Starting phenix.real_space_refine on Thu Mar 5 10:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.map" model { file = "/net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzc_9298/03_2026/6mzc_9298.cif" } resolution = 4.5 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= 0.000 sd= 0.005 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 117 5.16 5 C 13453 2.51 5 N 3718 2.21 5 O 3966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21254 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 7832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7832 Classifications: {'peptide': 968} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 923} Chain: "E" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 686 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 2, 'ASP:plan': 5, 'ARG:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 120 Chain: "G" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1447 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain breaks: 1 Chain: "G" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2199 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 10, 'TRANS': 289} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 40, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1943 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 243} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "I" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 551 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1969 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 10, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "K" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 722 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'UNK:plan-1': 51} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 697 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain breaks: 1 Chain: "R" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 611 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "Z" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1190 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 238} Link IDs: {'TRANS': 237} Chain breaks: 8 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 714 Unresolved non-hydrogen dihedrals: 238 Planarities with less than four sites: {'UNK:plan-1': 238} Unresolved non-hydrogen planarities: 238 Time building chain proxies: 4.67, per 1000 atoms: 0.22 Number of scatterers: 21254 At special positions: 0 Unit cell: (161.04, 225.72, 135.96, 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 117 16.00 O 3966 8.00 N 3718 7.00 C 13453 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 Links applied TRANS " UNK G 497 " - " VAL G 496 " " UNK K 121 " - " THR K 120 " " UNK M 110 " - " PRO M 109 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 968.7 milliseconds 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 16 sheets defined 59.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.948A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.127A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 337 through 358 removed outlier: 4.731A pdb=" N LEU B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.533A pdb=" N GLU B 367 " --> pdb=" O TRP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 387 through 409 Processing helix chain 'B' and resid 442 through 464 Processing helix chain 'B' and resid 465 through 484 Processing helix chain 'B' and resid 493 through 497 removed outlier: 4.191A pdb=" N MET B 496 " --> pdb=" O TRP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'B' and resid 514 through 523 removed outlier: 3.759A pdb=" N LEU B 518 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 Processing helix chain 'B' and resid 658 through 672 removed outlier: 3.925A pdb=" N PHE B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 687 removed outlier: 3.640A pdb=" N LEU B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 708 Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 743 through 759 Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 768 through 781 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 824 through 843 removed outlier: 3.682A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 863 Processing helix chain 'B' and resid 871 through 876 Processing helix chain 'B' and resid 883 through 901 Processing helix chain 'B' and resid 903 through 916 removed outlier: 3.632A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 removed outlier: 3.941A pdb=" N ARG B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 959 Processing helix chain 'B' and resid 964 through 978 removed outlier: 4.238A pdb=" N ARG B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 889 removed outlier: 3.543A pdb=" N LEU E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 925 Processing helix chain 'E' and resid 940 through 971 Processing helix chain 'G' and resid 211 through 227 Processing helix chain 'G' and resid 229 through 237 Processing helix chain 'G' and resid 239 through 255 removed outlier: 3.535A pdb=" N LEU G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 268 Processing helix chain 'G' and resid 275 through 284 removed outlier: 3.631A pdb=" N SER G 284 " --> pdb=" O ARG G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.711A pdb=" N MET G 291 " --> pdb=" O LYS G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.828A pdb=" N TYR G 314 " --> pdb=" O SER G 310 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN G 322 " --> pdb=" O LYS G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 337 removed outlier: 3.828A pdb=" N GLU G 335 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 510 removed outlier: 3.921A pdb=" N UNK G 510 " --> pdb=" O UNK G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 520 removed outlier: 3.534A pdb=" N UNK G 520 " --> pdb=" O UNK G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'H' and resid 218 through 233 Processing helix chain 'H' and resid 235 through 248 Processing helix chain 'H' and resid 255 through 274 Processing helix chain 'H' and resid 275 through 291 Processing helix chain 'H' and resid 297 through 299 No H-bonds generated for 'chain 'H' and resid 297 through 299' Processing helix chain 'H' and resid 300 through 311 removed outlier: 3.795A pdb=" N LEU H 304 " --> pdb=" O TYR H 300 " (cutoff:3.500A) Proline residue: H 306 - end of helix removed outlier: 3.997A pdb=" N CYS H 311 " --> pdb=" O ALA H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 345 removed outlier: 3.561A pdb=" N ALA H 333 " --> pdb=" O LEU H 329 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 338 " --> pdb=" O ALA H 334 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N HIS H 343 " --> pdb=" O GLN H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 365 removed outlier: 4.163A pdb=" N ASP H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 384 Processing helix chain 'H' and resid 384 through 392 Processing helix chain 'H' and resid 395 through 407 Processing helix chain 'H' and resid 413 through 439 Proline residue: H 433 - end of helix Processing helix chain 'H' and resid 443 through 451 Processing helix chain 'H' and resid 457 through 472 Processing helix chain 'I' and resid 15 through 26 removed outlier: 3.921A pdb=" N MET I 26 " --> pdb=" O VAL I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 59 removed outlier: 3.931A pdb=" N CYS I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 75 removed outlier: 3.652A pdb=" N ILE I 71 " --> pdb=" O THR I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 233 Processing helix chain 'I' and resid 235 through 248 Processing helix chain 'I' and resid 257 through 274 Processing helix chain 'I' and resid 275 through 291 Processing helix chain 'I' and resid 297 through 303 removed outlier: 4.748A pdb=" N HIS I 302 " --> pdb=" O LYS I 299 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU I 303 " --> pdb=" O TYR I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 314 removed outlier: 4.358A pdb=" N SER I 314 " --> pdb=" O THR I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 322 Processing helix chain 'I' and resid 323 through 342 removed outlier: 3.505A pdb=" N TRP I 327 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA I 328 " --> pdb=" O ASP I 324 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 365 Processing helix chain 'I' and resid 369 through 383 removed outlier: 3.695A pdb=" N ARG I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 407 removed outlier: 3.960A pdb=" N LEU I 393 " --> pdb=" O LYS I 389 " (cutoff:3.500A) Proline residue: I 394 - end of helix removed outlier: 4.893A pdb=" N GLN I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 439 Proline residue: I 433 - end of helix Processing helix chain 'I' and resid 443 through 450 Processing helix chain 'I' and resid 457 through 473 removed outlier: 3.543A pdb=" N GLN I 473 " --> pdb=" O GLN I 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 49 removed outlier: 4.134A pdb=" N ARG K 34 " --> pdb=" O HIS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 80 Processing helix chain 'K' and resid 89 through 100 Processing helix chain 'K' and resid 105 through 118 removed outlier: 4.639A pdb=" N ALA K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 198 Processing helix chain 'K' and resid 222 through 227 Processing helix chain 'M' and resid 14 through 26 Processing helix chain 'M' and resid 32 through 61 Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 87 through 101 Processing helix chain 'O' and resid 114 through 122 Processing helix chain 'O' and resid 123 through 125 No H-bonds generated for 'chain 'O' and resid 123 through 125' Processing helix chain 'O' and resid 131 through 142 Processing helix chain 'O' and resid 148 through 175 removed outlier: 4.272A pdb=" N ILE O 152 " --> pdb=" O ASP O 148 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS O 173 " --> pdb=" O ASP O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 204 Proline residue: O 202 - end of helix Processing helix chain 'R' and resid 59 through 71 removed outlier: 4.017A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 106 removed outlier: 4.083A pdb=" N GLU R 81 " --> pdb=" O ASP R 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 124 removed outlier: 3.952A pdb=" N VAL R 116 " --> pdb=" O GLU R 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 20 removed outlier: 3.531A pdb=" N UNK Z 20 " --> pdb=" O UNK Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 86 Processing helix chain 'Z' and resid 89 through 95 Processing helix chain 'Z' and resid 120 through 129 Processing helix chain 'Z' and resid 135 through 141 Processing helix chain 'Z' and resid 209 through 211 No H-bonds generated for 'chain 'Z' and resid 209 through 211' Processing helix chain 'Z' and resid 212 through 217 Processing helix chain 'Z' and resid 310 through 319 Processing helix chain 'Z' and resid 371 through 377 Processing helix chain 'Z' and resid 402 through 409 removed outlier: 4.154A pdb=" N UNK Z 409 " --> pdb=" O UNK Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 410 through 412 No H-bonds generated for 'chain 'Z' and resid 410 through 412' Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 5.377A pdb=" N ILE B 72 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER B 151 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 48 " --> pdb=" O CYS B 34 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS B 30 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 54 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 28 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N THR B 201 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 29 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS B 203 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR B 207 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 35 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TRP B 202 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 240 " --> pdb=" O TRP B 202 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU B 204 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 