6849 (mp-120) REVERT: G 121 HIS cc_start: 0.8492 (t-90) cc_final: 0.8247 (t-90) REVERT: G 170 TRP cc_start: 0.8280 (m100) cc_final: 0.8042 (m100) REVERT: G 191 LEU cc_start: 0.8837 (tt) cc_final: 0.8383 (tt) REVERT: G 196 ILE cc_start: 0.8558 (mm) cc_final: 0.8344 (mm) REVERT: G 210 ASP cc_start: 0.7541 (t70) cc_final: 0.6950 (t70) REVERT: G 232 TYR cc_start: 0.8583 (t80) cc_final: 0.8173 (t80) REVERT: G 248 PHE cc_start: 0.8718 (m-80) cc_final: 0.8442 (m-80) REVERT: G 324 ASN cc_start: 0.8322 (t0) cc_final: 0.7924 (t0) REVERT: G 338 ASP cc_start: 0.8449 (t0) cc_final: 0.8204 (t70) REVERT: G 372 GLU cc_start: 0.7050 (mp0) cc_final: 0.6544 (mp0) REVERT: G 378 PHE cc_start: 0.8164 (m-10) cc_final: 0.7802 (m-80) REVERT: G 402 ILE cc_start: 0.8278 (tp) cc_final: 0.8017 (tp) REVERT: G 405 ASN cc_start: 0.8142 (m110) cc_final: 0.7733 (m110) REVERT: G 473 LEU cc_start: 0.8465 (mm) cc_final: 0.8150 (mm) REVERT: H 35 TYR cc_start: 0.8085 (m-80) cc_final: 0.7274 (m-80) REVERT: H 92 TYR cc_start: 0.7155 (t80) cc_final: 0.6818 (t80) REVERT: H 93 ASN cc_start: 0.8071 (t0) cc_final: 0.7465 (t0) REVERT: H 97 GLN cc_start: 0.8187 (pm20) cc_final: 0.7943 (pm20) REVERT: H 121 HIS cc_start: 0.7855 (t-90) cc_final: 0.7570 (t-90) REVERT: H 169 HIS cc_start: 0.8366 (p90) cc_final: 0.7820 (p90) REVERT: H 245 ASP cc_start: 0.7407 (p0) cc_final: 0.6833 (p0) REVERT: H 263 ASN cc_start: 0.7739 (t0) cc_final: 0.7436 (t0) REVERT: H 320 GLN cc_start: 0.8531 (pp30) cc_final: 0.8318 (pp30) REVERT: H 333 PHE cc_start: 0.7803 (m-80) cc_final: 0.7476 (m-80) REVERT: H 367 TYR cc_start: 0.8140 (m-10) cc_final: 0.7903 (m-10) REVERT: H 372 GLU cc_start: 0.7289 (mp0) cc_final: 0.7023 (mp0) REVERT: H 465 GLN cc_start: 0.8078 (mp10) cc_final: 0.7730 (mp10) REVERT: H 473 LEU cc_start: 0.8526 (mm) cc_final: 0.8250 (mm) REVERT: H 475 GLN cc_start: 0.8641 (pp30) cc_final: 0.7883 (pp30) REVERT: I 93 ASN cc_start: 0.8041 (t0) cc_final: 0.6823 (t0) REVERT: I 97 GLN cc_start: 0.6348 (mp10) cc_final: 0.6055 (mp10) REVERT: I 114 LEU cc_start: 0.8460 (mm) cc_final: 0.8241 (mm) REVERT: I 162 CYS cc_start: 0.7019 (m) cc_final: 0.6416 (m) REVERT: I 163 VAL cc_start: 0.8863 (t) cc_final: 0.8618 (m) REVERT: I 229 ILE cc_start: 0.8728 (mt) cc_final: 0.8422 (tp) REVERT: I 232 TYR cc_start: 0.8887 (t80) cc_final: 0.8512 (t80) REVERT: I 248 PHE cc_start: 0.8793 (m-10) cc_final: 0.8459 (m-80) REVERT: I 305 SER cc_start: 0.8629 (p) cc_final: 0.8317 (m) REVERT: I 333 PHE cc_start: 0.8081 (m-10) cc_final: 0.7843 (m-10) REVERT: I 370 HIS cc_start: 0.7767 (t-90) cc_final: 0.7468 (t-90) REVERT: I 374 TYR cc_start: 0.7939 (m-10) cc_final: 0.7493 (m-80) REVERT: I 375 ASP cc_start: 0.7346 (t0) cc_final: 0.6922 (t0) REVERT: I 377 GLN cc_start: 0.7351 (mp10) cc_final: 0.6889 (mp10) REVERT: I 399 ASN cc_start: 0.8386 (t0) cc_final: 0.8041 (t0) outliers start: 57 outliers final: 45 residues processed: 749 average time/residue: 0.0849 time to fit residues: 104.0227 Evaluate side-chains 768 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 722 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 322 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 475 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 77 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 164 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 323 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 311 ASN H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.077315 restraints weight = 32354.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079962 restraints weight = 16748.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.081691 restraints weight = 10486.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082832 restraints weight = 7535.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083599 restraints weight = 5969.843| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 14880 Z= 0.302 Angle : 0.713 11.528 20546 Z= 0.365 Chirality : 0.048 0.189 2527 Planarity : 0.004 0.047 2658 Dihedral : 5.326 47.372 2151 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.30 % Favored : 90.60 % Rotamer: Outliers : 6.97 % Allowed : 23.67 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.18), residues: 2022 helix: -0.49 (0.37), residues: 194 sheet: -1.80 (0.21), residues: 516 loop : -2.21 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 341 TYR 0.021 0.002 TYR D 27 PHE 0.036 0.003 PHE H 249 TRP 0.050 0.002 TRP I 406 HIS 0.005 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00577 (14880) covalent geometry : angle 0.71328 (20546) hydrogen bonds : bond 0.04064 ( 351) hydrogen bonds : angle 5.57182 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 717 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7744 (pp) REVERT: D 147 ASN cc_start: 0.8522 (t0) cc_final: 0.8106 (t0) REVERT: D 210 ASP cc_start: 0.8636 (t0) cc_final: 0.8359 (t70) REVERT: D 241 ASP cc_start: 0.8440 (t0) cc_final: 0.8115 (t0) REVERT: D 316 LEU cc_start: 0.8577 (mm) cc_final: 0.8166 (mm) REVERT: D 320 GLN cc_start: 0.8816 (pp30) cc_final: 0.8526 (pp30) REVERT: D 324 ASN cc_start: 0.7713 (t0) cc_final: 0.7512 (t0) REVERT: D 465 GLN cc_start: 0.7869 (mp10) cc_final: 0.7235 (mp10) REVERT: E 69 TYR cc_start: 0.8002 (m-80) cc_final: 0.7553 (m-10) REVERT: E 93 ASN cc_start: 0.8682 (t0) cc_final: 0.8428 (t0) REVERT: E 163 VAL cc_start: 0.8959 (m) cc_final: 0.8487 (m) REVERT: E 196 ILE cc_start: 0.8915 (mm) cc_final: 0.8693 (mm) REVERT: E 198 ASP cc_start: 0.8716 (t0) cc_final: 0.8166 (t0) REVERT: E 217 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8455 (p) REVERT: E 245 ASP cc_start: 0.7334 (p0) cc_final: 0.6945 (p0) REVERT: E 324 ASN cc_start: 0.8073 (t0) cc_final: 0.7624 (t0) REVERT: E 335 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8501 (p) REVERT: E 399 ASN cc_start: 0.8466 (t0) cc_final: 0.8069 (t0) REVERT: F 80 ASP cc_start: 0.8739 (t0) cc_final: 0.8443 (t0) REVERT: F 97 GLN cc_start: 0.5924 (mp10) cc_final: 0.5389 (mp10) REVERT: F 114 LEU cc_start: 0.8378 (mm) cc_final: 0.8164 (mp) REVERT: F 121 HIS cc_start: 0.8197 (t-90) cc_final: 0.7576 (t-90) REVERT: F 169 HIS cc_start: 0.8799 (p90) cc_final: 0.8179 (p-80) REVERT: F 210 ASP cc_start: 0.8595 (t0) cc_final: 0.8361 (t0) REVERT: F 217 THR cc_start: 0.8331 (p) cc_final: 0.8044 (t) REVERT: F 232 TYR cc_start: 0.8545 (t80) cc_final: 0.8285 (t80) REVERT: F 248 PHE cc_start: 0.8700 (m-10) cc_final: 0.7987 (m-80) REVERT: F 399 ASN cc_start: 0.9165 (t0) cc_final: 0.8858 (t0) REVERT: F 405 ASN cc_start: 0.8820 (m110) cc_final: 0.8551 (m110) REVERT: G 44 THR cc_start: 0.7525 (p) cc_final: 0.6387 (t) REVERT: G 45 VAL cc_start: 0.8730 (t) cc_final: 0.8414 (p) REVERT: G 47 ASN cc_start: 0.9064 (t0) cc_final: 0.8756 (t0) REVERT: G 92 TYR cc_start: 0.6989 (t80) cc_final: 0.6535 (t80) REVERT: G 93 ASN cc_start: 0.7579 (t0) cc_final: 0.6114 (t0) REVERT: G 97 GLN cc_start: 0.7445 (mp-120) cc_final: 0.6993 (mp-120) REVERT: G 99 LEU cc_start: 0.8183 (mt) cc_final: 0.7870 (mt) REVERT: G 121 HIS cc_start: 0.8594 (t-90) cc_final: 0.8374 (t-90) REVERT: G 170 TRP cc_start: 0.8343 (m100) cc_final: 0.7992 (m100) REVERT: G 191 LEU cc_start: 0.8879 (tt) cc_final: 0.8435 (tt) REVERT: G 196 ILE cc_start: 0.8533 (mm) cc_final: 0.8332 (mm) REVERT: G 210 ASP cc_start: 0.7782 (t70) cc_final: 0.7212 (t70) REVERT: G 232 TYR cc_start: 0.8576 (t80) cc_final: 0.8262 (t80) REVERT: G 248 PHE cc_start: 0.8758 (m-80) cc_final: 0.8461 (m-80) REVERT: G 324 ASN cc_start: 0.8393 (t0) cc_final: 0.7977 (t0) REVERT: G 338 ASP cc_start: 0.8433 (t0) cc_final: 0.8220 (t70) REVERT: G 372 GLU cc_start: 0.7136 (mp0) cc_final: 0.6592 (mp0) REVERT: G 402 ILE cc_start: 0.8329 (tp) cc_final: 0.8036 (tp) REVERT: G 405 ASN cc_start: 0.8174 (m110) cc_final: 0.7782 (m110) REVERT: G 473 LEU cc_start: 0.8638 (mm) cc_final: 0.8329 (mm) REVERT: H 35 TYR cc_start: 0.8086 (m-80) cc_final: 0.7299 (m-80) REVERT: H 92 TYR cc_start: 0.7151 (t80) cc_final: 0.6858 (t80) REVERT: H 93 ASN cc_start: 0.8129 (t0) cc_final: 0.6854 (t0) REVERT: H 97 GLN cc_start: 0.8222 (pm20) cc_final: 0.7549 (pm20) REVERT: H 121 HIS cc_start: 0.7897 (t-90) cc_final: 0.7583 (t-90) REVERT: H 169 HIS cc_start: 0.8391 (p90) cc_final: 0.7808 (p90) REVERT: H 204 THR cc_start: 0.8082 (p) cc_final: 0.7790 (m) REVERT: H 221 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8323 (p) REVERT: H 245 ASP cc_start: 0.7567 (p0) cc_final: 0.7049 (p0) REVERT: H 263 ASN cc_start: 0.7745 (t0) cc_final: 0.7142 (t0) REVERT: H 333 PHE cc_start: 0.7876 (m-80) cc_final: 0.7478 (m-80) REVERT: H 344 ASN cc_start: 0.8520 (p0) cc_final: 0.8190 (p0) REVERT: H 367 TYR cc_start: 0.8209 (m-10) cc_final: 0.7924 (m-10) REVERT: H 372 GLU cc_start: 0.7347 (mp0) cc_final: 0.7081 (mp0) REVERT: H 390 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: H 465 GLN cc_start: 0.8283 (mp10) cc_final: 0.7808 (mp10) REVERT: H 473 LEU cc_start: 0.8633 (mm) cc_final: 0.8325 (mm) REVERT: H 475 GLN cc_start: 0.8670 (pp30) cc_final: 0.7937 (pp30) REVERT: I 93 ASN cc_start: 0.8111 (t0) cc_final: 0.6790 (t0) REVERT: I 114 LEU cc_start: 0.8573 (mm) cc_final: 0.8344 (mm) REVERT: I 162 CYS cc_start: 0.6993 (m) cc_final: 0.6282 (m) REVERT: I 163 VAL cc_start: 0.8898 (t) cc_final: 0.8588 (m) REVERT: I 198 ASP cc_start: 0.8022 (t0) cc_final: 0.7590 (m-30) REVERT: I 245 ASP cc_start: 0.7755 (p0) cc_final: 0.7405 (p0) REVERT: I 248 PHE cc_start: 0.8850 (m-10) cc_final: 0.8496 (m-80) REVERT: I 263 ASN cc_start: 0.6682 (p0) cc_final: 0.6433 (p0) REVERT: I 305 SER cc_start: 0.8666 (p) cc_final: 0.8232 (t) REVERT: I 333 PHE cc_start: 0.8063 (m-10) cc_final: 0.7854 (m-10) REVERT: I 341 ARG cc_start: 0.8776 (mmt90) cc_final: 0.8574 (mmt90) REVERT: I 375 ASP cc_start: 0.7606 (t0) cc_final: 0.7098 (t0) REVERT: I 377 GLN cc_start: 0.7439 (mp10) cc_final: 0.6860 (mp10) REVERT: I 399 ASN cc_start: 0.8445 (t0) cc_final: 0.8090 (t0) REVERT: I 465 GLN cc_start: 0.8274 (mp10) cc_final: 0.7825 (mp10) outliers start: 96 outliers final: 77 residues processed: 748 average time/residue: 0.0839 time to fit residues: 102.7848 Evaluate side-chains 793 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 711 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 323 ASN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 158 CYS Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 322 HIS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 136 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 323 ASN F 193 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 311 ASN H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.079070 restraints weight = 31977.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081747 restraints weight = 16734.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083461 restraints weight = 10568.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084601 restraints weight = 7658.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085368 restraints weight = 6109.788| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 14880 Z= 0.242 Angle : 0.693 10.222 20546 Z= 0.351 Chirality : 0.047 0.191 2527 Planarity : 0.004 0.046 2658 Dihedral : 5.181 45.812 2151 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 6.90 % Allowed : 24.55 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.18), residues: 2022 helix: -0.40 (0.37), residues: 207 sheet: -1.75 (0.21), residues: 517 loop : -2.18 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 341 TYR 0.021 0.002 TYR I 27 PHE 0.036 0.003 PHE H 249 TRP 0.072 0.002 TRP I 406 HIS 0.003 0.001 HIS F 370 Details of bonding type rmsd covalent geometry : bond 0.00469 (14880) covalent geometry : angle 0.69253 (20546) hydrogen bonds : bond 0.03627 ( 351) hydrogen bonds : angle 5.44540 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 718 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 ASN cc_start: 0.8508 (t0) cc_final: 0.8083 (t0) REVERT: D 210 ASP cc_start: 0.8643 (t0) cc_final: 0.8340 (t70) REVERT: D 241 ASP cc_start: 0.8417 (t0) cc_final: 0.8096 (t0) REVERT: D 320 GLN cc_start: 0.8837 (pp30) cc_final: 0.8529 (pp30) REVERT: D 465 GLN cc_start: 0.7896 (mp10) cc_final: 0.7301 (mp10) REVERT: D 470 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8143 (mtm-85) REVERT: E 69 TYR cc_start: 0.7968 (m-80) cc_final: 0.7567 (m-10) REVERT: E 93 ASN cc_start: 0.8616 (t0) cc_final: 0.8335 (t0) REVERT: E 163 VAL cc_start: 0.8929 (m) cc_final: 0.8364 (m) REVERT: E 196 ILE cc_start: 0.8938 (mm) cc_final: 0.8594 (mm) REVERT: E 198 ASP cc_start: 0.8707 (t0) cc_final: 0.8130 (t0) REVERT: E 217 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8464 (p) REVERT: E 245 ASP cc_start: 0.7372 (p0) cc_final: 0.6955 (p0) REVERT: E 323 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7956 (p0) REVERT: E 324 ASN cc_start: 0.8022 (t0) cc_final: 0.7673 (t0) REVERT: E 399 ASN cc_start: 0.8468 (t0) cc_final: 0.8107 (t0) REVERT: F 80 ASP cc_start: 0.8711 (t0) cc_final: 0.8424 (t0) REVERT: F 97 GLN cc_start: 0.5858 (mp10) cc_final: 0.5328 (mp10) REVERT: F 114 LEU cc_start: 0.8340 (mm) cc_final: 0.8128 (mp) REVERT: F 121 HIS cc_start: 0.8146 (t-90) cc_final: 0.7598 (t-90) REVERT: F 169 HIS cc_start: 0.8808 (p90) cc_final: 0.8157 (p-80) REVERT: F 217 THR cc_start: 0.8355 (p) cc_final: 0.8078 (t) REVERT: F 232 TYR cc_start: 0.8548 (t80) cc_final: 0.8280 (t80) REVERT: F 248 PHE cc_start: 0.8698 (m-10) cc_final: 0.7986 (m-80) REVERT: F 399 ASN