Starting phenix.real_space_refine on Mon Mar 18 14:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_9298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_9298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_9298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_9298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/03_2024/6mzc_9298.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 239": "NH1" <-> "NH2" Residue "H TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 284": "NH1" <-> "NH2" Residue "H ARG 320": "NH1" <-> "NH2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H ARG 373": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 284": "NH1" <-> "NH2" Residue "I ARG 373": "NH1" <-> "NH2" Residue "K PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21254 Number of models: 1 Model: "" Number of chains: 10 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: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "G" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3646 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 1 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: {'PHE:plan': 2, 'GLU:plan': 2, 'UNK:plan-1': 40, '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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "I" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2520 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 10, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "K" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1449 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 195} 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: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 732 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 96} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'UNK:plan-1': 7, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 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: 10.83, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 2.09 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: 6.64 Time building geometry restraints manager: 9.04 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: 6626 1.33 - 1.45: 3857 1.45 - 1.57: 10990 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 21657 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 21652 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.47: 436 105.47 - 112.69: 11630 112.69 - 119.92: 7558 119.92 - 127.14: 9570 127.14 - 134.36: 252 Bond angle restraints: 29446 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 29441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 12112 15.19 - 30.38: 825 30.38 - 45.56: 100 45.56 - 60.75: 13 60.75 - 75.94: 7 Dihedral angle restraints: 13057 sinusoidal: 4668 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 13054 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 2.440 nonbonded pdb=" OD1 ASN B 184 " pdb=" OG SER B 195 " model vdw 2.227 2.440 nonbonded pdb=" OG SER B 44 " pdb=" O LEU B 152 " model vdw 2.234 2.440 nonbonded pdb=" O LEU B 956 " pdb=" OG1 THR B 961 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR G 464 " pdb=" O UNK K 150 " model vdw 2.254 2.440 ... (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 ========== 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: 1.480 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: 0.020 Extract box with map and model: 5.990 Check model and map are aligned: 0.300 Set scattering table: 0.160 Process input model: 53.900 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.160 ------------------------------------------------------------------------------- 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= 0.636 Angle : 1.333 16.629 29446 Z= 0.721 Chirality : 0.066 0.419 3433 Planarity : 0.009 0.122 3798 Dihedral : 10.662 75.941 7579 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.14), residues: 2465 helix: -2.21 (0.11), residues: 1239 sheet: -2.54 (0.32), residues: 231 loop : -4.14 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP B 189 HIS 0.032 0.005 HIS H 422 PHE 0.059 0.005 PHE I 262 TYR 0.043 0.005 TYR I 45 ARG 0.022 0.002 ARG B 344 *********************** 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 fitting. rotamer outliers: 15 poor density : 943 time to evaluate : 2.193 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: 0.7852 (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: 0.9331 (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: 0.8649 (t) cc_final: 0.8405 (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: 0.8545 (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: 0.8716 (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: 0.8946 (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: 0.8267 (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: 0.8945 (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: 0.3583 time to fit residues: 503.8281 Evaluate side-chains 607 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 599 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 203 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 895 HIS ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 HIS G 290 HIS ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 HIS ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 700 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 784 HIS ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 