238 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 206 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR B 236 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 208 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B 234 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS B 235 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 257 removed outlier: 6.588A pdb=" N LYS B 305 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 325 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 307 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AA7, first strand: chain 'B' and resid 547 through 550 Processing sheet with id=AA8, first strand: chain 'B' and resid 575 through 579 Processing sheet with id=AA9, first strand: chain 'G' and resid 474 through 477 Processing sheet with id=AB1, first strand: chain 'G' and resid 548 through 551 Processing sheet with id=AB2, first strand: chain 'G' and resid 590 through 593 Processing sheet with id=AB3, first strand: chain 'G' and resid 630 through 635 removed outlier: 4.063A pdb=" N ARG G 663 " --> pdb=" O LEU G 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 672 through 677 removed outlier: 3.525A pdb=" N SER G 674 " --> pdb=" O GLY G 687 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP G 697 " --> pdb=" O MET G 703 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET G 703 " --> pdb=" O ASP G 697 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 714 through 719 Processing sheet with id=AB6, first strand: chain 'G' and resid 766 through 769 removed outlier: 4.733A pdb=" N LEU G 768 " --> pdb=" O VAL G 781 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 65 through 66 removed outlier: 3.646A pdb=" N LEU I 66 " --> pdb=" O GLU M 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1124 hydrogen bonds defined for protein. 3276 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: 3.99 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6624 1.33 - 1.45: 3856 1.45 - 1.57: 10990 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 21654 Sorted by residual: bond pdb=" CB TRP B 443 " pdb=" CG TRP B 443 " ideal model delta sigma weight residual 1.498 1.364 0.134 3.10e-02 1.04e+03 1.87e+01 bond pdb=" C ASP B 870 " pdb=" N PRO B 871 " ideal model delta sigma weight residual 1.336 1.296 0.040 9.80e-03 1.04e+04 1.66e+01 bond pdb=" CG GLN G 766 " pdb=" CD GLN G 766 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.83e+00 bond pdb=" CB TRP B 381 " pdb=" CG TRP B 381 " ideal model delta sigma weight residual 1.498 1.407 0.091 3.10e-02 1.04e+03 8.67e+00 bond pdb=" CA LEU G 717 " pdb=" CB LEU G 717 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 7.13e+00 ... (remaining 21649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 28521 3.33 - 6.65: 788 6.65 - 9.98: 111 9.98 - 13.30: 15 13.30 - 16.63: 2 Bond angle restraints: 29437 Sorted by residual: angle pdb=" C THR I 261 " pdb=" N PHE I 262 " pdb=" CA PHE I 262 " ideal model delta sigma weight residual 122.56 109.75 12.81 1.72e+00 3.38e-01 5.55e+01 angle pdb=" N ILE I 392 " pdb=" CA ILE I 392 " pdb=" C ILE I 392 " ideal model delta sigma weight residual 111.91 106.41 5.50 8.90e-01 1.26e+00 3.82e+01 angle pdb=" C UNK Z 367 " pdb=" N UNK Z 368 " pdb=" CA UNK Z 368 " ideal model delta sigma weight residual 121.70 131.97 -10.27 1.80e+00 3.09e-01 3.26e+01 angle pdb=" N GLY B 252 " pdb=" CA GLY B 252 " pdb=" C GLY B 252 " ideal model delta sigma weight residual 112.34 123.28 -10.94 2.04e+00 2.40e-01 2.88e+01 angle pdb=" CA ARG G 607 " pdb=" CB ARG G 607 " pdb=" CG ARG G 607 " ideal model delta sigma weight residual 114.10 124.79 -10.69 2.00e+00 2.50e-01 2.86e+01 ... (remaining 29432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 12112 15.19 - 30.38: 829 30.38 - 45.56: 102 45.56 - 60.75: 13 60.75 - 75.94: 7 Dihedral angle restraints: 13063 sinusoidal: 4674 harmonic: 8389 Sorted by residual: dihedral pdb=" CA LEU I 256 " pdb=" C LEU I 256 " pdb=" N PRO I 257 " pdb=" CA PRO I 257 " ideal model delta harmonic sigma weight residual -180.00 -115.80 -64.20 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA LEU B 843 " pdb=" C LEU B 843 " pdb=" N PRO B 844 " pdb=" CA PRO B 844 " ideal model delta harmonic sigma weight residual -180.00 -117.19 -62.81 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA ARG K 217 " pdb=" C ARG K 217 " pdb=" N PRO K 218 " pdb=" CA PRO K 218 " ideal model delta harmonic sigma weight residual -180.00 -119.08 -60.92 0 5.00e+00 4.00e-02 1.48e+02 ... (remaining 13060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2811 0.084 - 0.168: 554 0.168 - 0.252: 57 0.252 - 0.335: 8 0.335 - 0.419: 3 Chirality restraints: 3433 Sorted by residual: chirality pdb=" CB ILE B 666 " pdb=" CA ILE B 666 " pdb=" CG1 ILE B 666 " pdb=" CG2 ILE B 666 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA PHE I 262 " pdb=" N PHE I 262 " pdb=" C PHE I 262 " pdb=" CB PHE I 262 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CG LEU G 790 " pdb=" CB LEU G 790 " pdb=" CD1 LEU G 790 " pdb=" CD2 LEU G 790 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 3430 not shown) Planarity restraints: 3798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 217 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO K 218 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO K 218 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO K 218 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 441 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO H 442 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO H 442 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 442 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 843 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO B 844 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 844 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 844 " -0.055 5.00e-02 4.00e+02 ... (remaining 3795 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2965 2.75 - 3.28: 22153 3.28 - 3.82: 36397 3.82 - 4.36: 42481 4.36 - 4.90: 65869 Nonbonded interactions: 169865 Sorted by model distance: nonbonded pdb=" O ILE M 28 " pdb=" OH TYR M 31 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN B 184 " pdb=" OG SER B 195 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 44 " pdb=" O LEU B 152 " model vdw 2.234 3.040 nonbonded pdb=" O LEU B 956 " pdb=" OG1 THR B 961 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR G 464 " pdb=" O UNK K 150 " model vdw 2.254 3.040 ... (remaining 169860 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.010 0.134 21657 Z= 0.466 Angle : 1.333 16.629 29446 Z= 0.721 Chirality : 0.066 0.419 3433 Planarity : 0.009 0.122 3795 Dihedral : 10.663 75.941 7576 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.36 % Favored : 85.40 % Rotamer: Outliers : 0.72 % Allowed : 2.50 % Favored : 96.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 7.62 % Twisted General : 1.18 % 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: -4.52 (0.14), residues: 2465 helix: -2.21 (0.11), residues: 1239 sheet: -2.43 (0.33), residues: 223 loop : -4.14 (0.17), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG B 344 TYR 0.043 0.005 TYR I 45 PHE 0.059 0.005 PHE I 262 TRP 0.047 0.005 TRP B 189 HIS 0.032 0.005 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00971 (21654) covalent geometry : angle 1.33307 (29437) hydrogen bonds : bond 0.15139 ( 1124) hydrogen bonds : angle 7.81651 ( 3276) link_TRANS : bond 0.00756 ( 3) link_TRANS : angle 0.53646 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 943 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7952 (Cg_exo) REVERT: B 170 MET cc_start: 0.7851 (mtp) cc_final: 0.7615 (mmm) REVERT: B 206 PHE cc_start: 0.7010 (m-10) cc_final: 0.6631 (m-80) REVERT: B 217 ASN cc_start: 0.8481 (m-40) cc_final: 0.8045 (m-40) REVERT: B 265 VAL cc_start: 0.8599 (t) cc_final: 0.8356 (m) REVERT: B 294 ILE cc_start: 0.9330 (mt) cc_final: 0.8919 (mt) REVERT: B 295 LEU cc_start: 0.9186 (mt) cc_final: 0.8983 (mm) REVERT: B 314 VAL cc_start: 0.8648 (t) cc_final: 0.8404 (m) REVERT: B 324 ILE cc_start: 0.8290 (mt) cc_final: 0.7988 (mt) REVERT: B 357 CYS cc_start: 0.8594 (m) cc_final: 0.6182 (m) REVERT: B 396 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8263 (mmmt) REVERT: B 398 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7793 (tp30) REVERT: B 448 MET cc_start: 0.8653 (mmp) cc_final: 0.8382 (mmm) REVERT: B 451 CYS cc_start: 0.7832 (m) cc_final: 0.7418 (m) REVERT: B 470 LEU cc_start: 0.9273 (mt) cc_final: 0.8965 (mt) REVERT: B 520 LYS cc_start: 0.9206 (mttt) cc_final: 0.8881 (tptp) REVERT: B 579 LEU cc_start: 0.8874 (mt) cc_final: 0.7981 (mt) REVERT: B 614 MET cc_start: 0.8094 (mtp) cc_final: 0.7889 (mmt) REVERT: B 642 PHE cc_start: 0.8366 (p90) cc_final: 0.7953 (p90) REVERT: B 648 MET cc_start: 0.8873 (mtp) cc_final: 0.8360 (mtt) REVERT: B 649 TRP cc_start: 0.7622 (m100) cc_final: 0.7415 (m100) REVERT: B 757 MET cc_start: 0.9028 (mtp) cc_final: 0.7394 (mtm) REVERT: B 797 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7865 (mm-30) REVERT: B 888 ILE cc_start: 0.8707 (tt) cc_final: 0.8479 (pt) REVERT: B 914 ILE cc_start: 0.8771 (mt) cc_final: 0.8568 (mt) REVERT: B 916 ASN cc_start: 0.8895 (t0) cc_final: 0.7911 (p0) REVERT: B 939 ASN cc_start: 0.8630 (m-40) cc_final: 0.8299 (p0) REVERT: E 889 HIS cc_start: 0.7889 (m90) cc_final: 0.7054 (m90) REVERT: G 221 LEU cc_start: 0.9664 (tp) cc_final: 0.9376 (pp) REVERT: G 223 HIS cc_start: 0.9494 (t70) cc_final: 0.9274 (t70) REVERT: G 243 LEU cc_start: 0.9368 (tp) cc_final: 0.9101 (mt) REVERT: G 263 PHE cc_start: 0.8710 (t80) cc_final: 0.8111 (t80) REVERT: G 329 ILE cc_start: 0.8700 (mt) cc_final: 0.8445 (mp) REVERT: G 477 ASP cc_start: 0.7313 (p0) cc_final: 0.6950 (p0) REVERT: G 551 PHE cc_start: 0.7828 (m-80) cc_final: 0.7626 (m-80) REVERT: G 563 GLU cc_start: 0.7746 (tt0) cc_final: 0.7471 (tt0) REVERT: G 599 TYR cc_start: 0.8446 (m-80) cc_final: 0.7552 (m-80) REVERT: G 607 ARG cc_start: 0.7214 (pmm150) cc_final: 0.6962 (ptp90) REVERT: G 622 ILE cc_start: 0.9238 (tt) cc_final: 0.8451 (mm) REVERT: G 623 PHE cc_start: 0.8387 (m-80) cc_final: 0.6794 (m-10) REVERT: G 627 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6839 (pp) REVERT: G 654 TRP cc_start: 0.8096 (m100) cc_final: 0.6825 (m100) REVERT: G 656 VAL cc_start: 0.8729 (p) cc_final: 0.8477 (p) REVERT: G 657 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8194 (pp) REVERT: G 696 TRP cc_start: 0.8425 (m100) cc_final: 0.7457 (m100) REVERT: H 219 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7579 (tt0) REVERT: H 225 LYS cc_start: 0.9177 (mttt) cc_final: 0.8840 (tppt) REVERT: H 241 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8348 (tt0) REVERT: H 246 ILE cc_start: 0.9048 (mt) cc_final: 0.8692 (mm) REVERT: H 259 PHE cc_start: 0.8228 (t80) cc_final: 0.7976 (t80) REVERT: H 263 ILE cc_start: 0.9731 (mt) cc_final: 0.9464 (tp) REVERT: H 279 LEU cc_start: 0.9156 (mt) cc_final: 0.8717 (mt) REVERT: H 282 LEU cc_start: 0.9606 (mt) cc_final: 0.9389 (mt) REVERT: H 285 MET cc_start: 0.8670 (ttt) cc_final: 0.8041 (mtp) REVERT: H 305 ILE cc_start: 0.9274 (mm) cc_final: 0.8945 (mm) REVERT: H 335 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8100 (ttp-110) REVERT: H 336 LEU cc_start: 0.9538 (mt) cc_final: 0.9032 (mm) REVERT: H 339 GLN cc_start: 0.8270 (mt0) cc_final: 0.7913 (mt0) REVERT: H 363 TRP cc_start: 0.8408 (t60) cc_final: 0.8008 (t60) REVERT: H 389 LYS cc_start: 0.8286 (ttmt) cc_final: 0.8004 (tttt) REVERT: H 414 ASN cc_start: 0.8877 (m-40) cc_final: 0.7552 (m110) REVERT: H 421 ASP cc_start: 0.9132 (t0) cc_final: 0.8897 (m-30) REVERT: H 423 VAL cc_start: 0.9593 (t) cc_final: 0.9168 (t) REVERT: H 428 LEU cc_start: 0.8727 (tp) cc_final: 0.8407 (mm) REVERT: H 435 LEU cc_start: 0.9250 (mt) cc_final: 0.8952 (pp) REVERT: I 50 ILE cc_start: 0.9281 (mt) cc_final: 0.8971 (mm) REVERT: I 60 MET cc_start: 0.8358 (mmt) cc_final: 0.8023 (mmm) REVERT: I 219 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7934 (mt-10) REVERT: I 220 GLN cc_start: 0.8733 (pt0) cc_final: 0.8290 (tm-30) REVERT: I 221 GLN cc_start: 0.8988 (pt0) cc_final: 0.8485 (pp30) REVERT: I 222 LEU cc_start: 0.9361 (mt) cc_final: 0.9084 (mt) REVERT: I 226 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8266 (mm-30) REVERT: I 227 ILE cc_start: 0.9266 (mt) cc_final: 0.9040 (mt) REVERT: I 228 THR cc_start: 0.9220 (p) cc_final: 0.9000 (p) REVERT: I 229 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8653 (tp30) REVERT: I 244 GLN cc_start: 0.9159 (tp40) cc_final: 0.8593 (tp-100) REVERT: I 259 PHE cc_start: 0.7498 (t80) cc_final: 0.7004 (t80) REVERT: I 270 ASN cc_start: 0.8597 (m-40) cc_final: 0.8077 (t0) REVERT: I 273 GLN cc_start: 0.8939 (mm110) cc_final: 0.8538 (tm-30) REVERT: I 295 LEU cc_start: 0.6119 (mt) cc_final: 0.5800 (pp) REVERT: I 330 ARG cc_start: 0.8978 (mtt90) cc_final: 0.8531 (mtm-85) REVERT: I 332 PHE cc_start: 0.9069 (t80) cc_final: 0.8726 (t80) REVERT: I 335 ARG cc_start: 0.9206 (ttt180) cc_final: 0.8766 (ttm-80) REVERT: I 337 VAL cc_start: 0.9392 (t) cc_final: 0.9039 (t) REVERT: I 341 CYS cc_start: 0.8944 (m) cc_final: 0.8112 (t) REVERT: I 347 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8171 (p) REVERT: I 363 TRP cc_start: 0.7413 (t60) cc_final: 0.6939 (t60) REVERT: K 38 GLN cc_start: 0.9132 (mt0) cc_final: 0.8919 (mt0) REVERT: K 64 MET cc_start: 0.9239 (mtp) cc_final: 0.8653 (mmp) REVERT: K 87 GLN cc_start: 0.8229 (mm-40) cc_final: 0.6526 (pp30) REVERT: K 182 GLN cc_start: 0.8954 (tt0) cc_final: 0.8579 (pt0) REVERT: K 187 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6667 (mt-10) REVERT: K 223 TYR cc_start: 0.7897 (p90) cc_final: 0.7446 (p90) REVERT: K 224 LEU cc_start: 0.8966 (mt) cc_final: 0.8509 (mt) REVERT: M 14 LYS cc_start: 0.9216 (mttt) cc_final: 0.8689 (tptt) REVERT: M 22 ILE cc_start: 0.8705 (mt) cc_final: 0.8329 (mt) REVERT: M 24 LYS cc_start: 0.7957 (mttt) cc_final: 0.7702 (mtmm) REVERT: M 34 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7711 (ttt180) REVERT: M 35 VAL cc_start: 0.8405 (t) cc_final: 0.7838 (t) REVERT: M 40 LEU cc_start: 0.9305 (mt) cc_final: 0.9073 (mt) REVERT: M 46 TYR cc_start: 0.9210 (m-80) cc_final: 0.8943 (m-80) REVERT: M 49 THR cc_start: 0.9541 (p) cc_final: 0.9147 (p) REVERT: M 78 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8555 (tpt-90) REVERT: O 169 ASP cc_start: 0.9231 (t0) cc_final: 0.8917 (t70) REVERT: O 173 HIS cc_start: 0.9012 (m90) cc_final: 0.8516 (m90) REVERT: O 198 GLU cc_start: 0.9143 (tt0) cc_final: 0.8899 (tt0) REVERT: R 75 GLN cc_start: 0.8497 (tp40) cc_final: 0.8246 (mp10) REVERT: R 80 VAL cc_start: 0.7798 (t) cc_final: 0.7563 (t) REVERT: R 120 LEU cc_start: 0.9860 (mt) cc_final: 0.9645 (mt) REVERT: R 121 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8949 (mm-30) outliers start: 15 outliers final: 5 residues processed: 951 average time/residue: 0.1561 time to fit residues: 221.0619 Evaluate side-chains 607 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 599 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 147 HIS B 217 ASN B 430 HIS B 454 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 ASN B 864 ASN B 908 GLN E 895 HIS ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 GLN G 255 GLN G 256 HIS G 290 HIS ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN G 336 HIS H 343 HIS ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS O 122 GLN R 101 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.087541 restraints weight = 72212.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090019 restraints weight = 44014.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091678 restraints weight = 30914.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092795 restraints weight = 24114.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093567 restraints weight = 20290.667| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21657 Z= 0.174 Angle : 0.832 11.379 29446 Z= 0.436 Chirality : 0.048 0.343 3433 Planarity : 0.007 0.100 3795 Dihedral : 7.865 59.649 3033 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.32 % Favored : 88.64 % Rotamer: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.21 % 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: -3.21 (0.15), residues: 2465 helix: -0.90 (0.13), residues: 1292 sheet: -1.94 (0.34), residues: 214 loop : -3.97 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 859 TYR 0.047 0.002 TYR B 196 PHE 0.043 0.002 PHE I 262 TRP 0.021 0.002 TRP H 370 HIS 0.013 0.002 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00363 (21654) covalent geometry : angle 0.83241 (29437) hydrogen bonds : bond 0.04911 ( 1124) hydrogen bonds : angle 6.07348 ( 3276) link_TRANS : bond 0.00066 ( 3) link_TRANS : angle 0.54856 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 809 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8264 (tptm) cc_final: 0.7968 (tptm) REVERT: B 31 GLN cc_start: 0.8100 (mp-120) cc_final: 0.7763 (mp10) REVERT: B 66 ASN cc_start: 0.7637 (p0) cc_final: 0.7389 (p0) REVERT: B 206 PHE cc_start: 0.6878 (m-10) cc_final: 0.6570 (m-80) REVERT: B 217 ASN cc_start: 0.8548 (m110) cc_final: 0.8126 (m-40) REVERT: B 262 MET cc_start: 0.8315 (tpt) cc_final: 0.7715 (tpt) REVERT: B 276 LEU cc_start: 0.9117 (mp) cc_final: 0.8865 (mt) REVERT: B 324 ILE cc_start: 0.8373 (mt) cc_final: 0.7938 (mt) REVERT: B 362 MET cc_start: 0.6672 (tpt) cc_final: 0.6440 (tpp) REVERT: B 364 TRP cc_start: 0.8456 (t-100) cc_final: 0.7851 (t-100) REVERT: B 390 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8031 (tp30) REVERT: B 396 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8174 (tppt) REVERT: B 459 LEU cc_start: 0.8900 (mt) cc_final: 0.8595 (mt) REVERT: B 468 PHE cc_start: 0.9395 (m-10) cc_final: 0.9169 (m-80) REVERT: B 470 LEU cc_start: 0.9108 (mt) cc_final: 0.8765 (mt) REVERT: B 488 PHE cc_start: 0.8388 (t80) cc_final: 0.7460 (t80) REVERT: B 520 LYS cc_start: 0.9209 (mttt) cc_final: 0.8963 (tptt) REVERT: B 531 PHE cc_start: 0.8700 (m-80) cc_final: 0.8309 (m-80) REVERT: B 578 THR cc_start: 0.8301 (m) cc_final: 0.7808 (m) REVERT: B 588 HIS cc_start: 0.7463 (m-70) cc_final: 0.7197 (m-70) REVERT: B 642 PHE cc_start: 0.8743 (p90) cc_final: 0.8426 (p90) REVERT: B 653 LEU cc_start: 0.9210 (mt) cc_final: 0.8989 (mt) REVERT: B 660 VAL cc_start: 0.8849 (t) cc_final: 0.8639 (t) REVERT: B 753 MET cc_start: 0.7488 (ppp) cc_final: 0.7104 (ppp) REVERT: B 776 LEU cc_start: 0.8621 (mt) cc_final: 0.8386 (mt) REVERT: B 797 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 798 MET cc_start: 0.7670 (mtp) cc_final: 0.7427 (mtp) REVERT: B 833 ILE cc_start: 0.8844 (pt) cc_final: 0.8553 (pt) REVERT: B 837 LEU cc_start: 0.8942 (mt) cc_final: 0.8621 (mt) REVERT: B 854 CYS cc_start: 0.8327 (m) cc_final: 0.7693 (t) REVERT: B 914 ILE cc_start: 0.8723 (mt) cc_final: 0.8302 (mt) REVERT: B 916 ASN cc_start: 0.8764 (t0) cc_final: 0.8362 (p0) REVERT: B 955 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8879 (mttt) REVERT: E 889 HIS cc_start: 0.7875 (m90) cc_final: 0.7356 (m-70) REVERT: E 904 HIS cc_start: 0.9490 (t70) cc_final: 0.9254 (t70) REVERT: E 915 GLU cc_start: 0.9270 (pp20) cc_final: 0.8891 (pp20) REVERT: E 922 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8894 (mm-40) REVERT: G 214 TYR cc_start: 0.8428 (m-80) cc_final: 0.8026 (m-80) REVERT: G 223 HIS cc_start: 0.9442 (t70) cc_final: 0.9133 (t70) REVERT: G 246 HIS cc_start: 0.8632 (p-80) cc_final: 0.8126 (p-80) REVERT: G 261 LYS cc_start: 0.9574 (mtpt) cc_final: 0.9374 (ptmm) REVERT: G 265 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9074 (mt-10) REVERT: G 342 PHE cc_start: 0.8486 (m-10) cc_final: 0.8246 (m-10) REVERT: G 464 TYR cc_start: 0.4969 (m-10) cc_final: 0.4577 (m-10) REVERT: G 484 LEU cc_start: 0.7758 (mt) cc_final: 0.7409 (mt) REVERT: G 538 ILE cc_start: 0.9133 (tt) cc_final: 0.8870 (mm) REVERT: G 563 GLU cc_start: 0.6996 (tt0) cc_final: 0.6696 (tt0) REVERT: G 566 THR cc_start: 0.7727 (t) cc_final: 0.7425 (m) REVERT: G 568 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.6725 (mtt-85) REVERT: G 599 TYR cc_start: 0.8257 (m-80) cc_final: 0.7554 (m-80) REVERT: G 612 TRP cc_start: 0.8021 (m100) cc_final: 0.7561 (m100) REVERT: G 622 ILE cc_start: 0.9095 (tt) cc_final: 0.8383 (mm) REVERT: G 623 PHE cc_start: 0.8334 (m-80) cc_final: 0.6980 (m-10) REVERT: G 636 HIS cc_start: 0.7948 (t70) cc_final: 0.7299 (t-90) REVERT: G 640 ASN cc_start: 0.6900 (t0) cc_final: 0.6657 (t0) REVERT: G 654 TRP cc_start: 0.7990 (m100) cc_final: 0.6767 (m100) REVERT: G 696 TRP cc_start: 0.8172 (m100) cc_final: 0.7028 (m100) REVERT: G 713 THR cc_start: 0.6953 (m) cc_final: 0.6631 (m) REVERT: G 766 GLN cc_start: 0.5642 (mt0) cc_final: 0.4966 (pm20) REVERT: G 774 MET cc_start: 0.6136 (mtt) cc_final: 0.5880 (mtp) REVERT: G 780 VAL cc_start: 0.7976 (t) cc_final: 0.7257 (t) REVERT: H 224 TYR cc_start: 0.8510 (t80) cc_final: 0.8059 (t80) REVERT: H 226 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7350 (mt-10) REVERT: H 241 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8181 (tt0) REVERT: H 246 ILE cc_start: 0.8693 (mt) cc_final: 0.8418 (mm) REVERT: H 259 PHE cc_start: 0.8553 (t80) cc_final: 0.7869 (t80) REVERT: H 263 ILE cc_start: 0.9649 (mt) cc_final: 0.9436 (tp) REVERT: H 285 MET cc_start: 0.8644 (ttt) cc_final: 0.8154 (tpp) REVERT: H 302 HIS cc_start: 0.9227 (p-80) cc_final: 0.8993 (p-80) REVERT: H 336 LEU cc_start: 0.9562 (mt) cc_final: 0.8899 (mm) REVERT: H 339 GLN cc_start: 0.7857 (mt0) cc_final: 0.7546 (mt0) REVERT: H 354 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8495 (tpp80) REVERT: H 363 TRP cc_start: 0.8478 (t60) cc_final: 0.8148 (t60) REVERT: H 398 GLN cc_start: 0.8912 (mp10) cc_final: 0.8677 (mp10) REVERT: H 424 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 428 LEU cc_start: 0.8509 (tp) cc_final: 0.8182 (mm) REVERT: H 435 LEU cc_start: 0.9122 (mt) cc_final: 0.8836 (pp) REVERT: I 49 GLU cc_start: 0.9177 (tp30) cc_final: 0.8890 (tp30) REVERT: I 50 ILE cc_start: 0.9196 (mt) cc_final: 0.8893 (mm) REVERT: I 72 ASP cc_start: 0.7984 (m-30) cc_final: 0.7780 (m-30) REVERT: I 219 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7778 (mt-10) REVERT: I 220 GLN cc_start: 0.8686 (pt0) cc_final: 0.8477 (pt0) REVERT: I 221 GLN cc_start: 0.8832 (pt0) cc_final: 0.7953 (pp30) REVERT: I 222 LEU cc_start: 0.9259 (mt) cc_final: 0.9017 (mt) REVERT: I 227 ILE cc_start: 0.9207 (mt) cc_final: 0.8957 (mt) REVERT: I 228 THR cc_start: 0.9028 (p) cc_final: 0.8804 (p) REVERT: I 229 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8691 (tp30) REVERT: I 259 PHE cc_start: 0.6461 (t80) cc_final: 0.6139 (t80) REVERT: I 267 VAL cc_start: 0.8812 (t) cc_final: 0.8603 (t) REVERT: I 330 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8565 (mtm180) REVERT: I 332 PHE cc_start: 0.8932 (t80) cc_final: 0.8646 (t80) REVERT: I 335 ARG cc_start: 0.9016 (ttt180) cc_final: 0.8722 (ttm-80) REVERT: I 336 LEU cc_start: 0.9445 (mt) cc_final: 0.9147 (mt) REVERT: I 337 VAL cc_start: 0.9529 (t) cc_final: 0.9288 (t) REVERT: I 349 ASN cc_start: 0.7808 (p0) cc_final: 0.7435 (p0) REVERT: I 412 LEU cc_start: 0.8553 (tp) cc_final: 0.8341 (tp) REVERT: K 64 MET cc_start: 0.9123 (mtp) cc_final: 0.8383 (mmp) REVERT: K 87 GLN cc_start: 0.8418 (mm-40) cc_final: 0.6581 (pp30) REVERT: K 175 LEU cc_start: 0.8731 (tt) cc_final: 0.8047 (tt) REVERT: K 178 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8826 (pttp) REVERT: K 194 MET cc_start: 0.8720 (mmm) cc_final: 0.8239 (mmt) REVERT: K 196 LYS cc_start: 0.6345 (mppt) cc_final: 0.6109 (mppt) REVERT: K 201 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7347 (mm-40) REVERT: K 223 TYR cc_start: 0.7891 (p90) cc_final: 0.7521 (p90) REVERT: M 14 LYS cc_start: 0.9195 (mttt) cc_final: 0.8627 (tptp) REVERT: M 24 LYS cc_start: 0.7981 (mttt) cc_final: 0.7541 (tptp) REVERT: O 169 ASP cc_start: 0.9042 (t0) cc_final: 0.8715 (t0) REVERT: O 173 HIS cc_start: 0.8735 (m90) cc_final: 0.8264 (m90) REVERT: R 93 GLU cc_start: 0.9383 (tp30) cc_final: 0.9092 (tp30) REVERT: R 112 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8568 (mt-10) REVERT: R 114 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8013 (ttpt) REVERT: R 119 HIS cc_start: 0.9016 (t70) cc_final: 0.8670 (t-90) REVERT: R 120 LEU cc_start: 0.9727 (mt) cc_final: 0.9329 (mt) REVERT: R 121 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8603 (mm-30) REVERT: R 126 MET cc_start: 0.6247 (ttp) cc_final: 0.5642 (tmm) outliers start: 3 outliers final: 0 residues processed: 809 average time/residue: 0.1496 time to fit residues: 183.0865 Evaluate side-chains 605 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 172 optimal weight: 0.6980 chunk 198 optimal weight: 0.3980 chunk 98 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 454 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN E 895 HIS ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN R 56 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084500 restraints weight = 73798.