cc_start: 0.9177 (t0) cc_final: 0.8541 (t0) REVERT: G 44 THR cc_start: 0.7625 (p) cc_final: 0.6515 (t) REVERT: G 45 VAL cc_start: 0.8712 (t) cc_final: 0.8394 (p) REVERT: G 47 ASN cc_start: 0.9062 (t0) cc_final: 0.8760 (t0) REVERT: G 50 PHE cc_start: 0.7463 (p90) cc_final: 0.7133 (p90) REVERT: G 92 TYR cc_start: 0.7034 (t80) cc_final: 0.6581 (t80) REVERT: G 93 ASN cc_start: 0.7624 (t0) cc_final: 0.6241 (t0) REVERT: G 97 GLN cc_start: 0.7073 (mp-120) cc_final: 0.6716 (mp-120) REVERT: G 99 LEU cc_start: 0.8172 (mt) cc_final: 0.7839 (mt) REVERT: G 170 TRP cc_start: 0.8324 (m100) cc_final: 0.8023 (m100) REVERT: G 191 LEU cc_start: 0.8871 (tt) cc_final: 0.8456 (tt) REVERT: G 196 ILE cc_start: 0.8528 (mm) cc_final: 0.8328 (mm) REVERT: G 210 ASP cc_start: 0.7790 (t70) cc_final: 0.7212 (t70) REVERT: G 232 TYR cc_start: 0.8572 (t80) cc_final: 0.8187 (t80) REVERT: G 248 PHE cc_start: 0.8740 (m-80) cc_final: 0.8447 (m-80) REVERT: G 324 ASN cc_start: 0.8386 (t0) cc_final: 0.7998 (t0) REVERT: G 338 ASP cc_start: 0.8425 (t0) cc_final: 0.8195 (t70) REVERT: G 372 GLU cc_start: 0.7167 (mp0) cc_final: 0.6594 (mp0) REVERT: G 473 LEU cc_start: 0.8607 (mm) cc_final: 0.8278 (mm) REVERT: H 35 TYR cc_start: 0.8060 (m-80) cc_final: 0.7284 (m-80) REVERT: H 93 ASN cc_start: 0.8121 (t0) cc_final: 0.7506 (t0) REVERT: H 121 HIS cc_start: 0.7923 (t-90) cc_final: 0.7629 (t-90) REVERT: H 169 HIS cc_start: 0.8368 (p90) cc_final: 0.7785 (p90) REVERT: H 202 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7439 (p) REVERT: H 221 VAL cc_start: 0.8693 (t) cc_final: 0.8320 (p) REVERT: H 245 ASP cc_start: 0.7539 (p0) cc_final: 0.7061 (p0) REVERT: H 263 ASN cc_start: 0.7732 (t0) cc_final: 0.7124 (t0) REVERT: H 320 GLN cc_start: 0.8564 (pp30) cc_final: 0.8326 (pp30) REVERT: H 333 PHE cc_start: 0.7885 (m-80) cc_final: 0.7503 (m-80) REVERT: H 344 ASN cc_start: 0.8490 (p0) cc_final: 0.8148 (p0) REVERT: H 367 TYR cc_start: 0.8176 (m-10) cc_final: 0.7889 (m-10) REVERT: H 372 GLU cc_start: 0.7374 (mp0) cc_final: 0.7029 (mp0) REVERT: H 390 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: H 465 GLN cc_start: 0.8182 (mp10) cc_final: 0.7732 (mp10) REVERT: H 473 LEU cc_start: 0.8606 (mm) cc_final: 0.8311 (mm) REVERT: H 475 GLN cc_start: 0.8671 (pp30) cc_final: 0.7943 (pp30) REVERT: I 93 ASN cc_start: 0.8005 (t0) cc_final: 0.7036 (t0) REVERT: I 114 LEU cc_start: 0.8573 (mm) cc_final: 0.8321 (mm) REVERT: I 162 CYS cc_start: 0.6966 (m) cc_final: 0.6431 (m) REVERT: I 163 VAL cc_start: 0.8848 (t) cc_final: 0.8519 (m) REVERT: I 198 ASP cc_start: 0.8038 (t0) cc_final: 0.7559 (m-30) REVERT: I 245 ASP cc_start: 0.7753 (p0) cc_final: 0.7376 (p0) REVERT: I 248 PHE cc_start: 0.8863 (m-10) cc_final: 0.8508 (m-80) REVERT: I 305 SER cc_start: 0.8652 (p) cc_final: 0.8208 (t) REVERT: I 333 PHE cc_start: 0.8041 (m-10) cc_final: 0.7838 (m-10) REVERT: I 370 HIS cc_start: 0.7868 (t-90) cc_final: 0.7480 (t-90) REVERT: I 375 ASP cc_start: 0.7626 (t0) cc_final: 0.7060 (t0) REVERT: I 377 GLN cc_start: 0.7518 (mp10) cc_final: 0.6887 (mp10) REVERT: I 399 ASN cc_start: 0.8440 (t0) cc_final: 0.8081 (t0) REVERT: I 465 GLN cc_start: 0.8301 (mp10) cc_final: 0.7908 (mp10) outliers start: 95 outliers final: 79 residues processed: 749 average time/residue: 0.0835 time to fit residues: 102.2922 Evaluate side-chains 788 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 705 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 323 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 6 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 103 optimal weight: 0.0170 chunk 76 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 323 ASN F 323 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 311 ASN H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 370 HIS I 475 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.080418 restraints weight = 31691.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083145 restraints weight = 16592.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.084891 restraints weight = 10469.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086053 restraints weight = 7568.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086858 restraints weight = 6020.587| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14880 Z= 0.141 Angle : 0.662 15.407 20546 Z= 0.327 Chirality : 0.046 0.156 2527 Planarity : 0.004 0.046 2658 Dihedral : 4.779 45.827 2151 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 6.03 % Allowed : 27.02 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.18), residues: 2022 helix: -0.16 (0.37), residues: 208 sheet: -1.64 (0.21), residues: 529 loop : -1.99 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 341 TYR 0.020 0.001 TYR D 232 PHE 0.036 0.002 PHE H 249 TRP 0.071 0.002 TRP I 406 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00295 (14880) covalent geometry : angle 0.66245 (20546) hydrogen bonds : bond 0.02903 ( 351) hydrogen bonds : angle 5.15806 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 718 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 ASN cc_start: 0.8506 (t0) cc_final: 0.8081 (t0) REVERT: D 162 CYS cc_start: 0.7929 (t) cc_final: 0.7677 (m) REVERT: D 210 ASP cc_start: 0.8617 (t0) cc_final: 0.8293 (t70) REVERT: D 241 ASP cc_start: 0.8321 (t0) cc_final: 0.8044 (t0) REVERT: D 320 GLN cc_start: 0.8904 (pp30) cc_final: 0.8542 (pp30) REVERT: D 330 ASN cc_start: 0.8133 (m-40) cc_final: 0.7848 (m-40) REVERT: D 465 GLN cc_start: 0.7795 (mp10) cc_final: 0.7210 (mp10) REVERT: D 470 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7838 (mtt-85) REVERT: E 69 TYR cc_start: 0.7911 (m-80) cc_final: 0.7590 (m-10) REVERT: E 93 ASN cc_start: 0.8309 (t0) cc_final: 0.8035 (t0) REVERT: E 163 VAL cc_start: 0.8921 (m) cc_final: 0.8385 (m) REVERT: E 196 ILE cc_start: 0.8910 (mm) cc_final: 0.8594 (mm) REVERT: E 198 ASP cc_start: 0.8658 (t0) cc_final: 0.8115 (t0) REVERT: E 217 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8448 (p) REVERT: E 245 ASP cc_start: 0.7356 (p0) cc_final: 0.6924 (p0) REVERT: E 324 ASN cc_start: 0.7918 (t0) cc_final: 0.7469 (t0) REVERT: E 335 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8535 (p) REVERT: E 399 ASN cc_start: 0.8513 (t0) cc_final: 0.8155 (t0) REVERT: F 80 ASP cc_start: 0.8674 (t0) cc_final: 0.8381 (t0) REVERT: F 97 GLN cc_start: 0.5729 (mp10) cc_final: 0.5263 (mp10) REVERT: F 114 LEU cc_start: 0.8404 (mm) cc_final: 0.8194 (mp) REVERT: F 121 HIS cc_start: 0.8060 (t-90) cc_final: 0.7574 (t-90) REVERT: F 162 CYS cc_start: 0.7887 (t) cc_final: 0.7166 (t) REVERT: F 169 HIS cc_start: 0.8725 (p90) cc_final: 0.8067 (p-80) REVERT: F 217 THR cc_start: 0.8338 (p) cc_final: 0.8062 (t) REVERT: F 232 TYR cc_start: 