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087044 restraints weight = 47982.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089464 restraints weight = 31219.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.089786 restraints weight = 22371.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089661 restraints weight = 20549.292| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21657 Z= 0.209 Angle : 0.839 10.883 29446 Z= 0.438 Chirality : 0.047 0.349 3433 Planarity : 0.006 0.105 3795 Dihedral : 7.382 58.438 3033 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.37 % Favored : 87.55 % Rotamer: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.17 % 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: -2.62 (0.16), residues: 2465 helix: -0.33 (0.13), residues: 1301 sheet: -1.80 (0.35), residues: 219 loop : -3.82 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 392 TYR 0.036 0.002 TYR M 46 PHE 0.054 0.003 PHE I 262 TRP 0.021 0.002 TRP B 381 HIS 0.014 0.002 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00440 (21654) covalent geometry : angle 0.83952 (29437) hydrogen bonds : bond 0.04802 ( 1124) hydrogen bonds : angle 5.80699 ( 3276) link_TRANS : bond 0.00215 ( 3) link_TRANS : angle 0.50465 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 743 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LYS cc_start: 0.8174 (mttt) cc_final: 0.7653 (mtpt) REVERT: B 203 LYS cc_start: 0.8773 (tttt) cc_final: 0.8424 (tttp) REVERT: B 206 PHE cc_start: 0.6634 (m-10) cc_final: 0.6420 (m-80) REVERT: B 262 MET cc_start: 0.8024 (tpt) cc_final: 0.7573 (tpt) REVERT: B 270 LEU cc_start: 0.8689 (mm) cc_final: 0.8309 (mm) REVERT: B 278 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8250 (mttt) REVERT: B 322 MET cc_start: 0.8294 (ttp) cc_final: 0.8083 (ppp) REVERT: B 326 SER cc_start: 0.8256 (p) cc_final: 0.8053 (p) REVERT: B 355 PHE cc_start: 0.7850 (m-10) cc_final: 0.7435 (m-10) REVERT: B 358 PHE cc_start: 0.8794 (m-10) cc_final: 0.8537 (m-10) REVERT: B 364 TRP cc_start: 0.7987 (t-100) cc_final: 0.7158 (t-100) REVERT: B 390 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8034 (tp30) REVERT: B 392 ARG cc_start: 0.8628 (mpp-170) cc_final: 0.8232 (mtm110) REVERT: B 412 VAL cc_start: 0.9052 (t) cc_final: 0.8811 (t) REVERT: B 452 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7785 (ttmt) REVERT: B 461 GLU cc_start: 0.8186 (tp30) cc_final: 0.7798 (tp30) REVERT: B 505 LYS cc_start: 0.9481 (mttt) cc_final: 0.9198 (mttt) REVERT: B 508 SER cc_start: 0.9520 (m) cc_final: 0.9310 (p) REVERT: B 588 HIS cc_start: 0.7421 (m-70) cc_final: 0.7208 (m-70) REVERT: B 599 ASN cc_start: 0.8947 (p0) cc_final: 0.8672 (m-40) REVERT: B 696 MET cc_start: 0.7870 (mtt) cc_final: 0.7622 (mtt) REVERT: B 794 TYR cc_start: 0.8293 (t80) cc_final: 0.7719 (t80) REVERT: B 797 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 854 CYS cc_start: 0.8507 (m) cc_final: 0.8301 (m) REVERT: B 859 ARG cc_start: 0.8623 (tpt170) cc_final: 0.8316 (tpt-90) REVERT: B 914 ILE cc_start: 0.8886 (mt) cc_final: 0.8630 (mt) REVERT: B 952 GLN cc_start: 0.8633 (mt0) cc_final: 0.8263 (tt0) REVERT: E 904 HIS cc_start: 0.9438 (t70) cc_final: 0.9182 (t70) REVERT: E 915 GLU cc_start: 0.9273 (pp20) cc_final: 0.9015 (pp20) REVERT: E 922 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8985 (mm-40) REVERT: G 223 HIS cc_start: 0.9406 (t70) cc_final: 0.9042 (t70) REVERT: G 261 LYS cc_start: 0.9592 (mtpt) cc_final: 0.9367 (mtmm) REVERT: G 265 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9129 (mt-10) REVERT: G 329 ILE cc_start: 0.8683 (mt) cc_final: 0.8450 (mp) REVERT: G 563 GLU cc_start: 0.6841 (tt0) cc_final: 0.6631 (tt0) REVERT: G 568 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7278 (mtt-85) REVERT: G 599 TYR cc_start: 0.8127 (m-80) cc_final: 0.7535 (m-80) REVERT: G 600 PHE cc_start: 0.8650 (p90) cc_final: 0.8395 (p90) REVERT: G 612 TRP cc_start: 0.7921 (m100) cc_final: 0.7464 (m100) REVERT: G 622 ILE cc_start: 0.9178 (tt) cc_final: 0.8573 (mm) REVERT: G 623 PHE cc_start: 0.8351 (m-80) cc_final: 0.6960 (m-10) REVERT: G 636 HIS cc_start: 0.7802 (t70) cc_final: 0.7477 (t-90) REVERT: G 640 ASN cc_start: 0.6903 (t0) cc_final: 0.6688 (t0) REVERT: G 654 TRP cc_start: 0.8182 (m100) cc_final: 0.6860 (m100) REVERT: G 696 TRP cc_start: 0.8727 (m100) cc_final: 0.6988 (m100) REVERT: G 774 MET cc_start: 0.6351 (mtt) cc_final: 0.6112 (mtp) REVERT: H 224 TYR cc_start: 0.8328 (t80) cc_final: 0.7859 (t80) REVERT: H 241 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8215 (tt0) REVERT: H 246 ILE cc_start: 0.8763 (mt) cc_final: 0.8482 (mm) REVERT: H 255 MET cc_start: 0.8450 (ppp) cc_final: 0.7869 (ppp) REVERT: H 256 LEU cc_start: 0.9121 (tp) cc_final: 0.8526 (tp) REVERT: H 279 LEU cc_start: 0.8923 (mt) cc_final: 0.8688 (mt) REVERT: H 282 LEU cc_start: 0.9550 (mt) cc_final: 0.9224 (mt) REVERT: H 285 MET cc_start: 0.8296 (ttt) cc_final: 0.7978 (mtp) REVERT: H 335 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8284 (ttp-110) REVERT: H 336 LEU cc_start: 0.9516 (mt) cc_final: 0.8788 (mm) REVERT: H 363 TRP cc_start: 0.8372 (t60) cc_final: 0.8106 (t60) REVERT: H 370 TRP cc_start: 0.7601 (m100) cc_final: 0.7293 (m100) REVERT: H 424 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8451 (tm-30) REVERT: H 427 LEU cc_start: 0.9421 (mt) cc_final: 0.9109 (mt) REVERT: H 428 LEU cc_start: 0.8522 (tp) cc_final: 0.8100 (mm) REVERT: H 435 LEU cc_start: 0.9092 (mt) cc_final: 0.8853 (pp) REVERT: I 49 GLU cc_start: 0.9061 (tp30) cc_final: 0.8800 (tp30) REVERT: I 219 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7861 (mt-10) REVERT: I 220 GLN cc_start: 0.8600 (pt0) cc_final: 0.8375 (tm-30) REVERT: I 226 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8002 (mm-30) REVERT: I 228 THR cc_start: 0.8938 (p) cc_final: 0.8661 (p) REVERT: I 229 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8759 (tp30) REVERT: I 309 MET cc_start: 0.9000 (mmm) cc_final: 0.8757 (mmp) REVERT: I 316 GLN cc_start: 0.7960 (mp10) cc_final: 0.7612 (mp10) REVERT: I 326 HIS cc_start: 0.8903 (m-70) cc_final: 0.8580 (m170) REVERT: I 332 PHE cc_start: 0.8832 (t80) cc_final: 0.8614 (t80) REVERT: I 342 LYS cc_start: 0.8604 (pttt) cc_final: 0.8235 (pttm) REVERT: K 64 MET cc_start: 0.8914 (mtp) cc_final: 0.8235 (mmp) REVERT: K 77 LYS cc_start: 0.8943 (tttt) cc_final: 0.8170 (tttt) REVERT: K 87 GLN cc_start: 0.8274 (mm-40) cc_final: 0.6653 (pp30) REVERT: K 99 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8717 (mt-10) REVERT: K 175 LEU cc_start: 0.8714 (tt) cc_final: 0.8122 (tt) REVERT: K 194 MET cc_start: 0.8321 (mmm) cc_final: 0.8087 (mmm) REVERT: K 196 LYS cc_start: 0.6463 (mppt) cc_final: 0.6003 (mppt) REVERT: K 201 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7353 (mm110) REVERT: M 19 MET cc_start: 0.7808 (mtp) cc_final: 0.6898 (ptp) REVERT: M 22 ILE cc_start: 0.8650 (mt) cc_final: 0.8284 (mt) REVERT: M 24 LYS cc_start: 0.8029 (mttt) cc_final: 0.7533 (tptp) REVERT: M 28 ILE cc_start: 0.8298 (tp) cc_final: 0.7856 (tp) REVERT: M 36 ILE cc_start: 0.8113 (mm) cc_final: 0.7420 (mm) REVERT: M 49 THR cc_start: 0.9327 (p) cc_final: 0.9084 (p) REVERT: M 50 ILE cc_start: 0.9509 (mt) cc_final: 0.9278 (mt) REVERT: M 53 ASP cc_start: 0.9436 (m-30) cc_final: 0.9131 (m-30) REVERT: M 78 ARG cc_start: 0.8467 (mtp180) cc_final: 0.8029 (mtp180) REVERT: O 169 ASP cc_start: 0.9062 (t0) cc_final: 0.8702 (t0) REVERT: O 173 HIS cc_start: 0.8779 (m90) cc_final: 0.8228 (m90) REVERT: O 198 GLU cc_start: 0.9090 (tt0) cc_final: 0.8819 (tt0) REVERT: R 76 LEU cc_start: 0.8593 (tp) cc_final: 0.8355 (tp) REVERT: R 93 GLU cc_start: 0.9307 (tp30) cc_final: 0.9032 (tp30) REVERT: R 100 CYS cc_start: 0.9547 (t) cc_final: 0.9309 (t) REVERT: R 114 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8348 (ttpt) REVERT: R 126 MET cc_start: 0.6332 (ttp) cc_final: 0.6089 (tmm) outliers start: 1 outliers final: 0 residues processed: 743 average time/residue: 0.1497 time to fit residues: 168.8933 Evaluate side-chains 566 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 72 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 170 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 85 optimal weight: 0.0070 chunk 213 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 454 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 946 ASN G 238 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 HIS H 316 GLN H 414 ASN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089771 restraints weight = 71698.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091986 restraints weight = 47058.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093942 restraints weight = 32039.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094439 restraints weight = 23724.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094392 restraints weight = 21787.505| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21657 Z= 0.147 Angle : 0.781 11.804 29446 Z= 0.404 Chirality : 0.046 0.336 3433 Planarity : 0.006 0.099 3795 Dihedral : 6.927 55.738 3033 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.32 % Favored : 88.64 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.13 % 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: -2.24 (0.16), residues: 2465 helix: -0.04 (0.14), residues: 1311 sheet: -1.55 (0.35), residues: 216 loop : -3.67 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 392 TYR 0.033 0.002 TYR B 846 PHE 0.042 0.002 PHE I 262 TRP 0.016 0.002 TRP B 443 HIS 0.015 0.001 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00311 (21654) covalent geometry : angle 0.78148 (29437) hydrogen bonds : bond 0.04351 ( 1124) hydrogen bonds : angle 5.50461 ( 3276) link_TRANS : bond 0.00027 ( 3) link_TRANS : angle 0.40221 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 731 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8571 (mt) cc_final: 0.8365 (mt) REVERT: B 44 SER cc_start: 0.6645 (t) cc_final: 0.5651 (t) REVERT: B 145 LYS cc_start: 0.8140 (mttt) cc_final: 0.7769 (mmtm) REVERT: B 148 ILE cc_start: 0.8791 (mp) cc_final: 0.8581 (mm) REVERT: B 153 ASP cc_start: 0.8049 (p0) cc_final: 0.7761 (t70) REVERT: B 180 CYS cc_start: 0.6250 (m) cc_final: 0.5189 (m) REVERT: B 206 PHE cc_start: 0.6565 (m-10) cc_final: 0.6360 (m-80) REVERT: B 270 LEU cc_start: 0.8517 (mm) cc_final: 0.8125 (mm) REVERT: B 278 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8303 (mttt) REVERT: B 323 SER cc_start: 0.7995 (t) cc_final: 0.7777 (t) REVERT: B 355 PHE cc_start: 0.8160 (m-10) cc_final: 0.7841 (m-10) REVERT: B 362 MET cc_start: 0.7063 (tpt) cc_final: 0.6730 (tpp) REVERT: B 468 PHE cc_start: 0.8962 (m-80) cc_final: 0.8465 (m-80) REVERT: B 505 LYS cc_start: 0.9468 (mttt) cc_final: 0.9118 (mttt) REVERT: B 753 MET cc_start: 0.8025 (ppp) cc_final: 0.7640 (ppp) REVERT: B 776 LEU cc_start: 0.8606 (mt) cc_final: 0.8378 (mt) REVERT: B 797 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 839 MET cc_start: 0.6127 (ttt) cc_final: 0.5825 (ttt) REVERT: B 840 GLU cc_start: 0.7992 (tp30) cc_final: 0.7791 (mm-30) REVERT: B 913 MET cc_start: 0.9001 (mtt) cc_final: 0.8749 (mtp) REVERT: B 914 ILE cc_start: 0.8937 (mt) cc_final: 0.8668 (mt) REVERT: B 949 LEU cc_start: 0.8636 (mm) cc_final: 0.8003 (mm) REVERT: E 889 HIS cc_start: 0.8062 (m-70) cc_final: 0.7770 (m-70) REVERT: E 915 GLU cc_start: 0.9444 (pp20) cc_final: 0.8814 (pp20) REVERT: E 922 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9026 (mm-40) REVERT: G 213 MET cc_start: 0.9342 (ptp) cc_final: 0.9030 (ptt) REVERT: G 214 TYR cc_start: 0.8315 (m-10) cc_final: 0.7950 (m-80) REVERT: G 261 LYS cc_start: 0.9581 (mtpt) cc_final: 0.9308 (mtmm) REVERT: G 265 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8939 (mt-10) REVERT: G 342 PHE cc_start: 0.8468 (m-10) cc_final: 0.7869 (m-10) REVERT: G 477 ASP cc_start: 0.6408 (t0) cc_final: 0.6070 (t0) REVERT: G 559 LEU cc_start: 0.8425 (tp) cc_final: 0.7948 (tp) REVERT: G 568 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7143 (mtt-85) REVERT: G 599 TYR cc_start: 0.8026 (m-80) cc_final: 0.7449 (m-80) REVERT: G 612 TRP cc_start: 0.7847 (m100) cc_final: 0.7553 (m100) REVERT: G 622 ILE cc_start: 0.9146 (tt) cc_final: 0.8499 (mm) REVERT: G 623 PHE cc_start: 0.8267 (m-80) cc_final: 0.7061 (m-10) REVERT: G 636 HIS cc_start: 0.7619 (t70) cc_final: 0.7264 (t-90) REVERT: G 654 TRP cc_start: 0.8070 (m100) cc_final: 0.6681 (m100) REVERT: G 696 TRP cc_start: 0.8369 (m100) cc_final: 0.7106 (m100) REVERT: G 774 MET cc_start: 0.6370 (mtt) cc_final: 0.6128 (mtp) REVERT: H 224 TYR cc_start: 0.8370 (t80) cc_final: 0.7908 (t80) REVERT: H 265 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8018 (mm-30) REVERT: H 336 LEU cc_start: 0.9535 (mt) cc_final: 0.8600 (mm) REVERT: H 398 GLN cc_start: 0.8899 (mp10) cc_final: 0.8662 (mp10) REVERT: H 435 LEU cc_start: 0.9020 (mt) cc_final: 0.8802 (pp) REVERT: I 49 GLU cc_start: 0.9079 (tp30) cc_final: 0.8597 (tp30) REVERT: I 64 GLN cc_start: 0.6078 (pm20) cc_final: 0.5365 (mm-40) REVERT: I 219 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7754 (mt-10) REVERT: I 226 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8057 (mm-30) REVERT: I 228 THR cc_start: 0.8750 (p) cc_final: 0.8519 (p) REVERT: I 342 LYS cc_start: 0.8528 (pttt) cc_final: 0.8141 (pttm) REVERT: K 64 MET cc_start: 0.8916 (mtp) cc_final: 0.8233 (mmp) REVERT: K 77 LYS cc_start: 0.8784 (tttt) cc_final: 0.8200 (tttt) REVERT: K 87 GLN cc_start: 0.8183 (mm-40) cc_final: 0.6469 (pp30) REVERT: K 99 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8593 (mt-10) REVERT: K 176 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7251 (mmt90) REVERT: K 194 MET cc_start: 0.8294 (mmm) cc_final: 0.8037 (mmm) REVERT: K 221 ILE cc_start: 0.7977 (tt) cc_final: 0.7476 (mt) REVERT: M 24 LYS cc_start: 0.8149 (mttt) cc_final: 0.7649 (tptp) REVERT: M 28 ILE cc_start: 0.8209 (tp) cc_final: 0.7812 (tp) REVERT: O 169 ASP cc_start: 0.9053 (t0) cc_final: 0.8610 (t0) REVERT: O 173 HIS cc_start: 0.8724 (m90) cc_final: 0.8250 (m90) REVERT: O 198 GLU cc_start: 0.9041 (tt0) cc_final: 0.8772 (tt0) REVERT: R 58 LEU cc_start: 0.8983 (tp) cc_final: 0.8680 (tp) REVERT: R 76 LEU cc_start: 0.8334 (tp) cc_final: 0.8114 (tp) REVERT: R 93 GLU cc_start: 0.9243 (tp30) cc_final: 0.8965 (tp30) REVERT: R 114 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8254 (tttt) outliers start: 1 outliers final: 0 residues processed: 732 average time/residue: 0.1446 time to fit residues: 161.1442 Evaluate side-chains 548 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 228 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 147 HIS B 235 HIS B 331 HIS B 393 HIS ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN G 238 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN O 122 GLN R 101 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.109642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088010 restraints weight = 72817.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090360 restraints weight = 48253.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091446 restraints weight = 33017.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092104 restraints weight = 27169.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092253 restraints weight = 24396.679| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21657 Z= 0.172 Angle : 0.797 10.857 29446 Z= 0.413 Chirality : 0.047 0.281 3433 Planarity : 0.006 0.102 3795 Dihedral : 6.759 55.313 3033 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.62 % Favored : 87.34 % Rotamer: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.13 % 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: -2.00 (0.17), residues: 2465 helix: 0.14 (0.14), residues: 1315 sheet: -1.31 (0.35), residues: 217 loop : -3.58 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 392 TYR 0.037 0.002 TYR B 846 PHE 0.047 0.002 PHE I 262 TRP 0.029 0.002 TRP B 443 HIS 0.014 0.001 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00372 (21654) covalent geometry : angle 0.79681 (29437) hydrogen bonds : bond 0.04372 ( 1124) hydrogen bonds : angle 5.48158 ( 3276) link_TRANS : bond 0.00129 ( 3) link_TRANS : angle 0.46132 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 684 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8543 (mt) cc_final: 0.8291 (mt) REVERT: B 42 ARG cc_start: 0.7424 (tmt170) cc_final: 0.7005 (tpt90) REVERT: B 44 SER cc_start: 0.7536 (t) cc_final: 0.6720 (t) REVERT: B 118 ASP cc_start: 0.9133 (m-30) cc_final: 0.8911 (m-30) REVERT: B 145 LYS cc_start: 0.8196 (mttt) cc_final: 0.7787 (mmtm) REVERT: B 270 LEU cc_start: 0.8629 (mm) cc_final: 0.8196 (mm) REVERT: B 323 SER cc_start: 0.7976 (t) cc_final: 0.7682 (t) REVERT: B 362 MET cc_start: 0.7133 (tpt) cc_final: 0.6763 (tpp) REVERT: B 364 TRP cc_start: 0.8311 (t-100) cc_final: 0.7468 (t-100) REVERT: B 392 ARG cc_start: 0.8741 (mpp-170) cc_final: 0.8513 (mtm110) REVERT: B 452 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7628 (ttmt) REVERT: B 468 PHE cc_start: 0.9022 (m-80) cc_final: 0.8560 (m-80) REVERT: B 469 MET cc_start: 0.8954 (ptt) cc_final: 0.8712 (ptt) REVERT: B 505 LYS cc_start: 0.9447 (mttt) cc_final: 0.9156 (mttt) REVERT: B 508 SER cc_start: 0.9493 (m) cc_final: 0.9247 (p) REVERT: B 531 PHE cc_start: 0.8614 (m-80) cc_final: 0.8203 (m-80) REVERT: B 588 HIS cc_start: 0.7676 (m-70) cc_final: 0.7464 (m-70) REVERT: B 614 MET cc_start: 0.7329 (mmm) cc_final: 0.6896 (mmm) REVERT: B 726 MET cc_start: 0.8426 (mtm) cc_final: 0.8024 (mpp) REVERT: B 753 MET cc_start: 0.8155 (ppp) cc_final: 0.7638 (ppp) REVERT: B 776 LEU cc_start: 0.8686 (mt) cc_final: 0.8453 (mt) REVERT: B 797 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 837 LEU cc_start: 0.8755 (mt) cc_final: 0.8495 (mt) REVERT: B 840 GLU cc_start: 0.8295 (tp30) cc_final: 0.8028 (mm-30) REVERT: B 850 ILE cc_start: 0.9067 (mp) cc_final: 0.8663 (mp) REVERT: B 854 CYS cc_start: 0.8112 (m) cc_final: 0.7039 (t) REVERT: B 899 LYS cc_start: 0.9095 (tttt) cc_final: 0.8665 (pttm) REVERT: B 913 MET cc_start: 0.9154 (mtt) cc_final: 0.8847 (mtt) REVERT: B 914 ILE cc_start: 0.8818 (mt) cc_final: 0.8416 (mm) REVERT: B 955 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8774 (mttt) REVERT: B 964 ASP cc_start: 0.6541 (m-30) cc_final: 0.4547 (m-30) REVERT: E 889 HIS cc_start: 0.7975 (m-70) cc_final: 0.7583 (m-70) REVERT: E 904 HIS cc_start: 0.8990 (m90) cc_final: 0.8394 (m90) REVERT: E 915 GLU cc_start: 0.9360 (pp20) cc_final: 0.9008 (pp20) REVERT: E 922 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9083 (mm-40) REVERT: G 261 LYS cc_start: 0.9592 (mtpt) cc_final: 0.9286 (ptpp) REVERT: G 265 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8956 (mt-10) REVERT: G 342 PHE cc_start: 0.8343 (m-10) cc_final: 0.7898 (m-10) REVERT: G 477 ASP cc_start: 0.6491 (t0) cc_final: 0.6212 (t0) REVERT: G 559 LEU cc_start: 0.8566 (tp) cc_final: 0.8350 (tp) REVERT: G 568 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7149 (mtt-85) REVERT: G 599 TYR cc_start: 0.8119 (m-80) cc_final: 0.7462 (m-80) REVERT: G 600 PHE cc_start: 0.8752 (p90) cc_final: 0.8482 (p90) REVERT: G 612 TRP cc_start: 0.7929 (m100) cc_final: 0.7345 (m100) REVERT: G 622 ILE cc_start: 0.9214 (tt) cc_final: 0.8814 (mm) REVERT: G 623 PHE cc_start: 0.8310 (m-80) cc_final: 0.7042 (m-10) REVERT: G 654 TRP cc_start: 0.8547 (m100) cc_final: 0.7011 (m100) REVERT: G 684 LEU cc_start: 0.8074 (tp) cc_final: 0.7864 (tp) REVERT: G 696 TRP cc_start: 0.8646 (m100) cc_final: 0.6829 (m100) REVERT: G 766 GLN cc_start: 0.5930 (mt0) cc_final: 0.4947 (pm20) REVERT: G 780 VAL cc_start: 0.8061 (t) cc_final: 0.7464 (t) REVERT: H 219 GLU cc_start: 0.6576 (tt0) cc_final: 0.6112 (tt0) REVERT: H 224 TYR cc_start: 0.8429 (t80) cc_final: 0.8041 (t80) REVERT: H 260 SER cc_start: 0.9051 (t) cc_final: 0.8759 (t) REVERT: H 335 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8479 (ttp-110) REVERT: H 336 LEU cc_start: 0.9540 (mt) cc_final: 0.8952 (tt) REVERT: H 398 GLN cc_start: 0.8944 (mp10) cc_final: 0.8392 (mp10) REVERT: H 401 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7742 (mm-30) REVERT: H 404 ARG cc_start: 0.8058 (mtt90) cc_final: 0.6711 (mtt-85) REVERT: H 435 LEU cc_start: 0.9023 (mt) cc_final: 0.8799 (pp) REVERT: I 49 GLU cc_start: 0.9103 (tp30) cc_final: 0.8836 (tp30) REVERT: I 219 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7809 (mt-10) REVERT: I 228 THR cc_start: 0.8909 (p) cc_final: 0.8670 (p) REVERT: I 289 LEU cc_start: 0.9379 (mt) cc_final: 0.9098 (mt) REVERT: I 326 HIS cc_start: 0.8746 (m170) cc_final: 0.8442 (m170) REVERT: I 342 LYS cc_start: 0.8501 (pttt) cc_final: 0.8119 (pttm) REVERT: K 60 THR cc_start: 0.9210 (m) cc_final: 0.8915 (p) REVERT: K 64 MET cc_start: 0.8897 (mtp) cc_final: 0.8277 (mmp) REVERT: K 77 LYS cc_start: 0.8702 (tttt) cc_final: 0.8307 (tppt) REVERT: K 81 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7924 (mm-30) REVERT: K 87 GLN cc_start: 0.8186 (mm-40) cc_final: 0.6448 (pp30) REVERT: K 99 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8696 (mt-10) REVERT: K 178 LYS cc_start: 0.8360 (pptt) cc_final: 0.7355 (pptt) REVERT: K 201 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7689 (mm110) REVERT: M 21 GLN cc_start: 0.8738 (tp40) cc_final: 0.8331 (tp40) REVERT: M 22 ILE cc_start: 0.8522 (mt) cc_final: 0.8164 (mt) REVERT: M 24 LYS cc_start: 0.8270 (mttt) cc_final: 0.7893 (tptp) REVERT: M 25 ASP cc_start: 0.8034 (m-30) cc_final: 0.7606 (m-30) REVERT: M 28 ILE cc_start: 0.8296 (tp) cc_final: 0.7831 (tp) REVERT: M 57 TYR cc_start: 0.9356 (m-10) cc_final: 0.9091 (m-10) REVERT: O 169 ASP cc_start: 0.9059 (t0) cc_final: 0.8581 (t0) REVERT: O 173 HIS cc_start: 0.8814 (m90) cc_final: 0.8316 (m90) REVERT: O 198 GLU cc_start: 0.9038 (tt0) cc_final: 0.8768 (tt0) REVERT: R 76 LEU cc_start: 0.8332 (tp) cc_final: 0.8105 (tp) REVERT: R 85 LEU cc_start: 0.9396 (mt) cc_final: 0.9192 (mt) REVERT: R 93 GLU cc_start: 0.9227 (tp30) cc_final: 0.8941 (tp30) REVERT: R 111 LEU cc_start: 0.9106 (tt) cc_final: 0.8367 (mm) REVERT: R 114 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8814 (tttt) REVERT: R 126 MET cc_start: 0.6579 (tmm) cc_final: 0.5920 (tmm) outliers start: 1 outliers final: 0 residues processed: 684 average time/residue: 0.1394 time to fit residues: 146.2523 Evaluate side-chains 536 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 191 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 98 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 217 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN R 101 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.109057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086420 restraints weight = 73056.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088701 restraints weight = 45550.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090245 restraints weight = 32601.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091300 restraints weight = 25752.