0.8524 (t80) cc_final: 0.8235 (t80) REVERT: F 248 PHE cc_start: 0.8660 (m-10) cc_final: 0.8003 (m-80) REVERT: F 399 ASN cc_start: 0.9139 (t0) cc_final: 0.8538 (t0) REVERT: F 460 SER cc_start: 0.8613 (t) cc_final: 0.8373 (t) REVERT: G 45 VAL cc_start: 0.8692 (t) cc_final: 0.8323 (p) REVERT: G 47 ASN cc_start: 0.9003 (t0) cc_final: 0.8716 (t0) REVERT: G 93 ASN cc_start: 0.7717 (t0) cc_final: 0.6325 (t0) REVERT: G 97 GLN cc_start: 0.7009 (mp-120) cc_final: 0.6610 (mp10) REVERT: G 121 HIS cc_start: 0.8467 (t-90) cc_final: 0.8179 (t-90) REVERT: G 170 TRP cc_start: 0.8301 (m100) cc_final: 0.8040 (m100) REVERT: G 191 LEU cc_start: 0.8867 (tt) cc_final: 0.8465 (tt) REVERT: G 210 ASP cc_start: 0.7750 (t70) cc_final: 0.7154 (t70) REVERT: G 232 TYR cc_start: 0.8570 (t80) cc_final: 0.8214 (t80) REVERT: G 248 PHE cc_start: 0.8701 (m-80) cc_final: 0.8402 (m-80) REVERT: G 324 ASN cc_start: 0.8351 (t0) cc_final: 0.7953 (t0) REVERT: G 338 ASP cc_start: 0.8471 (t0) cc_final: 0.8130 (t70) REVERT: G 372 GLU cc_start: 0.7173 (mp0) cc_final: 0.6494 (mp0) REVERT: G 473 LEU cc_start: 0.8588 (mm) cc_final: 0.8266 (mm) REVERT: H 35 TYR cc_start: 0.8042 (m-80) cc_final: 0.7249 (m-80) REVERT: H 92 TYR cc_start: 0.7040 (t80) cc_final: 0.6501 (t80) REVERT: H 93 ASN cc_start: 0.8112 (t0) cc_final: 0.6801 (t0) REVERT: H 97 GLN cc_start: 0.8224 (pm20) cc_final: 0.7582 (pm20) REVERT: H 121 HIS cc_start: 0.7850 (t-90) cc_final: 0.7542 (t-90) REVERT: H 169 HIS cc_start: 0.8312 (p90) cc_final: 0.7726 (p90) REVERT: H 202 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7468 (p) REVERT: H 221 VAL cc_start: 0.8605 (t) cc_final: 0.8177 (p) REVERT: H 245 ASP cc_start: 0.7535 (p0) cc_final: 0.7003 (p0) REVERT: H 263 ASN cc_start: 0.7660 (t0) cc_final: 0.7075 (t0) REVERT: H 333 PHE cc_start: 0.7907 (m-80) cc_final: 0.7511 (m-80) REVERT: H 367 TYR cc_start: 0.8131 (m-10) cc_final: 0.7856 (m-10) REVERT: H 372 GLU cc_start: 0.7314 (mp0) cc_final: 0.6989 (mp0) REVERT: H 390 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: H 465 GLN cc_start: 0.8128 (mp10) cc_final: 0.7668 (mp10) REVERT: H 473 LEU cc_start: 0.8586 (mm) cc_final: 0.8285 (mm) REVERT: H 475 GLN cc_start: 0.8688 (pp30) cc_final: 0.7952 (pp30) REVERT: I 44 THR cc_start: 0.8562 (m) cc_final: 0.8203 (p) REVERT: I 93 ASN cc_start: 0.8272 (t0) cc_final: 0.7994 (t0) REVERT: I 162 CYS cc_start: 0.6953 (m) cc_final: 0.6557 (m) REVERT: I 163 VAL cc_start: 0.8811 (t) cc_final: 0.8379 (m) REVERT: I 198 ASP cc_start: 0.7986 (t0) cc_final: 0.7508 (m-30) REVERT: I 229 ILE cc_start: 0.8705 (mm) cc_final: 0.8041 (tp) REVERT: I 245 ASP cc_start: 0.7727 (p0) cc_final: 0.7294 (p0) REVERT: I 248 PHE cc_start: 0.8810 (m-10) cc_final: 0.8457 (m-80) REVERT: I 305 SER cc_start: 0.8626 (p) cc_final: 0.8302 (m) REVERT: I 333 PHE cc_start: 0.8025 (m-10) cc_final: 0.7801 (m-10) REVERT: I 370 HIS cc_start: 0.7778 (t70) cc_final: 0.7322 (t-90) REVERT: I 374 TYR cc_start: 0.7950 (m-10) cc_final: 0.7386 (m-80) REVERT: I 375 ASP cc_start: 0.7579 (t0) cc_final: 0.6989 (t0) REVERT: I 377 GLN cc_start: 0.7553 (mp10) cc_final: 0.7024 (mp10) REVERT: I 399 ASN cc_start: 0.8392 (t0) cc_final: 0.8060 (t0) REVERT: I 457 GLU cc_start: 0.8254 (pp20) cc_final: 0.7864 (pp20) REVERT: I 465 GLN cc_start: 0.8280 (mp10) cc_final: 0.7987 (mp10) outliers start: 83 outliers final: 65 residues processed: 747 average time/residue: 0.0839 time to fit residues: 102.1588 Evaluate side-chains 782 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 713 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 199 optimal weight: 0.0170 chunk 58 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 2.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 ASN ** H 330 ASN ** 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 = 0.3233 r_free = 0.3233 target = 0.094494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079490 restraints weight = 31526.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082173 restraints weight = 16605.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.083915 restraints weight = 10538.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085073 restraints weight = 7654.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085810 restraints weight = 6107.744| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14880 Z= 0.209 Angle : 0.691 15.343 20546 Z= 0.345 Chirality : 0.047 0.171 2527 Planarity : 0.004 0.061 2658 Dihedral : 4.857 46.101 2151 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.01 % Favored : 91.94 % Rotamer: Outliers : 6.25 % Allowed : 28.03 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.18), residues: 2022 helix: 0.01 (0.38), residues: 201 sheet: -1.64 (0.21), residues: 529 loop : -1.95 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 341 TYR 0.022 0.002 TYR E 232 PHE 0.038 0.002 PHE H 249 TRP 0.074 0.002 TRP I 406 HIS 0.005 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00417 (14880) covalent geometry : angle 0.69080 (20546) hydrogen bonds : bond 0.03227 ( 351) hydrogen bonds : angle 5.19105 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 715 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 LEU cc_start: 0.8765 (mm) cc_final: 0.8537 (mp) REVERT: D 147 ASN cc_start: 0.8498 (t0) cc_final: 0.8056 (t0) REVERT: D 162 CYS cc_start: 0.7990 (t) cc_final: 0.7683 (m) REVERT: D 210 ASP cc_start: 0.8671 (t0) cc_final: 0.8389 (t70) REVERT: D 241 ASP cc_start: 0.8332 (t0) cc_final: 0.8034 (t0) REVERT: D 314 TYR cc_start: 0.7751 (m-80) cc_final: 0.7519 (m-80) REVERT: D 316 LEU cc_start: 0.8605 (mm) cc_final: 0.8333 (mm) REVERT: D 320 GLN cc_start: 0.8876 (pp30) cc_final: 0.8516 (pp30) REVERT: D 330 ASN cc_start: 0.8195 (m-40) cc_final: 0.7923 (m-40) REVERT: D 465 GLN cc_start: 0.7823 (mp10) cc_final: 0.7210 (mp10) REVERT: D 470 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.7941 (mtt-85) REVERT: E 44 THR cc_start: 0.8498 (t) cc_final: 0.8212 (m) REVERT: E 69 TYR cc_start: 0.7931 (m-80) cc_final: 0.7621 (m-10) REVERT: E 93 ASN cc_start: 0.8358 (t0) cc_final: 0.8091 (t0) REVERT: E 163 VAL cc_start: 0.8774 (m) cc_final: 0.8241 (m) REVERT: E 196 ILE cc_start: 0.8964 (mm) cc_final: 0.8601 (mm) REVERT: E 198 ASP cc_start: 0.8687 (t0) cc_final: 0.8156 (t0) REVERT: E 217 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8480 (p) REVERT: E 245 ASP cc_start: 0.7336 (p0) cc_final: 0.6946 (p0) REVERT: E 309 LEU cc_start: 0.8358 (mt) cc_final: 0.8149 (mt) REVERT: E 324 ASN cc_start: 0.7982 (t0) cc_final: 0.7648 (t0) REVERT: E 335 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8512 (p) REVERT: E 399 ASN cc_start: 0.8495 (t0) cc_final: 0.8145 (t0) REVERT: F 80 ASP cc_start: 0.8709 (t0) cc_final: 0.8483 (t0) REVERT: F 97 GLN cc_start: 0.5721 (mp10) cc_final: 0.5250 (mp10) REVERT: F 112 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7847 (mm-40) REVERT: F 121 HIS cc_start: 0.8048 (t-90) cc_final: 0.7562 (t-90) REVERT: F 162 CYS cc_start: 0.7879 (t) cc_final: 0.7532 (t) REVERT: F 169 HIS cc_start: 0.8804 (p90) cc_final: 0.8141 (p-80) REVERT: F 217 THR cc_start: 0.8346 (p) cc_final: 0.8066 (t) REVERT: F 232 TYR cc_start: 0.8534 (t80) cc_final: 0.8261 (t80) REVERT: F 399 ASN cc_start: 0.9138 (t0) cc_final: 0.8548 (t0) REVERT: F 460 SER cc_start: 0.8640 (t) cc_final: 0.8419 (t) REVERT: G 45 VAL cc_start: 0.8714 (t) cc_final: 0.8324 (p) REVERT: G 47 ASN cc_start: 0.9022 (t0) cc_final: 0.8740 (t0) REVERT: G 93 ASN cc_start: 0.7719 (t0) cc_final: 0.6411 (t0) REVERT: G 97 GLN cc_start: 0.7023 (mp-120) cc_final: 0.6660 (mp10) REVERT: G 121 HIS cc_start: 0.8544 (t-90) cc_final: 0.8188 (t-90) REVERT: G 170 TRP cc_start: 0.8303 (m100) cc_final: 0.8082 (m100) REVERT: G 191 LEU cc_start: 0.8866 (tt) cc_final: 0.8466 (tt) REVERT: G 210 ASP cc_start: 0.7812 (t70) cc_final: 0.7220 (t70) REVERT: G 232 TYR cc_start: 0.8570 (t80) cc_final: 0.8245 (t80) REVERT: G 248 PHE cc_start: 0.8711 (m-80) cc_final: 0.8459 (m-80) REVERT: G 309 LEU cc_start: 0.8134 (mt) cc_final: 0.7906 (tt) REVERT: G 324 ASN cc_start: 0.8347 (t0) cc_final: 0.7945 (t0) REVERT: G 338 ASP cc_start: 0.8472 (t0) cc_final: 0.8222 (t70) REVERT: G 372 GLU cc_start: 0.7082 (mp0) cc_final: 0.6535 (mp0) REVERT: G 473 LEU cc_start: 0.8640 (mm) cc_final: 0.8337 (mm) REVERT: H 35 TYR cc_start: 0.8027 (m-80) cc_final: 0.7182 (m-80) REVERT: H 92 TYR cc_start: 0.6965 (t80) cc_final: 0.6598 (t80) REVERT: H 93 ASN cc_start: 0.8154 (t0) cc_final: 0.7519 (t0) REVERT: H 97 GLN cc_start: 0.8313 (pm20) cc_final: 0.8059 (pm20) REVERT: H 121 HIS cc_start: 0.7856 (t-90) cc_final: 0.7545 (t-90) REVERT: H 169 HIS cc_start: 0.8305 (p90) cc_final: 0.7716 (p90) REVERT: H 221 VAL cc_start: 0.8637 (t) cc_final: 0.8234 (p) REVERT: H 245 ASP cc_start: 0.7555 (p0) cc_final: 0.6990 (p0) REVERT: H 263 ASN cc_start: 0.7727 (t0) cc_final: 0.7146 (t0) REVERT: H 333 PHE cc_start: 0.7920 (m-80) cc_final: 0.7516 (m-80) REVERT: H 367 TYR cc_start: 0.8148 (m-10) cc_final: 0.7858 (m-10) REVERT: H 372 GLU cc_start: 0.7413 (mp0) cc_final: 0.7160 (mp0) REVERT: H 378 PHE cc_start: 0.8776 (m-80) cc_final: 0.8575 (m-80) REVERT: H 390 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: H 465 GLN cc_start: 0.8139 (mp10) cc_final: 0.7647 (mp10) REVERT: H 473 LEU cc_start: 0.8610 (mm) cc_final: 0.8325 (mm) REVERT: H 475 GLN cc_start: 0.8697 (pp30) cc_final: 0.7959 (pp30) REVERT: I 44 THR cc_start: 0.8589 (m) cc_final: 0.8252 (p) REVERT: I 162 CYS cc_start: 0.6965 (m) cc_final: 0.6534 (m) REVERT: I 163 VAL cc_start: 0.8837 (t) cc_final: 0.8377 (m) REVERT: I 198 ASP cc_start: 0.8114 (t0) cc_final: 0.7692 (m-30) REVERT: I 229 ILE cc_start: 0.8710 (mm) cc_final: 0.8007 (tp) REVERT: I 237 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: I 245 ASP cc_start: 0.7708 (p0) cc_final: 0.7218 (p0) REVERT: I 248 PHE cc_start: 0.8816 (m-10) cc_final: 0.8477 (m-80) REVERT: I 305 SER cc_start: 0.8641 (p) cc_final: 0.8309 (m) REVERT: I 333 PHE cc_start: 0.8021 (m-10) cc_final: 0.7819 (m-10) REVERT: I 370 HIS cc_start: 0.7865 (t70) cc_final: 0.7438 (t-90) REVERT: I 374 TYR cc_start: 0.7758 (m-10) cc_final: 0.7274 (m-80) REVERT: I 375 ASP cc_start: 0.7506 (t0) cc_final: 0.6996 (t0) REVERT: I 377 GLN cc_start: 0.7590 (mp10) cc_final: 0.6917 (mp10) REVERT: I 399 ASN cc_start: 0.8395 (t0) cc_final: 0.8058 (t0) REVERT: I 457 GLU cc_start: 0.8268 (pp20) cc_final: 0.7843 (pp20) REVERT: I 465 GLN cc_start: 0.8302 (mp10) cc_final: 0.7965 (mp10) outliers start: 86 outliers final: 74 residues processed: 746 average time/residue: 0.0830 time to fit residues: 101.2894 Evaluate side-chains 790 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 712 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 323 ASN F 193 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078478 restraints weight = 31799.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081164 restraints weight = 16665.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.082910 restraints weight = 10552.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084090 restraints weight = 7646.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.084866 restraints weight = 6098.340| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14880 Z= 0.220 Angle : 0.706 15.124 20546 Z= 0.355 Chirality : 0.047 0.186 2527 Planarity : 0.004 0.075 2658 Dihedral : 4.929 46.069 2151 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 7.12 % Allowed : 28.18 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.18), residues: 2022 helix: -0.05 (0.38), residues: 202 sheet: -1.63 (0.21), residues: 525 loop : -1.91 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 341 TYR 0.022 0.002 TYR E 232 PHE 0.040 0.003 PHE H 249 TRP 0.068 0.002 TRP I 406 HIS 0.004 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00432 (14880) covalent geometry : angle 0.70643 (20546) hydrogen bonds : bond 0.03315 ( 351) hydrogen bonds : angle 5.14983 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 716 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 ASN cc_start: 0.8545 (t0) cc_final: 0.8100 (t0) REVERT: D 162 CYS cc_start: 0.7975 (t) cc_final: 0.7678 (m) REVERT: D 210 ASP cc_start: 0.8708 (t0) cc_final: 0.8500 (t70) REVERT: D 241 ASP cc_start: 0.8334 (t0) cc_final: 0.8042 (t0) REVERT: D 314 TYR cc_start: 0.7757 (m-80) cc_final: 0.7463 (m-80) REVERT: D 320 GLN cc_start: 0.8879 (pp30) cc_final: 0.8515 (pp30) REVERT: D 330 ASN cc_start: 0.8208 (m-40) cc_final: 0.7931 (m-40) REVERT: D 465 GLN cc_start: 0.7827 (mp10) cc_final: 0.7219 (mp10) REVERT: D 470 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: E 44 THR cc_start: 0.8494 (t) cc_final: 0.8212 (m) REVERT: E 69 TYR cc_start: 0.7958 (m-80) cc_final: 0.7620 (m-10) REVERT: E 93 ASN cc_start: 0.8396 (t0) cc_final: 0.8111 (t0) REVERT: E 196 ILE cc_start: 0.8924 (mm) cc_final: 0.8565 (mm) REVERT: E 198 ASP cc_start: 0.8694 (t0) cc_final: 0.8171 (t0) REVERT: E 217 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8468 (p) REVERT: E 324 ASN cc_start: 0.8005 (t0) cc_final: 0.7611 (t0) REVERT: E 335 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 399 ASN cc_start: 0.8492 (t0) cc_final: 0.8097 (t0) REVERT: F 80 ASP cc_start: 0.8711 (t0) cc_final: 0.8480 (t0) REVERT: F 97 GLN cc_start: 0.5731 (mp10) cc_final: 0.5241 (mp-120) REVERT: F 112 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7852 (mm-40) REVERT: F 121 HIS cc_start: 0.8088 (t-90) cc_final: 0.7513 (t-90) REVERT: F 162 