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092003 restraints weight = 21839.877| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21657 Z= 0.190 Angle : 0.806 12.260 29446 Z= 0.419 Chirality : 0.047 0.340 3433 Planarity : 0.006 0.103 3795 Dihedral : 6.704 56.094 3033 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.17 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.13 % 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: -1.91 (0.17), residues: 2465 helix: 0.22 (0.14), residues: 1313 sheet: -1.32 (0.35), residues: 218 loop : -3.54 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 678 TYR 0.045 0.002 TYR B 794 PHE 0.046 0.002 PHE I 262 TRP 0.020 0.002 TRP B 443 HIS 0.019 0.002 HIS G 782 Details of bonding type rmsd covalent geometry : bond 0.00411 (21654) covalent geometry : angle 0.80635 (29437) hydrogen bonds : bond 0.04307 ( 1124) hydrogen bonds : angle 5.51740 ( 3276) link_TRANS : bond 0.00140 ( 3) link_TRANS : angle 0.52753 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8452 (mt) cc_final: 0.8229 (mt) REVERT: B 44 SER cc_start: 0.6974 (t) cc_final: 0.5411 (t) REVERT: B 145 LYS cc_start: 0.8251 (mttt) cc_final: 0.7831 (mmtm) REVERT: B 180 CYS cc_start: 0.6175 (m) cc_final: 0.5868 (m) REVERT: B 270 LEU cc_start: 0.8581 (mm) cc_final: 0.8136 (mm) REVERT: B 355 PHE cc_start: 0.8202 (m-10) cc_final: 0.7824 (m-10) REVERT: B 362 MET cc_start: 0.6951 (tpt) cc_final: 0.6574 (tpp) REVERT: B 452 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7550 (ttmt) REVERT: B 468 PHE cc_start: 0.8938 (m-80) cc_final: 0.8570 (m-80) REVERT: B 469 MET cc_start: 0.8891 (ptt) cc_final: 0.8691 (ptt) REVERT: B 505 LYS cc_start: 0.9450 (mttt) cc_final: 0.9166 (mttt) REVERT: B 508 SER cc_start: 0.9543 (m) cc_final: 0.9309 (p) REVERT: B 531 PHE cc_start: 0.8745 (m-80) cc_final: 0.8291 (m-80) REVERT: B 588 HIS cc_start: 0.7709 (m-70) cc_final: 0.7201 (m-70) REVERT: B 614 MET cc_start: 0.7275 (mmm) cc_final: 0.6860 (mmm) REVERT: B 753 MET cc_start: 0.8214 (ppp) cc_final: 0.7899 (ppp) REVERT: B 797 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 823 ASN cc_start: 0.8007 (p0) cc_final: 0.6974 (p0) REVERT: B 840 GLU cc_start: 0.8342 (tp30) cc_final: 0.7913 (mm-30) REVERT: B 914 ILE cc_start: 0.8754 (mt) cc_final: 0.8474 (mt) REVERT: B 964 ASP cc_start: 0.6704 (m-30) cc_final: 0.4748 (m-30) REVERT: E 870 GLU cc_start: 0.7919 (pp20) cc_final: 0.7688 (pp20) REVERT: E 885 ILE cc_start: 0.6872 (mp) cc_final: 0.6519 (mm) REVERT: E 889 HIS cc_start: 0.8119 (m-70) cc_final: 0.7710 (m-70) REVERT: E 904 HIS cc_start: 0.9102 (m90) cc_final: 0.8532 (m90) REVERT: E 915 GLU cc_start: 0.9349 (pp20) cc_final: 0.8981 (pp20) REVERT: E 922 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9096 (mm-40) REVERT: G 214 TYR cc_start: 0.8661 (m-80) cc_final: 0.8427 (m-80) REVERT: G 246 HIS cc_start: 0.8690 (p-80) cc_final: 0.7920 (p90) REVERT: G 261 LYS cc_start: 0.9592 (mtpt) cc_final: 0.9328 (mtmm) REVERT: G 265 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8957 (mt-10) REVERT: G 342 PHE cc_start: 0.8039 (m-10) cc_final: 0.7603 (m-10) REVERT: G 477 ASP cc_start: 0.6422 (t0) cc_final: 0.6189 (t0) REVERT: G 559 LEU cc_start: 0.8331 (tp) cc_final: 0.8068 (tp) REVERT: G 568 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7246 (mtt-85) REVERT: G 599 TYR cc_start: 0.8078 (m-80) cc_final: 0.7447 (m-80) REVERT: G 600 PHE cc_start: 0.8814 (p90) cc_final: 0.8571 (p90) REVERT: G 612 TRP cc_start: 0.7811 (m100) cc_final: 0.7153 (m100) REVERT: G 623 PHE cc_start: 0.8367 (m-10) cc_final: 0.7798 (m-10) REVERT: G 640 ASN cc_start: 0.7504 (t0) cc_final: 0.7067 (t0) REVERT: G 684 LEU cc_start: 0.8203 (tp) cc_final: 0.7889 (tp) REVERT: H 224 TYR cc_start: 0.8575 (t80) cc_final: 0.8163 (t80) REVERT: H 282 LEU cc_start: 0.9643 (mt) cc_final: 0.9430 (mt) REVERT: H 335 ARG cc_start: 0.8844 (ttp-110) cc_final: 0.8478 (ttp-110) REVERT: H 336 LEU cc_start: 0.9574 (mt) cc_final: 0.8918 (tt) REVERT: H 398 GLN cc_start: 0.8845 (mp10) cc_final: 0.8619 (mp10) REVERT: H 404 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7862 (ptp-170) REVERT: H 435 LEU cc_start: 0.9070 (mt) cc_final: 0.8843 (pp) REVERT: I 49 GLU cc_start: 0.9163 (tp30) cc_final: 0.8861 (tp30) REVERT: I 219 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7902 (mt-10) REVERT: I 326 HIS cc_start: 0.8871 (m170) cc_final: 0.8640 (m170) REVERT: I 342 LYS cc_start: 0.8449 (pttt) cc_final: 0.8011 (pttm) REVERT: K 59 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8661 (mm-30) REVERT: K 60 THR cc_start: 0.9245 (m) cc_final: 0.8945 (p) REVERT: K 64 MET cc_start: 0.8863 (mtp) cc_final: 0.8268 (mmp) REVERT: K 77 LYS cc_start: 0.8672 (tttt) cc_final: 0.8165 (tppt) REVERT: K 81 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8274 (mm-30) REVERT: K 87 GLN cc_start: 0.8225 (mm-40) cc_final: 0.6448 (pp30) REVERT: K 99 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8587 (mt-10) REVERT: K 201 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7773 (mm110) REVERT: K 221 ILE cc_start: 0.8000 (tt) cc_final: 0.7668 (mt) REVERT: M 21 GLN cc_start: 0.8662 (tp40) cc_final: 0.8097 (tp40) REVERT: M 22 ILE cc_start: 0.8560 (mt) cc_final: 0.8144 (mt) REVERT: M 24 LYS cc_start: 0.8313 (mttt) cc_final: 0.7898 (tptp) REVERT: M 25 ASP cc_start: 0.7999 (m-30) cc_final: 0.7482 (m-30) REVERT: M 57 TYR cc_start: 0.9360 (m-10) cc_final: 0.9066 (m-10) REVERT: M 78 ARG cc_start: 0.8659 (mtp180) cc_final: 0.7991 (mmm-85) REVERT: O 169 ASP cc_start: 0.9004 (t0) cc_final: 0.8533 (t0) REVERT: O 173 HIS cc_start: 0.8815 (m90) cc_final: 0.8379 (m90) REVERT: O 198 GLU cc_start: 0.9047 (tt0) cc_final: 0.8835 (tt0) REVERT: R 76 LEU cc_start: 0.8316 (tp) cc_final: 0.8099 (tp) REVERT: R 93 GLU cc_start: 0.9310 (tp30) cc_final: 0.9039 (tp30) REVERT: R 111 LEU cc_start: 0.9165 (tt) cc_final: 0.8456 (mm) REVERT: R 114 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8556 (tttt) REVERT: R 119 HIS cc_start: 0.8856 (t-90) cc_final: 0.8645 (t-90) REVERT: R 124 TRP cc_start: 0.6862 (m100) cc_final: 0.6552 (m100) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.1363 time to fit residues: 141.0964 Evaluate side-chains 532 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 263 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 161 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 235 HIS B 272 GLN B 331 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 848 HIS ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 HIS ** H 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084773 restraints weight = 73815.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087444 restraints weight = 47461.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089442 restraints weight = 30820.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089891 restraints weight = 23017.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089879 restraints weight = 20889.575| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21657 Z= 0.232 Angle : 0.862 11.002 29446 Z= 0.447 Chirality : 0.049 0.346 3433 Planarity : 0.006 0.102 3795 Dihedral : 6.834 58.286 3033 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.02 % Favored : 86.94 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.08 % 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: -1.94 (0.17), residues: 2465 helix: 0.19 (0.14), residues: 1311 sheet: -1.36 (0.35), residues: 220 loop : -3.51 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 678 TYR 0.026 0.002 TYR M 31 PHE 0.047 0.002 PHE I 262 TRP 0.035 0.003 TRP G 696 HIS 0.022 0.002 HIS G 782 Details of bonding type rmsd covalent geometry : bond 0.00498 (21654) covalent geometry : angle 0.86174 (29437) hydrogen bonds : bond 0.04587 ( 1124) hydrogen bonds : angle 5.60420 ( 3276) link_TRANS : bond 0.00248 ( 3) link_TRANS : angle 0.62352 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 SER cc_start: 0.7307 (t) cc_final: 0.6064 (t) REVERT: B 129 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7732 (tppt) REVERT: B 145 LYS cc_start: 0.8282 (mttt) cc_final: 0.7948 (mmtm) REVERT: B 270 LEU cc_start: 0.8540 (mm) cc_final: 0.8127 (mm) REVERT: B 290 PHE cc_start: 0.8440 (t80) cc_final: 0.7833 (t80) REVERT: B 299 TYR cc_start: 0.8275 (t80) cc_final: 0.7916 (t80) REVERT: B 364 TRP cc_start: 0.8446 (t-100) cc_final: 0.7604 (t-100) REVERT: B 452 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7641 (ttmt) REVERT: B 464 ILE cc_start: 0.8872 (mm) cc_final: 0.8584 (mm) REVERT: B 468 PHE cc_start: 0.8909 (m-80) cc_final: 0.8534 (m-80) REVERT: B 469 MET cc_start: 0.8946 (ptt) cc_final: 0.8718 (ptt) REVERT: B 505 LYS cc_start: 0.9449 (mttt) cc_final: 0.9173 (mttt) REVERT: B 508 SER cc_start: 0.9562 (m) cc_final: 0.9312 (p) REVERT: B 531 PHE cc_start: 0.8695 (m-80) cc_final: 0.8210 (m-80) REVERT: B 588 HIS cc_start: 0.7447 (m-70) cc_final: 0.7220 (m-70) REVERT: B 614 MET cc_start: 0.7458 (mmm) cc_final: 0.7042 (mmm) REVERT: B 726 MET cc_start: 0.8452 (mtm) cc_final: 0.8214 (mtp) REVERT: B 774 PHE cc_start: 0.8862 (t80) cc_final: 0.8622 (t80) REVERT: B 797 GLU cc_start: 0.8359 (mm-30) cc_final: 0.6969 (tp30) REVERT: B 837 LEU cc_start: 0.8832 (mt) cc_final: 0.8594 (mt) REVERT: B 850 ILE cc_start: 0.9059 (mp) cc_final: 0.8846 (mp) REVERT: B 854 CYS cc_start: 0.8524 (m) cc_final: 0.7681 (t) REVERT: B 955 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8964 (mttt) REVERT: E 885 ILE cc_start: 0.6960 (mp) cc_final: 0.6439 (mp) REVERT: E 889 HIS cc_start: 0.8153 (m-70) cc_final: 0.7727 (m-70) REVERT: E 904 HIS cc_start: 0.9165 (m90) cc_final: 0.8561 (m90) REVERT: E 915 GLU cc_start: 0.9376 (pp20) cc_final: 0.9161 (pp20) REVERT: E 919 GLU cc_start: 0.9028 (mp0) cc_final: 0.8768 (mp0) REVERT: E 922 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9166 (mm-40) REVERT: G 214 TYR cc_start: 0.8758 (m-80) cc_final: 0.8482 (m-80) REVERT: G 261 LYS cc_start: 0.9587 (mtpt) cc_final: 0.9300 (ptpp) REVERT: G 265 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8972 (mt-10) REVERT: G 292 LYS cc_start: 0.8949 (mttt) cc_final: 0.8442 (mmtt) REVERT: G 342 PHE cc_start: 0.8246 (m-10) cc_final: 0.8017 (m-10) REVERT: G 559 LEU cc_start: 0.8555 (tp) cc_final: 0.8341 (tp) REVERT: G 568 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7394 (mtt-85) REVERT: G 590 ASP cc_start: 0.7668 (t0) cc_final: 0.7222 (p0) REVERT: G 591 THR cc_start: 0.9015 (p) cc_final: 0.8730 (p) REVERT: G 599 TYR cc_start: 0.8097 (m-80) cc_final: 0.7477 (m-80) REVERT: G 600 PHE cc_start: 0.8875 (p90) cc_final: 0.8639 (p90) REVERT: G 612 TRP cc_start: 0.7854 (m100) cc_final: 0.7063 (m100) REVERT: G 633 THR cc_start: 0.7370 (p) cc_final: 0.5716 (p) REVERT: G 640 ASN cc_start: 0.7435 (t0) cc_final: 0.6990 (t0) REVERT: G 686 THR cc_start: 0.8457 (p) cc_final: 0.8093 (p) REVERT: H 224 TYR cc_start: 0.8634 (t80) cc_final: 0.8120 (t80) REVERT: H 241 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8417 (tt0) REVERT: H 259 PHE cc_start: 0.8116 (t80) cc_final: 0.7864 (t80) REVERT: H 260 SER cc_start: 0.9148 (t) cc_final: 0.8886 (t) REVERT: H 326 HIS cc_start: 0.8648 (m-70) cc_final: 0.7433 (m-70) REVERT: H 335 ARG cc_start: 0.8893 (ttp-110) cc_final: 0.8506 (ttp-110) REVERT: H 336 LEU cc_start: 0.9554 (mt) cc_final: 0.8930 (tt) REVERT: H 398 GLN cc_start: 0.8867 (mp10) cc_final: 0.8639 (mp10) REVERT: H 435 LEU cc_start: 0.9127 (mt) cc_final: 0.8845 (pp) REVERT: I 49 GLU cc_start: 0.9162 (tp30) cc_final: 0.8930 (tp30) REVERT: I 219 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7744 (mt-10) REVERT: I 226 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8047 (mm-30) REVERT: I 228 THR cc_start: 0.8955 (p) cc_final: 0.8738 (p) REVERT: I 289 LEU cc_start: 0.9249 (mt) cc_final: 0.8950 (mt) REVERT: I 326 HIS cc_start: 0.8937 (m170) cc_final: 0.8320 (m170) REVERT: I 336 LEU cc_start: 0.9427 (mt) cc_final: 0.9221 (mt) REVERT: I 374 TYR cc_start: 0.8288 (t80) cc_final: 0.8077 (t80) REVERT: K 64 MET cc_start: 0.8851 (mtp) cc_final: 0.8373 (mmp) REVERT: K 77 LYS cc_start: 0.8661 (tttt) cc_final: 0.8172 (tppt) REVERT: K 81 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8516 (mm-30) REVERT: K 87 GLN cc_start: 0.8059 (mm-40) cc_final: 0.6461 (pp30) REVERT: K 99 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8574 (mt-10) REVERT: M 18 MET cc_start: 0.8933 (ppp) cc_final: 0.8626 (ppp) REVERT: M 21 GLN cc_start: 0.8492 (tp40) cc_final: 0.7795 (tp40) REVERT: M 24 LYS cc_start: 0.8479 (mttt) cc_final: 0.8011 (tptp) REVERT: M 25 ASP cc_start: 0.7982 (m-30) cc_final: 0.7292 (m-30) REVERT: M 26 MET cc_start: 0.7234 (mmp) cc_final: 0.6924 (mmm) REVERT: M 49 THR cc_start: 0.9323 (p) cc_final: 0.8947 (p) REVERT: M 50 ILE cc_start: 0.9501 (mt) cc_final: 0.9218 (mt) REVERT: M 53 ASP cc_start: 0.9510 (m-30) cc_final: 0.8297 (m-30) REVERT: M 57 TYR cc_start: 0.9396 (m-10) cc_final: 0.9113 (m-10) REVERT: M 78 ARG cc_start: 0.8729 (mtp180) cc_final: 0.7979 (mmm-85) REVERT: O 169 ASP cc_start: 0.9078 (t0) cc_final: 0.8575 (t0) REVERT: O 173 HIS cc_start: 0.8751 (m90) cc_final: 0.8395 (m90) REVERT: O 198 GLU cc_start: 0.9087 (tt0) cc_final: 0.8772 (tt0) REVERT: R 76 LEU cc_start: 0.8383 (tp) cc_final: 0.8128 (tp) REVERT: R 93 GLU cc_start: 0.9307 (tp30) cc_final: 0.9045 (tp30) REVERT: R 114 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8523 (tttt) REVERT: R 124 TRP cc_start: 0.7013 (m100) cc_final: 0.6774 (m-10) outliers start: 0 outliers final: 0 residues processed: 644 average time/residue: 0.1382 time to fit residues: 138.1084 Evaluate side-chains 532 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 210 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 251 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 235 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 848 HIS G 238 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.108740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086390 restraints weight = 73055.