CYS cc_start: 0.7861 (t) cc_final: 0.7110 (t) REVERT: F 169 HIS cc_start: 0.8814 (p90) cc_final: 0.8147 (p-80) REVERT: F 217 THR cc_start: 0.8351 (p) cc_final: 0.8063 (t) REVERT: F 232 TYR cc_start: 0.8540 (t80) cc_final: 0.8319 (t80) REVERT: F 248 PHE cc_start: 0.8565 (m-10) cc_final: 0.7837 (m-80) REVERT: F 320 GLN cc_start: 0.8153 (pp30) cc_final: 0.7744 (pp30) REVERT: F 399 ASN cc_start: 0.9132 (t0) cc_final: 0.8518 (t0) REVERT: F 464 ASP cc_start: 0.7746 (p0) cc_final: 0.7371 (p0) REVERT: G 45 VAL cc_start: 0.8721 (t) cc_final: 0.8360 (p) REVERT: G 47 ASN cc_start: 0.9049 (t0) cc_final: 0.8766 (t0) REVERT: G 97 GLN cc_start: 0.7058 (mp-120) cc_final: 0.6689 (mp10) REVERT: G 121 HIS cc_start: 0.8520 (t-90) cc_final: 0.8246 (t-90) REVERT: G 170 TRP cc_start: 0.8355 (m100) cc_final: 0.8043 (m100) REVERT: G 191 LEU cc_start: 0.8866 (tt) cc_final: 0.8476 (tt) REVERT: G 210 ASP cc_start: 0.7827 (t70) cc_final: 0.7231 (t70) REVERT: G 232 TYR cc_start: 0.8592 (t80) cc_final: 0.8313 (t80) REVERT: G 248 PHE cc_start: 0.8794 (m-80) cc_final: 0.8566 (m-80) REVERT: G 324 ASN cc_start: 0.8368 (t0) cc_final: 0.7979 (t0) REVERT: G 338 ASP cc_start: 0.8476 (t0) cc_final: 0.8143 (t70) REVERT: G 372 GLU cc_start: 0.7162 (mp0) cc_final: 0.6787 (mp0) REVERT: G 406 TRP cc_start: 0.7810 (m-10) cc_final: 0.7377 (m-10) REVERT: G 473 LEU cc_start: 0.8641 (mm) cc_final: 0.8330 (mm) REVERT: H 23 SER cc_start: 0.8640 (p) cc_final: 0.8241 (m) REVERT: H 35 TYR cc_start: 0.7997 (m-80) cc_final: 0.7115 (m-80) REVERT: H 92 TYR cc_start: 0.6955 (t80) cc_final: 0.6579 (t80) REVERT: H 93 ASN cc_start: 0.8170 (t0) cc_final: 0.7516 (t0) REVERT: H 97 GLN cc_start: 0.8332 (pm20) cc_final: 0.8074 (pm20) REVERT: H 121 HIS cc_start: 0.7881 (t-90) cc_final: 0.7475 (t-90) REVERT: H 147 ASN cc_start: 0.8200 (t0) cc_final: 0.7971 (t0) REVERT: H 169 HIS cc_start: 0.8319 (p90) cc_final: 0.7720 (p90) REVERT: H 202 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7458 (p) REVERT: H 221 VAL cc_start: 0.8659 (t) cc_final: 0.8265 (p) REVERT: H 245 ASP cc_start: 0.7427 (p0) cc_final: 0.6934 (p0) REVERT: H 263 ASN cc_start: 0.7740 (t0) cc_final: 0.7125 (t0) REVERT: H 333 PHE cc_start: 0.7972 (m-80) cc_final: 0.7533 (m-80) REVERT: H 367 TYR cc_start: 0.8158 (m-10) cc_final: 0.7858 (m-10) REVERT: H 372 GLU cc_start: 0.7427 (mp0) cc_final: 0.7163 (mp0) REVERT: H 390 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: H 465 GLN cc_start: 0.8213 (mp10) cc_final: 0.7678 (mp10) REVERT: H 473 LEU cc_start: 0.8632 (mm) cc_final: 0.8339 (mm) REVERT: H 475 GLN cc_start: 0.8699 (pp30) cc_final: 0.7970 (pp30) REVERT: I 44 THR cc_start: 0.8569 (m) cc_final: 0.8285 (p) REVERT: I 96 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7797 (p) REVERT: I 162 CYS cc_start: 0.6958 (m) cc_final: 0.6457 (m) REVERT: I 163 VAL cc_start: 0.8828 (t) cc_final: 0.8276 (m) REVERT: I 198 ASP cc_start: 0.8168 (t0) cc_final: 0.7746 (m-30) REVERT: I 229 ILE cc_start: 0.8737 (mm) cc_final: 0.8047 (tp) REVERT: I 237 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: I 245 ASP cc_start: 0.7753 (p0) cc_final: 0.7190 (p0) REVERT: I 248 PHE cc_start: 0.8756 (m-10) cc_final: 0.8392 (m-80) REVERT: I 305 SER cc_start: 0.8683 (p) cc_final: 0.8304 (t) REVERT: I 333 PHE cc_start: 0.8037 (m-10) cc_final: 0.7834 (m-10) REVERT: I 370 HIS cc_start: 0.7839 (t70) cc_final: 0.7353 (t-90) REVERT: I 374 TYR cc_start: 0.7578 (m-10) cc_final: 0.7234 (m-10) REVERT: I 375 ASP cc_start: 0.7552 (t0) cc_final: 0.7154 (t0) REVERT: I 377 GLN cc_start: 0.7612 (mp10) cc_final: 0.6934 (mp10) REVERT: I 399 ASN cc_start: 0.8390 (t0) cc_final: 0.8080 (t0) REVERT: I 457 GLU cc_start: 0.8275 (pp20) cc_final: 0.7843 (pp20) REVERT: I 465 GLN cc_start: 0.8259 (mp10) cc_final: 0.7942 (mp10) outliers start: 98 outliers final: 85 residues processed: 749 average time/residue: 0.0826 time to fit residues: 101.5647 Evaluate side-chains 803 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 712 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 323 ASN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 250 CYS Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 169 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 323 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.077848 restraints weight = 32093.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.080479 restraints weight = 16917.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082183 restraints weight = 10770.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083345 restraints weight = 7845.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084105 restraints weight = 6276.785| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 14880 Z= 0.305 Angle : 0.756 14.941 20546 Z= 0.386 Chirality : 0.049 0.223 2527 Planarity : 0.005 0.065 2658 Dihedral : 5.193 46.185 2151 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.99 % Favored : 89.91 % Rotamer: Outliers : 7.19 % Allowed : 28.90 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.18), residues: 2022 helix: -0.15 (0.38), residues: 202 sheet: -1.79 (0.21), residues: 540 loop : -1.95 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 341 TYR 0.024 0.002 TYR I 27 PHE 0.040 0.003 PHE H 249 TRP 0.069 0.003 TRP I 406 HIS 0.007 0.002 HIS I 322 Details of bonding type rmsd covalent geometry : bond 0.00587 (14880) covalent geometry : angle 0.75599 (20546) hydrogen bonds : bond 0.03812 ( 351) hydrogen bonds : angle 5.38091 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 711 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 ASN cc_start: 0.8538 (t0) cc_final: 0.8098 (t0) REVERT: D 162 CYS cc_start: 0.8112 (t) cc_final: 0.7753 (m) REVERT: D 234 ASP cc_start: 0.7726 (p0) cc_final: 0.7250 (p0) REVERT: D 241 ASP cc_start: 0.8365 (t0) cc_final: 0.8060 (t0) REVERT: D 251 LEU cc_start: 0.8539 (mt) cc_final: 0.8321 (mm) REVERT: D 314 TYR cc_start: 0.7767 (m-80) cc_final: 0.7408 (m-80) REVERT: D 320 GLN cc_start: 0.8869 (pp30) cc_final: 0.8458 (pp30) REVERT: D 330 ASN cc_start: 0.8225 (m-40) cc_final: 0.7947 (m-40) REVERT: D 465 GLN cc_start: 0.7921 (mp10) cc_final: 0.7293 (mp10) REVERT: D 470 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: E 69 TYR cc_start: 0.8011 (m-80) cc_final: 0.7672 (m-10) REVERT: E 93 ASN cc_start: 0.8431 (t0) cc_final: 0.8173 (t0) REVERT: E 196 ILE cc_start: 0.8953 (mm) cc_final: 0.8565 (mm) REVERT: E 198 ASP cc_start: 0.8722 (t0) cc_final: 0.8193 (t0) REVERT: E 217 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8493 (p) REVERT: E 324 ASN cc_start: 0.8069 (t0) cc_final: 0.7781 (t0) REVERT: E 335 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (p) REVERT: E 399 ASN cc_start: 0.8504 (t0) cc_final: 