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088972 restraints weight = 47110.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.090761 restraints weight = 31238.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091156 restraints weight = 24445.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091269 restraints weight = 21891.444| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21657 Z= 0.182 Angle : 0.814 10.818 29446 Z= 0.425 Chirality : 0.049 0.354 3433 Planarity : 0.006 0.101 3795 Dihedral : 6.707 59.604 3033 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.05 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.08 % 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: -1.80 (0.17), residues: 2465 helix: 0.35 (0.14), residues: 1300 sheet: -1.22 (0.36), residues: 214 loop : -3.51 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 46 TYR 0.030 0.002 TYR B 846 PHE 0.040 0.002 PHE I 262 TRP 0.055 0.003 TRP G 696 HIS 0.016 0.002 HIS G 782 Details of bonding type rmsd covalent geometry : bond 0.00396 (21654) covalent geometry : angle 0.81432 (29437) hydrogen bonds : bond 0.04364 ( 1124) hydrogen bonds : angle 5.49379 ( 3276) link_TRANS : bond 0.00143 ( 3) link_TRANS : angle 0.55547 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8622 (mt) cc_final: 0.8339 (mt) REVERT: B 44 SER cc_start: 0.7241 (t) cc_final: 0.6209 (t) REVERT: B 145 LYS cc_start: 0.8358 (mttt) cc_final: 0.8033 (mmtm) REVERT: B 170 MET cc_start: 0.8187 (mtp) cc_final: 0.7417 (mmm) REVERT: B 270 LEU cc_start: 0.8331 (mm) cc_final: 0.7951 (mm) REVERT: B 289 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 299 TYR cc_start: 0.8179 (t80) cc_final: 0.7902 (t80) REVERT: B 362 MET cc_start: 0.6927 (tpt) cc_final: 0.6583 (tpp) REVERT: B 364 TRP cc_start: 0.8427 (t-100) cc_final: 0.7615 (t-100) REVERT: B 444 GLU cc_start: 0.8356 (mp0) cc_final: 0.8148 (mt-10) REVERT: B 452 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7605 (ttmt) REVERT: B 464 ILE cc_start: 0.8799 (mm) cc_final: 0.8551 (mm) REVERT: B 468 PHE cc_start: 0.8940 (m-80) cc_final: 0.8463 (m-80) REVERT: B 469 MET cc_start: 0.8938 (ptt) cc_final: 0.8680 (ptt) REVERT: B 505 LYS cc_start: 0.9442 (mttt) cc_final: 0.9173 (mttt) REVERT: B 508 SER cc_start: 0.9534 (m) cc_final: 0.9298 (p) REVERT: B 531 PHE cc_start: 0.8846 (m-80) cc_final: 0.8553 (m-80) REVERT: B 588 HIS cc_start: 0.7557 (m-70) cc_final: 0.7287 (m-70) REVERT: B 614 MET cc_start: 0.7554 (mmm) cc_final: 0.7120 (mmm) REVERT: B 707 ASN cc_start: 0.9278 (m-40) cc_final: 0.8870 (m-40) REVERT: B 726 MET cc_start: 0.8395 (mtm) cc_final: 0.7867 (mtp) REVERT: B 797 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 854 CYS cc_start: 0.8360 (m) cc_final: 0.7591 (t) REVERT: B 899 LYS cc_start: 0.9255 (tttt) cc_final: 0.8714 (ptmt) REVERT: B 914 ILE cc_start: 0.8865 (mt) cc_final: 0.8614 (mm) REVERT: E 885 ILE cc_start: 0.6907 (mp) cc_final: 0.6430 (mp) REVERT: E 889 HIS cc_start: 0.8116 (m-70) cc_final: 0.7702 (m-70) REVERT: E 904 HIS cc_start: 0.9175 (m90) cc_final: 0.8524 (m90) REVERT: E 915 GLU cc_start: 0.9410 (pp20) cc_final: 0.9192 (pp20) REVERT: E 919 GLU cc_start: 0.9082 (mp0) cc_final: 0.8739 (mp0) REVERT: E 922 GLN cc_start: 0.9484 (mm-40) cc_final: 0.9199 (mm-40) REVERT: G 214 TYR cc_start: 0.8754 (m-80) cc_final: 0.8514 (m-80) REVERT: G 216 GLU cc_start: 0.9479 (mp0) cc_final: 0.9205 (mp0) REVERT: G 223 HIS cc_start: 0.9442 (t70) cc_final: 0.9019 (t70) REVERT: G 261 LYS cc_start: 0.9579 (mtpt) cc_final: 0.9292 (ptpp) REVERT: G 265 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9010 (mt-10) REVERT: G 342 PHE cc_start: 0.8381 (m-10) cc_final: 0.8165 (m-10) REVERT: G 559 LEU cc_start: 0.8379 (tp) cc_final: 0.8145 (tp) REVERT: G 568 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7383 (mtt-85) REVERT: G 590 ASP cc_start: 0.7626 (t0) cc_final: 0.7259 (p0) REVERT: G 591 THR cc_start: 0.8932 (p) cc_final: 0.8695 (p) REVERT: G 599 TYR cc_start: 0.7993 (m-80) cc_final: 0.7414 (m-80) REVERT: G 600 PHE cc_start: 0.8851 (p90) cc_final: 0.8596 (p90) REVERT: G 612 TRP cc_start: 0.7849 (m100) cc_final: 0.6969 (m100) REVERT: G 623 PHE cc_start: 0.8359 (m-10) cc_final: 0.7830 (m-10) REVERT: G 633 THR cc_start: 0.7657 (p) cc_final: 0.5880 (p) REVERT: G 640 ASN cc_start: 0.7261 (t0) cc_final: 0.6836 (t0) REVERT: G 664 ILE cc_start: 0.8840 (mp) cc_final: 0.8457 (pt) REVERT: G 684 LEU cc_start: 0.8306 (tp) cc_final: 0.8053 (tp) REVERT: G 766 GLN cc_start: 0.5977 (mt0) cc_final: 0.5030 (pm20) REVERT: G 780 VAL cc_start: 0.8042 (t) cc_final: 0.7760 (t) REVERT: H 224 TYR cc_start: 0.8532 (t80) cc_final: 0.8050 (t80) REVERT: H 241 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8458 (tt0) REVERT: H 335 ARG cc_start: 0.8771 (ttp-110) cc_final: 0.8484 (ttp-110) REVERT: H 336 LEU cc_start: 0.9575 (mt) cc_final: 0.8857 (tt) REVERT: H 398 GLN cc_start: 0.8907 (mp10) cc_final: 0.8647 (mp10) REVERT: H 404 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7731 (mtt180) REVERT: H 435 LEU cc_start: 0.9145 (mt) cc_final: 0.8875 (pp) REVERT: I 49 GLU cc_start: 0.9121 (tp30) cc_final: 0.8819 (tp30) REVERT: I 219 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7725 (mt-10) REVERT: I 326 HIS cc_start: 0.8974 (m170) cc_final: 0.8678 (m170) REVERT: I 374 TYR cc_start: 0.8320 (t80) cc_final: 0.8088 (t80) REVERT: K 64 MET cc_start: 0.8836 (mtp) cc_final: 0.8397 (mmp) REVERT: K 77 LYS cc_start: 0.8657 (tttt) cc_final: 0.7778 (tppt) REVERT: K 81 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8360 (mm-30) REVERT: K 87 GLN cc_start: 0.8057 (mm-40) cc_final: 0.6399 (pp30) REVERT: K 99 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8486 (mt-10) REVERT: M 18 MET cc_start: 0.8880 (ppp) cc_final: 0.8547 (ppp) REVERT: M 21 GLN cc_start: 0.8549 (tp40) cc_final: 0.7826 (tp40) REVERT: M 22 ILE cc_start: 0.8451 (mt) cc_final: 0.8206 (mt) REVERT: M 24 LYS cc_start: 0.8394 (mttt) cc_final: 0.7939 (tptp) REVERT: M 25 ASP cc_start: 0.7943 (m-30) cc_final: 0.7175 (m-30) REVERT: M 26 MET cc_start: 0.7034 (mmp) cc_final: 0.6798 (mmm) REVERT: M 28 ILE cc_start: 0.8312 (tp) cc_final: 0.7843 (tp) REVERT: M 49 THR cc_start: 0.9311 (p) cc_final: 0.9090 (p) REVERT: M 57 TYR cc_start: 0.9353 (m-10) cc_final: 0.9143 (m-10) REVERT: O 126 TYR cc_start: 0.7865 (m-10) cc_final: 0.7401 (m-80) REVERT: O 169 ASP cc_start: 0.9007 (t0) cc_final: 0.8324 (t0) REVERT: O 173 HIS cc_start: 0.8705 (m90) cc_final: 0.8343 (m90) REVERT: O 198 GLU cc_start: 0.9134 (tt0) cc_final: 0.8723 (tt0) REVERT: R 76 LEU cc_start: 0.8454 (tp) cc_final: 0.8211 (tp) REVERT: R 86 GLN cc_start: 0.9557 (mp10) cc_final: 0.9355 (mp10) REVERT: R 93 GLU cc_start: 0.9275 (tp30) cc_final: 0.9007 (tp30) REVERT: R 114 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8552 (tttt) REVERT: R 126 MET cc_start: 0.5670 (tmm) cc_final: 0.4785 (tmm) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.1348 time to fit residues: 136.9859 Evaluate side-chains 530 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 115 optimal weight: 0.2980 chunk 195 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN G 238 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN R 101 GLN ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088540 restraints weight = 72552.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091100 restraints weight = 46170.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092274 restraints weight = 31741.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092845 restraints weight = 25534.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093035 restraints weight = 23133.448| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21657 Z= 0.161 Angle : 0.814 13.577 29446 Z= 0.423 Chirality : 0.048 0.357 3433 Planarity : 0.006 0.102 3795 Dihedral : 6.557 59.564 3033 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.64 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.13 % 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: -1.71 (0.17), residues: 2465 helix: 0.40 (0.14), residues: 1301 sheet: -1.09 (0.36), residues: 212 loop : -3.46 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 46 TYR 0.049 0.002 TYR B 794 PHE 0.041 0.002 PHE I 262 TRP 0.044 0.002 TRP G 696 HIS 0.013 0.001 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00354 (21654) covalent geometry : angle 0.81445 (29437) hydrogen bonds : bond 0.04323 ( 1124) hydrogen bonds : angle 5.42025 ( 3276) link_TRANS : bond 0.00074 ( 3) link_TRANS : angle 0.46936 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8548 (mt) cc_final: 0.8320 (mt) REVERT: B 44 SER cc_start: 0.7631 (t) cc_final: 0.6664 (t) REVERT: B 129 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7759 (tppt) REVERT: B 145 LYS cc_start: 0.8341 (mttt) cc_final: 0.8049 (mmtm) REVERT: B 170 MET cc_start: 0.8270 (mtp) cc_final: 0.7648 (mmm) REVERT: B 270 LEU cc_start: 0.8205 (mm) cc_final: 0.7997 (mm) REVERT: B 272 GLN cc_start: 0.8466 (pm20) cc_final: 0.8244 (pm20) REVERT: B 285 HIS cc_start: 0.7291 (m-70) cc_final: 0.7007 (m170) REVERT: B 289 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 299 TYR cc_start: 0.8101 (t80) cc_final: 0.7781 (t80) REVERT: B 362 MET cc_start: 0.6946 (tpt) cc_final: 0.6660 (tpp) REVERT: B 364 TRP cc_start: 0.8473 (t-100) cc_final: 0.7716 (t-100) REVERT: B 452 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7513 (ttmt) REVERT: B 468 PHE cc_start: 0.8973 (m-80) cc_final: 0.8505 (m-80) REVERT: B 469 MET cc_start: 0.8979 (ptt) cc_final: 0.8743 (ptt) REVERT: B 505 LYS cc_start: 0.9444 (mttt) cc_final: 0.9179 (mttt) REVERT: B 508 SER cc_start: 0.9503 (m) cc_final: 0.9274 (p) REVERT: B 531 PHE cc_start: 0.8804 (m-80) cc_final: 0.8577 (m-80) REVERT: B 588 HIS cc_start: 0.7478 (m-70) cc_final: 0.7184 (m-70) REVERT: B 614 MET cc_start: 0.7517 (mmm) cc_final: 0.7037 (mmm) REVERT: B 707 ASN cc_start: 0.9299 (m-40) cc_final: 0.8866 (m-40) REVERT: B 726 MET cc_start: 0.8397 (mtm) cc_final: 0.7798 (mtp) REVERT: B 755 VAL cc_start: 0.9438 (m) cc_final: 0.9163 (m) REVERT: B 757 MET cc_start: 0.8194 (ptm) cc_final: 0.7967 (ptm) REVERT: B 774 PHE cc_start: 0.8688 (t80) cc_final: 0.8419 (t80) REVERT: B 797 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7095 (mm-30) REVERT: B 854 CYS cc_start: 0.8045 (m) cc_final: 0.7576 (t) REVERT: B 899 LYS cc_start: 0.9213 (tttt) cc_final: 0.8671 (ptmt) REVERT: E 885 ILE cc_start: 0.6717 (mp) cc_final: 0.6180 (mp) REVERT: E 889 HIS cc_start: 0.8079 (m-70) cc_final: 0.7668 (m-70) REVERT: E 904 HIS cc_start: 0.9177 (m90) cc_final: 0.8565 (m90) REVERT: E 915 GLU cc_start: 0.9359 (pp20) cc_final: 0.8954 (pp20) REVERT: E 916 LYS cc_start: 0.9317 (mmpt) cc_final: 0.8942 (mmmt) REVERT: E 919 GLU cc_start: 0.9099 (mp0) cc_final: 0.8864 (mp0) REVERT: E 922 GLN cc_start: 0.9504 (mm-40) cc_final: 0.9220 (mm-40) REVERT: G 261 LYS cc_start: 0.9616 (mtpt) cc_final: 0.9289 (ptpp) REVERT: G 265 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9010 (mt-10) REVERT: G 477 ASP cc_start: 0.6160 (t0) cc_final: 0.5930 (t0) REVERT: G 559 LEU cc_start: 0.8381 (tp) cc_final: 0.7702 (tp) REVERT: G 567 VAL cc_start: 0.8457 (p) cc_final: 0.8105 (t) REVERT: G 568 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7489 (mtt-85) REVERT: G 591 THR cc_start: 0.8860 (p) cc_final: 0.8487 (p) REVERT: G 599 TYR cc_start: 0.8038 (m-80) cc_final: 0.7439 (m-80) REVERT: G 612 TRP cc_start: 0.7784 (m100) cc_final: 0.6930 (m100) REVERT: G 623 PHE cc_start: 0.8268 (m-10) cc_final: 0.7768 (m-10) REVERT: G 633 THR cc_start: 0.7574 (p) cc_final: 0.5922 (p) REVERT: G 640 ASN cc_start: 0.7169 (t0) cc_final: 0.6910 (t0) REVERT: H 224 TYR cc_start: 0.8525 (t80) cc_final: 0.8016 (t80) REVERT: H 241 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8440 (tt0) REVERT: H 282 LEU cc_start: 0.9491 (mt) cc_final: 0.9285 (mt) REVERT: H 285 MET cc_start: 0.8518 (ttt) cc_final: 0.8301 (ttt) REVERT: H 335 ARG cc_start: 0.8824 (ttp-110) cc_final: 0.8467 (ttp-110) REVERT: H 336 LEU cc_start: 0.9552 (mt) cc_final: 0.8771 (tt) REVERT: H 366 GLU cc_start: 0.8681 (tp30) cc_final: 0.8332 (tp30) REVERT: H 398 GLN cc_start: 0.8882 (mp10) cc_final: 0.8640 (mp10) REVERT: H 404 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7645 (mtt180) REVERT: H 423 VAL cc_start: 0.9579 (t) cc_final: 0.9313 (t) REVERT: H 435 LEU cc_start: 0.9201 (mt) cc_final: 0.8922 (pp) REVERT: I 49 GLU cc_start: 0.9117 (tp30) cc_final: 0.8800 (tp30) REVERT: I 219 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7707 (mt-10) REVERT: I 259 PHE cc_start: 0.6317 (t80) cc_final: 0.6116 (t80) REVERT: I 326 HIS cc_start: 0.9028 (m170) cc_final: 0.8580 (m170) REVERT: I 336 LEU cc_start: 0.9418 (mt) cc_final: 0.9168 (mt) REVERT: K 64 MET cc_start: 0.8807 (mtp) cc_final: 0.8254 (mmp) REVERT: K 77 LYS cc_start: 0.8437 (tttt) cc_final: 0.8049 (tttt) REVERT: K 87 GLN cc_start: 0.8033 (mm-40) cc_final: 0.6391 (pp30) REVERT: K 99 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8463 (mt-10) REVERT: K 221 ILE cc_start: 0.8184 (tp) cc_final: 0.7673 (mm) REVERT: M 18 MET cc_start: 0.8897 (ppp) cc_final: 0.8572 (ppp) REVERT: M 21 GLN cc_start: 0.8509 (tp40) cc_final: 0.7733 (tp40) REVERT: M 24 LYS cc_start: 0.8536 (mttt) cc_final: 0.8016 (tptp) REVERT: M 25 ASP cc_start: 0.7979 (m-30) cc_final: 0.7066 (m-30) REVERT: M 26 MET cc_start: 0.6978 (mmp) cc_final: 0.6633 (mmm) REVERT: M 28 ILE cc_start: 0.8183 (tp) cc_final: 0.7799 (tp) REVERT: M 57 TYR cc_start: 0.9340 (m-10) cc_final: 0.9087 (m-10) REVERT: O 122 GLN cc_start: 0.9375 (tp-100) cc_final: 0.8992 (tp-100) REVERT: O 126 TYR cc_start: 0.8336 (m-10) cc_final: 0.7666 (m-10) REVERT: O 169 ASP cc_start: 0.9001 (t0) cc_final: 0.8281 (t0) REVERT: O 173 HIS cc_start: 0.8697 (m90) cc_final: 0.8345 (m90) REVERT: O 198 GLU cc_start: 0.9095 (tt0) cc_final: 0.8713 (pt0) REVERT: R 76 LEU cc_start: 0.8447 (tp) cc_final: 0.8200 (tp) REVERT: R 85 LEU cc_start: 0.9399 (mt) cc_final: 0.9190 (mt) REVERT: R 93 GLU cc_start: 0.9279 (tp30) cc_final: 0.9043 (tp30) REVERT: R 114 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8553 (tttt) REVERT: R 126 MET cc_start: 0.6466 (tmm) cc_final: 0.4787 (tmm) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.1373 time to fit residues: 139.7110 Evaluate side-chains 531 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 127 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 165 optimal weight: 0.0050 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS B 235 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.111843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089555 restraints weight = 73640.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091910 restraints weight = 47167.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093824 restraints weight = 32695.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094204 restraints weight = 24833.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094244 restraints weight = 22877.614| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21657 Z= 0.155 Angle : 0.818 10.960 29446 Z= 0.424 Chirality : 0.048 0.355 3433 Planarity : 0.006 0.098 3795 Dihedral : 6.390 57.665 3033 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.04 % 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: -1.69 (0.17), residues: 2465 helix: 0.48 (0.14), residues: 1297 sheet: -1.05 (0.36), residues: 211 loop : -3.53 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 787 TYR 0.038 0.002 TYR I 223 PHE 0.042 0.002 PHE I 262 TRP 0.039 0.002 TRP G 696 HIS 0.014 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00343 (21654) covalent geometry : angle 0.81818 (29437) hydrogen bonds : bond 0.04285 ( 1124) hydrogen bonds : angle 5.37712 ( 3276) link_TRANS : bond 0.00073 ( 3) link_TRANS : angle 0.42989 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8390 (mt) cc_final: 0.8187 (mt) REVERT: B 44 SER cc_start: 0.7372 (t) cc_final: 0.6419 (t) REVERT: B 145 LYS cc_start: 0.8407 (mttt) cc_final: 0.8089 (mmtm) REVERT: B 170 MET cc_start: 0.8219 (mtp) cc_final: 0.7598 (mmm) REVERT: B 270 LEU cc_start: 0.8130 (mm) cc_final: 0.7888 (mm) REVERT: B 285 HIS cc_start: 0.7353 (m-70) cc_final: 0.7114 (m170) REVERT: B 289 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 323 SER cc_start: 0.7951 (t) cc_final: 0.7656 (t) REVERT: B 331 HIS cc_start: 0.6241 (t-170) cc_final: 0.6009 (t-170) REVERT: B 362 MET cc_start: 0.6999 (tpt) cc_final: 0.6626 (tpp) REVERT: B 364 TRP cc_start: 0.8391 (t-100) cc_final: 0.7718 (t-100) REVERT: B 412 VAL cc_start: 0.9204 (t) cc_final: 0.8881 (t) REVERT: B 452 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7389 (ttmt) REVERT: B 468 PHE cc_start: 0.8910 (m-80) cc_final: 0.8445 (m-80) REVERT: B 505 LYS cc_start: 0.9512 (mttt) cc_final: 0.9202 (mttt) REVERT: B 508 SER cc_start: 0.9484 (m) cc_final: 0.9265 (p) REVERT: B 531 PHE cc_start: 0.8778 (m-80) cc_final: 0.8523 (m-80) REVERT: B 537 PHE cc_start: 0.8795 (p90) cc_final: 0.8186 (p90) REVERT: B 588 HIS cc_start: 0.7459 (m-70) cc_final: 0.7103 (m-70) REVERT: B 614 MET cc_start: 0.7399 (mmm) cc_final: 0.6952 (mmm) REVERT: B 707 ASN cc_start: 0.9305 (m-40) cc_final: 0.8885 (m-40) REVERT: B 726 MET cc_start: 0.8407 (mtm) cc_final: 0.7836 (mtp) REVERT: B 757 MET cc_start: 0.8201 (ptm) cc_final: 0.7991 (ptm) REVERT: B 774 PHE cc_start: 0.8741 (t80) cc_final: 0.8455 (t80) REVERT: B 797 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7060 (mm-30) REVERT: B 854 CYS cc_start: 0.7901 (m) cc_final: 0.7493 (t) REVERT: B 899 LYS cc_start: 0.9215 (tttt) cc_final: 0.8681 (ptmt) REVERT: B 913 MET cc_start: 0.8737 (mtt) cc_final: 0.8534 (mtt) REVERT: B 930 LEU cc_start: 0.9262 (tp) cc_final: 0.9027 (tp) REVERT: E 885 ILE cc_start: 0.6719 (mp) cc_final: 0.6300 (mp) REVERT: E 889 HIS cc_start: 0.8176 (m-70) cc_final: 0.7764 (m-70) REVERT: E 904 HIS cc_start: 0.9147 (m90) cc_final: 0.8563 (m90) REVERT: E 915 GLU cc_start: 0.9351 (pp20) cc_final: 0.8975 (pp20) REVERT: E 916 LYS cc_start: 0.9236 (mmpt) cc_final: 0.8865 (mmmt) REVERT: E 919 GLU cc_start: 0.9130 (mp0) cc_final: 0.8907 (mp0) REVERT: E 922 GLN cc_start: 0.9515 (mm-40) cc_final: 0.9235 (mm-40) REVERT: G 261 LYS cc_start: 0.9596 (mtpt) cc_final: 0.9264 (ptpp) REVERT: G 265 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8980 (mt-10) REVERT: G 477 ASP cc_start: 0.6099 (t0) cc_final: 0.5799 (t0) REVERT: G 559 LEU cc_start: 0.8418 (tp) cc_final: 0.7813 (tp) REVERT: G 567 VAL cc_start: 0.8478 (p) cc_final: 0.8090 (t) REVERT: G 568 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: G 612 TRP cc_start: 0.7667 (m100) cc_final: 0.7057 (m100) REVERT: G 623 PHE cc_start: 0.8254 (m-10) cc_final: 0.7768 (m-10) REVERT: G 633 THR cc_start: 0.6376 (p) cc_final: 0.6080 (p) REVERT: G 640 ASN cc_start: 0.7084 (t0) cc_final: 0.6857 (t0) REVERT: G 684 LEU cc_start: 0.8205 (tp) cc_final: 0.7989 (tp) REVERT: G 774 MET cc_start: 0.5822 (mtt) cc_final: 0.5613 (mtp) REVERT: G 788 ARG cc_start: 0.6049 (mtt180) cc_final: 0.5846 (mmt90) REVERT: H 224 TYR cc_start: 0.8459 (t80) cc_final: 0.8064 (t80) REVERT: H 244 GLN cc_start: 0.8560 (tp40) cc_final: 0.8275 (tp-100) REVERT: H 335 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.7752 (ttp-110) REVERT: H 357 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8163 (tppt) REVERT: H 398 GLN cc_start: 0.8887 (mp10) cc_final: 0.8614 (mp10) REVERT: H 404 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7603 (mtt180) REVERT: H 423 VAL cc_start: 0.9571 (t) cc_final: 0.9336 (t) REVERT: H 435 LEU cc_start: 0.9143 (mt) cc_final: 0.8813 (pp) REVERT: I 36 CYS cc_start: 0.9498 (m) cc_final: 0.9100 (t) REVERT: I 49 GLU cc_start: 0.9073 (tp30) cc_final: 0.8709 (tp30) REVERT: I 68 THR cc_start: 0.8166 (p) cc_final: 0.7576 (t) REVERT: I 72 ASP cc_start: 0.7840 (m-30) cc_final: 0.7633 (m-30) REVERT: I 219 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7657 (mt-10) REVERT: I 326 HIS cc_start: 0.9011 (m170) cc_final: 0.8538 (m170) REVERT: I 342 LYS cc_start: 0.8477 (pttt) cc_final: 0.7996 (pttm) REVERT: I 374 TYR cc_start: 0.8389 (t80) cc_final: 0.8015 (t80) REVERT: K 64 MET cc_start: 0.8793 (mtp) cc_final: 0.8248 (mmp) REVERT: K 77 LYS cc_start: 0.8353 (tttt) cc_final: 0.7703 (tppt) REVERT: K 87 GLN cc_start: 0.8080 (mm-40) cc_final: 0.6475 (pp30) REVERT: K 99 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8455 (mt-10) REVERT: K 194 MET cc_start: 0.8421 (mmm) cc_final: 0.7857 (mmm) REVERT: M 14 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8539 (tmtt) REVERT: M 18 MET cc_start: 0.8871 (ppp) cc_final: 0.8651 (ppp) REVERT: M 21 GLN cc_start: 0.8607 (tp40) cc_final: 0.7902 (tp40) REVERT: M 22 ILE cc_start: 0.8412 (mt) cc_final: 0.8053 (mt) REVERT: M 24 LYS cc_start: 0.8545 (mttt) cc_final: 0.8262 (mmmt) REVERT: M 25 ASP cc_start: 0.7977 (m-30) cc_final: 0.7690 (m-30) REVERT: M 57 TYR cc_start: 0.9311 (m-10) cc_final: 0.8975 (m-10) REVERT: O 122 GLN cc_start: 0.9397 (tp-100) cc_final: 0.9134 (tp-100) REVERT: O 126 TYR cc_start: 0.8203 (m-10) cc_final: 0.7698 (m-80) REVERT: O 169 ASP cc_start: 0.9043 (t0) cc_final: 0.8382 (t0) REVERT: O 173 HIS cc_start: 0.8718 (m90) cc_final: 0.8412 (m90) REVERT: O 198 GLU cc_start: 0.9108 (tt0) cc_final: 0.8735 (pt0) REVERT: R 76 LEU cc_start: 0.8494 (tp) cc_final: 0.8244 (tp) REVERT: R 86 GLN cc_start: 0.9506 (mp10) cc_final: 0.9193 (mp10) REVERT: R 93 GLU cc_start: 0.9261 (tp30) cc_final: 0.9028 (tp30) REVERT: R 101 GLN cc_start: 0.9328 (mp10) cc_final: 0.9085 (mm-40) REVERT: R 114 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8282 (tttt) REVERT: R 126 MET cc_start: 0.6441 (tmm) cc_final: 0.4752 (tmm) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.1351 time to fit residues: 136.4484 Evaluate side-chains 521 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 155 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.111761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089760 restraints weight = 72483.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092387 restraints weight = 47152.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093239 restraints weight = 32616.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093988 restraints weight = 26910.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094146 restraints weight = 24081.812| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21657 Z= 0.156 Angle : 0.807 11.316 29446 Z= 0.421 Chirality : 0.049 0.339 3433 Planarity : 0.006 0.099 3795 Dihedral : 6.319 56.921 3033 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.04 % 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: -1.66 (0.17), residues: 2465 helix: 0.47 (0.14), residues: 1304 sheet: -1.00 (0.36), residues: 207 loop : -3.50 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 787 TYR 0.023 0.002 TYR I 45 PHE 0.041 0.002 PHE I 262 TRP 0.038 0.002 TRP G 696 HIS 0.013 0.001 HIS H 422 Details of bonding type rmsd covalent geometry : bond 0.00341 (21654) covalent geometry : angle 0.80701 (29437) hydrogen bonds : bond 0.04299 ( 1124) hydrogen bonds : angle 5.38326 ( 3276) link_TRANS : bond 0.00081 ( 3) link_TRANS : angle 0.44787 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.42 seconds wall clock time: 70 minutes 17.93 seconds (4217.93 seconds total)