0.8087 (t0) REVERT: F 80 ASP cc_start: 0.8696 (t0) cc_final: 0.8336 (t0) REVERT: F 97 GLN cc_start: 0.5770 (mp10) cc_final: 0.5244 (mp10) REVERT: F 112 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7858 (mm-40) REVERT: F 121 HIS cc_start: 0.8119 (t-90) cc_final: 0.7617 (t-90) REVERT: F 169 HIS cc_start: 0.8874 (p90) cc_final: 0.8288 (p-80) REVERT: F 217 THR cc_start: 0.8360 (p) cc_final: 0.8087 (t) REVERT: F 232 TYR cc_start: 0.8557 (t80) cc_final: 0.8342 (t80) REVERT: F 248 PHE cc_start: 0.8608 (m-10) cc_final: 0.7856 (m-80) REVERT: F 399 ASN cc_start: 0.9156 (t0) cc_final: 0.8532 (t0) REVERT: F 464 ASP cc_start: 0.7787 (p0) cc_final: 0.7410 (p0) REVERT: G 44 THR cc_start: 0.7421 (p) cc_final: 0.5952 (p) REVERT: G 45 VAL cc_start: 0.8741 (t) cc_final: 0.8385 (p) REVERT: G 47 ASN cc_start: 0.9095 (t0) cc_final: 0.8808 (t0) REVERT: G 97 GLN cc_start: 0.7050 (mp-120) cc_final: 0.6643 (mp10) REVERT: G 121 HIS cc_start: 0.8600 (t-90) cc_final: 0.8299 (t-90) REVERT: G 170 TRP cc_start: 0.8377 (m100) cc_final: 0.8073 (m100) REVERT: G 191 LEU cc_start: 0.8863 (tt) cc_final: 0.8464 (tt) REVERT: G 210 ASP cc_start: 0.7872 (t70) cc_final: 0.7299 (t70) REVERT: G 232 TYR cc_start: 0.8594 (t80) cc_final: 0.8325 (t80) REVERT: G 248 PHE cc_start: 0.8818 (m-80) cc_final: 0.8567 (m-80) REVERT: G 251 LEU cc_start: 0.8716 (mt) cc_final: 0.8487 (mm) REVERT: G 309 LEU cc_start: 0.8128 (mt) cc_final: 0.7859 (tt) REVERT: G 324 ASN cc_start: 0.8413 (t0) cc_final: 0.8048 (t0) REVERT: G 338 ASP cc_start: 0.8480 (t0) cc_final: 0.8260 (t70) REVERT: G 372 GLU cc_start: 0.7119 (mp0) cc_final: 0.6345 (mp0) REVERT: G 406 TRP cc_start: 0.7712 (m-10) cc_final: 0.7399 (m-10) REVERT: G 473 LEU cc_start: 0.8684 (mm) cc_final: 0.8373 (mm) REVERT: H 35 TYR cc_start: 0.7989 (m-80) cc_final: 0.7100 (m-80) REVERT: H 92 TYR cc_start: 0.6973 (t80) cc_final: 0.6590 (t80) REVERT: H 93 ASN cc_start: 0.8204 (t0) cc_final: 0.7581 (t0) REVERT: H 97 GLN cc_start: 0.8335 (pm20) cc_final: 0.8068 (pm20) REVERT: H 121 HIS cc_start: 0.7894 (t-90) cc_final: 0.7450 (t-90) REVERT: H 147 ASN cc_start: 0.8182 (t0) cc_final: 0.7939 (t0) REVERT: H 169 HIS cc_start: 0.8352 (p90) cc_final: 0.7733 (p90) REVERT: H 202 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7475 (p) REVERT: H 221 VAL cc_start: 0.8769 (t) cc_final: 0.8446 (p) REVERT: H 245 ASP cc_start: 0.7497 (p0) cc_final: 0.7022 (p0) REVERT: H 263 ASN cc_start: 0.7793 (t0) cc_final: 0.7170 (t0) REVERT: H 316 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8488 (mp) REVERT: H 333 PHE cc_start: 0.8015 (m-80) cc_final: 0.7525 (m-80) REVERT: H 343 THR cc_start: 0.8236 (m) cc_final: 0.7835 (p) REVERT: H 367 TYR cc_start: 0.8193 (m-10) cc_final: 0.7905 (m-10) REVERT: H 372 GLU cc_start: 0.7477 (mp0) cc_final: 0.7177 (mp0) REVERT: H 390 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: H 465 GLN cc_start: 0.8224 (mp10) cc_final: 0.7683 (mp10) REVERT: H 473 LEU cc_start: 0.8666 (mm) cc_final: 0.8389 (mm) REVERT: H 475 GLN cc_start: 0.8693 (pp30) cc_final: 0.7973 (pp30) REVERT: I 44 THR cc_start: 0.8584 (m) cc_final: 0.8324 (p) REVERT: I 95 GLU cc_start: 0.7881 (pp20) cc_final: 0.7627 (pp20) REVERT: I 96 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7703 (p) REVERT: I 162 CYS cc_start: 0.6988 (m) cc_final: 0.6239 (m) REVERT: I 163 VAL cc_start: 0.8855 (t) cc_final: 0.8095 (m) REVERT: I 198 ASP cc_start: 0.8215 (t0) cc_final: 0.7828 (m-30) REVERT: I 229 ILE cc_start: 0.8752 (mm) cc_final: 0.8224 (tp) REVERT: I 237 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: I 245 ASP cc_start: 0.7763 (p0) cc_final: 0.7094 (p0) REVERT: I 248 PHE cc_start: 0.8753 (m-10) cc_final: 0.8392 (m-80) REVERT: I 370 HIS cc_start: 0.7918 (t70) cc_final: 0.7423 (t-90) REVERT: I 374 TYR cc_start: 0.7645 (m-10) cc_final: 0.7335 (m-10) REVERT: I 375 ASP cc_start: 0.7541 (t0) cc_final: 0.7175 (t0) REVERT: I 377 GLN cc_start: 0.7647 (mp10) cc_final: 0.7052 (mp10) REVERT: I 399 ASN cc_start: 0.8436 (t0) cc_final: 0.8119 (t0) REVERT: I 465 GLN cc_start: 0.8349 (mp10) cc_final: 0.8016 (mp10) outliers start: 99 outliers final: 84 residues processed: 746 average time/residue: 0.0839 time to fit residues: 102.0150 Evaluate side-chains 795 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 704 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 250 CYS Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 116 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 178 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 102 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 323 ASN F 193 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN H 323 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 GLN I 193 ASN I 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.079714 restraints weight = 31611.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082471 restraints weight = 16562.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084260 restraints weight = 10462.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085437 restraints weight = 7548.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086248 restraints weight = 6014.853| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14880 Z= 0.151 Angle : 0.722 15.374 20546 Z= 0.359 Chirality : 0.047 0.209 2527 Planarity : 0.004 0.076 2658 Dihedral : 4.749 45.748 2151 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.27 % Rotamer: Outliers : 5.59 % Allowed : 31.30 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.18), residues: 2022 helix: -0.03 (0.38), residues: 202 sheet: -1.54 (0.21), residues: 541 loop : -1.79 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 341 TYR 0.022 0.001 TYR E 232 PHE 0.038 0.003 PHE G 380 TRP 0.047 0.002 TRP E 406 HIS 0.009 0.001 HIS I 322 Details of bonding type rmsd covalent geometry : bond 0.00317 (14880) covalent geometry : angle 0.72234 (20546) hydrogen bonds : bond 0.02818 ( 351) hydrogen bonds : angle 5.01360 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 709 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 LEU cc_start: 0.8833 (mm) cc_final: 0.8593 (mp) REVERT: D 92 TYR cc_start: 0.8514 (p90) cc_final: 0.8207 (p90) REVERT: D 147 ASN cc_start: 0.8493 (t0) cc_final: 0.8063 (t0) REVERT: D 162 CYS cc_start: 0.7939 (t) cc_final: 0.7724 (m) REVERT: D 234 ASP cc_start: 0.7508 (p0) cc_final: 0.6968 (p0) REVERT: D 241 ASP cc_start: 0.8322 (t0) cc_final: 0.8040 (t0) REVERT: D 314 TYR cc_start: 0.7631 (m-80) cc_final: 0.7281 (m-80) REVERT: D 320 GLN cc_start: 0.8896 (pp30) cc_final: 0.8541 (pp30) REVERT: D 330 ASN cc_start: 0.8186 (m-40) cc_final: 0.7898 (m-40) REVERT: D 337 VAL cc_start: 0.8701 (t) cc_final: 0.8417 (p) REVERT: D 465 GLN cc_start: 0.7783 (mp10) cc_final: 0.7215 (mp10) REVERT: D 470 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7928 (mtt-85) REVERT: E 69 TYR cc_start: 0.7986 (m-80) cc_final: 0.7669 (m-10) REVERT: E 93 ASN cc_start: 0.8258 (t0) cc_final: 0.7973 (t0) REVERT: E 196 ILE cc_start: 0.8914 (mm) cc_final: 0.8539 (mm) REVERT: E 198 ASP cc_start: 0.8662 (t0) cc_final: 0.8128 (t0) REVERT: E 217 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8488 (p) REVERT: E 324 ASN cc_start: 0.7862 (t0) cc_final: 0.7504 (t0) REVERT: E 335 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8522 (p) REVERT: E 399 ASN cc_start: 0.8519 (t0) cc_final: 0.8069 (t0) REVERT: F 80 ASP cc_start: 0.8740 (t0) cc_final: 0.8463 (t0) REVERT: F 97 GLN cc_start: 0.5618 (mp10) cc_final: 0.5169 (mp10) REVERT: F 112 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7816 (mm-40) REVERT: F 121 HIS cc_start: 0.8099 (t-90) cc_final: 0.7495 (t-90) REVERT: F 162 CYS cc_start: 0.7787 (t) cc_final: 0.7023 (t) REVERT: F 169 HIS cc_start: 0.8761 (p90) cc_final: 0.8110 (p-80) REVERT: F 217 THR cc_start: 0.8351 (p) cc_final: 0.8068 (t) REVERT: F 232 TYR cc_start: 0.8544 (t80) cc_final: 0.8284 (t80) REVERT: F 248 PHE cc_start: 0.8526 (m-10) cc_final: 0.7817 (m-80) REVERT: F 320 GLN cc_start: 0.8155 (pp30) cc_final: 0.7787 (pp30) REVERT: F 372 GLU cc_start: 0.7490 (mp0) cc_final: 0.7031 (mp0) REVERT: F 399 ASN cc_start: 0.9095 (t0) cc_final: 0.8497 (t0) REVERT: F 464 ASP cc_start: 0.7801 (p0) cc_final: 0.7430 (p0) REVERT: G 45 VAL cc_start: 0.8717 (t) cc_final: 0.8355 (p) REVERT: G 47 ASN cc_start: 0.9025 (t0) cc_final: 0.8739 (t0) REVERT: G 97 GLN cc_start: 0.7039 (mp-120) cc_final: 0.6729 (mp10) REVERT: G 121 HIS cc_start: 0.8419 (t-90) cc_final: 0.8102 (t-90) REVERT: G 170 TRP cc_start: 0.8355 (m100) cc_final: 0.8075 (m100) REVERT: G 191 LEU cc_start: 0.8869 (tt) cc_final: 0.8483 (tt) REVERT: G 210 ASP cc_start: 0.7790 (t70) cc_final: 0.7175 (t70) REVERT: G 232 TYR cc_start: 0.8603 (t80) cc_final: 0.8294 (t80) REVERT: G 248 PHE cc_start: 0.8714 (m-80) cc_final: 0.8440 (m-80) REVERT: G 309 LEU cc_start: 0.8127 (mt) cc_final: 0.7911 (tt) REVERT: G 314 TYR cc_start: 0.7423 (m-10) cc_final: 0.7102 (m-10) REVERT: G 324 ASN cc_start: 0.8374 (t0) cc_final: 0.7969 (t0) REVERT: G 338 ASP cc_start: 0.8506 (t0) cc_final: 0.8110 (t70) REVERT: G 343 THR cc_start: 0.8241 (m) cc_final: 0.7798 (p) REVERT: G 372 GLU cc_start: 0.7144 (mp0) cc_final: 0.6725 (mp0) REVERT: G 377 GLN cc_start: 0.8265 (mp10) cc_final: 0.7596 (mp10) REVERT: G 473 LEU cc_start: 0.8578 (mm) cc_final: 0.8275 (mm) REVERT: H 35 TYR cc_start: 0.7931 (m-80) cc_final: 0.6964 (m-80) REVERT: H 92 TYR cc_start: 0.6981 (t80) cc_final: 0.6590 (t80) REVERT: H 93 ASN cc_start: 0.8166 (t0) cc_final: 0.7601 (t0) REVERT: H 97 GLN cc_start: 0.8311 (pm20) cc_final: 0.8062 (pm20) REVERT: H 121 HIS cc_start: 0.7900 (t-90) cc_final: 0.7486 (t-90) REVERT: H 147 ASN cc_start: 0.8189 (t0) cc_final: 0.7932 (t0) REVERT: H 169 HIS cc_start: 0.8304 (p90) cc_final: 0.7711 (p90) REVERT: H 202 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7532 (p) REVERT: H 221 VAL cc_start: 0.8700 (t) cc_final: 0.8249 (p) REVERT: H 245 ASP cc_start: 0.7414 (p0) cc_final: 0.6953 (p0) REVERT: H 263 ASN cc_start: 0.7767 (t0) cc_final: 0.7173 (t0) REVERT: H 333 PHE cc_start: 0.7971 (m-80) cc_final: 0.7448 (m-80) REVERT: H 343 THR cc_start: 0.8262 (m) cc_final: 0.7886 (p) REVERT: H 367 TYR cc_start: 0.8119 (m-10) cc_final: 0.7865 (m-10) REVERT: H 372 GLU cc_start: 0.7433 (mp0) cc_final: 0.7183 (mp0) REVERT: H 465 GLN cc_start: 0.8039 (mp10) cc_final: 0.7529 (mp10) REVERT: H 473 LEU cc_start: 0.8615 (mm) cc_final: 0.8315 (mm) REVERT: H 475 GLN cc_start: 0.8714 (pp30) cc_final: 0.7983 (pp30) REVERT: I 44 THR cc_start: 0.8584 (m) cc_final: 0.8276 (p) REVERT: I 96 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (p) REVERT: I 198 ASP cc_start: 0.8090 (t0) cc_final: 0.7581 (m-30) REVERT: I 229 ILE cc_start: 0.8650 (mm) cc_final: 0.7978 (tp) REVERT: I 237 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: I 245 ASP cc_start: 0.7667 (p0) cc_final: 0.7461 (p0) REVERT: I 248 PHE cc_start: 0.8669 (m-10) cc_final: 0.8426 (m-80) REVERT: I 370 HIS cc_start: 0.7887 (t70) cc_final: 0.7377 (t-90) REVERT: I 375 ASP cc_start: 0.7448 (t0) cc_final: 0.7017 (t0) REVERT: I 377 GLN cc_start: 0.7661 (mp10) cc_final: 0.6834 (mp10) REVERT: I 399 ASN cc_start: 0.8313 (t0) cc_final: 0.7963 (t0) REVERT: I 457 GLU cc_start: 0.8286 (pp20) cc_final: 0.7893 (pp20) REVERT: I 465 GLN cc_start: 0.8178 (mp10) cc_final: 0.7788 (mp10) outliers start: 77 outliers final: 66 residues processed: 740 average time/residue: 0.0838 time to fit residues: 101.7547 Evaluate side-chains 780 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 709 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 323 ASN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 392 MET Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 323 ASN Chi-restraints excluded: chain H residue 335 THR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 377 GLN Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 292 CYS Chi-restraints excluded: chain I residue 323 ASN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS E 47 ASN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN ** H 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079759 restraints weight = 31630.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082480 restraints weight = 16598.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084256 restraints weight = 10498.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085459 restraints weight = 7588.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086253 restraints weight = 6031.214| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 14880 Z= 0.291 Angle : 1.221 59.199 20546 Z= 0.751 Chirality : 0.053 0.805 2527 Planarity : 0.008 0.187 2658 Dihedral : 4.879 45.756 2151 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.27 % Rotamer: Outliers : 5.59 % Allowed : 31.52 % Favored : 62.89 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.18), residues: 2022 helix: -0.02 (0.38), residues: 202 sheet: -1.58 (0.21), residues: 554 loop : -1.77 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D 341 TYR 0.020 0.002 TYR I 374 PHE 0.034 0.003 PHE H 249 TRP 0.039 0.002 TRP E 406 HIS 0.007 0.001 HIS I 322 Details of bonding type rmsd covalent geometry : bond 0.00560 (14880) covalent geometry : angle 1.22082 (20546) hydrogen bonds : bond 0.02902 ( 351) hydrogen bonds : angle 5.03791 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.29 seconds wall clock time: 59 minutes 18.20 seconds (3558.20 seconds total)