GLN I 254 GLN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 GLN K 82 HIS O 122 GLN ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21657 Z= 0.238 Angle : 0.821 10.709 29446 Z= 0.429 Chirality : 0.047 0.350 3433 Planarity : 0.006 0.099 3798 Dihedral : 7.911 59.613 3036 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.13 % Favored : 87.83 % Rotamer: Outliers : 0.19 % Allowed : 3.60 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.15), residues: 2465 helix: -0.92 (0.13), residues: 1289 sheet: -2.12 (0.33), residues: 222 loop : -3.91 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 370 HIS 0.013 0.002 HIS G 246 PHE 0.043 0.002 PHE I 262 TYR 0.046 0.002 TYR B 196 ARG 0.012 0.001 ARG B 859 *********************** 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 805 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 801 time to evaluate : 2.215 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: B 27 LYS cc_start: 0.8353 (tptm) cc_final: 0.8061 (tptm) REVERT: B 31 GLN cc_start: 0.8068 (mp-120) cc_final: 0.7642 (mp10) REVERT: B 153 ASP cc_start: 0.8281 (p0) cc_final: 0.8009 (p0) REVERT: B 217 ASN cc_start: 0.8665 (m-40) cc_final: 0.8254 (m-40) REVERT: B 262 MET cc_start: 0.8577 (tpt) cc_final: 0.7960 (tpt) REVERT: B 265 VAL cc_start: 0.8212 (t) cc_final: 0.7955 (m) REVERT: B 307 VAL cc_start: 0.8922 (t) cc_final: 0.8716 (t) REVERT: B 324 ILE cc_start: 0.8362 (mt) cc_final: 0.7873 (mt) REVERT: B 358 PHE cc_start: 0.8632 (m-80) cc_final: 0.8406 (m-10) REVERT: B 364 TRP cc_start: 0.8415 (t-100) cc_final: 0.7850 (t-100) REVERT: B 390 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8198 (tp30) REVERT: B 456 VAL cc_start: 0.9120 (m) cc_final: 0.8889 (m) REVERT: B 459 LEU cc_start: 0.8773 (mt) cc_final: 0.8536 (mt) REVERT: B 467 GLU cc_start: 0.8798 (tp30) cc_final: 0.8571 (tp30) REVERT: B 468 PHE cc_start: 0.9328 (m-10) cc_final: 0.9001 (m-80) REVERT: B 470 LEU cc_start: 0.9095 (mt) cc_final: 0.8774 (mt) REVERT: B 488 PHE cc_start: 0.8396 (t80) cc_final: 0.7419 (t80) REVERT: B 520 LYS cc_start: 0.9231 (mttt) cc_final: 0.8972 (tptt) REVERT: B 531 PHE cc_start: 0.8599 (m-80) cc_final: 0.8304 (m-80) REVERT: B 578 THR cc_start: 0.8214 (m) cc_final: 0.7714 (m) REVERT: B 588 HIS cc_start: 0.7503 (m-70) cc_final: 0.7248 (m-70) REVERT: B 753 MET cc_start: 0.7664 (ppp) cc_final: 0.7226 (ppp) REVERT: B 776 LEU cc_start: 0.8760 (mt) cc_final: 0.8451 (mt) REVERT: B 797 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 798 MET cc_start: 0.7859 (mtp) cc_final: 0.7532 (mtp) REVERT: B 914 ILE cc_start: 0.8765 (mt) cc_final: 0.8381 (mt) REVERT: B 916 ASN cc_start: 0.8850 (t0) cc_final: 0.8280 (p0) REVERT: B 955 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8953 (mttt) REVERT: E 904 HIS cc_start: 0.9611 (t70) cc_final: 0.9357 (t70) REVERT: E 916 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9237 (mmmt) REVERT: E 922 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9037 (mm-40) REVERT: G 214 TYR cc_start: 0.8606 (m-80) cc_final: 0.8344 (m-80) REVERT: G 223 HIS cc_start: 0.9537 (t70) cc_final: 0.9291 (t70) REVERT: G 246 HIS cc_start: 0.8706 (p-80) cc_final: 0.8068 (p90) REVERT: G 265 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9038 (mt-10) REVERT: G 477 ASP cc_start: 0.7065 (p0) cc_final: 0.6810 (t0) REVERT: G 484 LEU cc_start: 0.7814 (mt) cc_final: 0.7501 (mt) REVERT: G 538 ILE cc_start: 0.9012 (tt) cc_final: 0.8679 (mm) REVERT: G 563 GLU cc_start: 0.7533 (tt0) cc_final: 0.7164 (tt0) REVERT: G 566 THR cc_start: 0.7932 (t) cc_final: 0.7631 (m) REVERT: G 568 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.6635 (mtt-85) REVERT: G 599 TYR cc_start: 0.8296 (m-80) cc_final: 0.7587 (m-80) REVERT: G 622 ILE cc_start: 0.9147 (tt) cc_final: 0.8440 (mm) REVERT: G 623 PHE cc_start: 0.8266 (m-80) cc_final: 0.6801 (m-10) REVERT: G 636 HIS cc_start: 0.7990 (t70) cc_final: 0.7328 (t-90) REVERT: G 640 ASN cc_start: 0.6931 (t0) cc_final: 0.6660 (t0) REVERT: G 654 TRP cc_start: 0.7994 (m100) cc_final: 0.6580 (m100) REVERT: G 696 TRP cc_start: 0.8094 (m100) cc_final: 0.7041 (m100) REVERT: G 726 LEU cc_start: 0.7719 (mt) cc_final: 0.7423 (tp) REVERT: G 766 GLN cc_start: 0.5915 (mt0) cc_final: 0.5102 (pm20) REVERT: G 774 MET cc_start: 0.6134 (mtt) cc_final: 0.5934 (mtp) REVERT: G 780 VAL cc_start: 0.8044 (t) cc_final: 0.7287 (t) REVERT: H 224 TYR cc_start: 0.8503 (t80) cc_final: 0.8072 (t80) REVERT: H 241 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8239 (tt0) REVERT: H 246 ILE cc_start: 0.8797 (mt) cc_final: 0.8541 (mm) REVERT: H 259 PHE cc_start: 0.8411 (t80) cc_final: 0.7924 (t80) REVERT: H 263 ILE cc_start: 0.9664 (mt) cc_final: 0.9447 (tp) REVERT: H 285 MET cc_start: 0.8680 (ttt) cc_final: 0.8254 (mtp) REVERT: H 302 HIS cc_start: 0.9217 (p-80) cc_final: 0.8990 (p-80) REVERT: H 336 LEU cc_start: 0.9552 (mt) cc_final: 0.8890 (mm) REVERT: H 339 GLN cc_start: 0.7775 (mt0) cc_final: 0.7563 (mt0) REVERT: H 354 ARG cc_start: 0.8804 (tpp-160) cc_final: 0.8589 (tpp80) REVERT: H 355 ILE cc_start: 0.9304 (pt) cc_final: 0.9068 (tp) REVERT: H 363 TRP cc_start: 0.8442 (t60) cc_final: 0.8149 (t60) REVERT: H 398 GLN cc_start: 0.8948 (mp10) cc_final: 0.8742 (mp10) REVERT: H 421 ASP cc_start: 0.9112 (t0) cc_final: 0.8888 (m-30) REVERT: H 424 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8582 (tm-30) REVERT: H 428 LEU cc_start: 0.8698 (tp) cc_final: 0.8395 (mm) REVERT: H 435 LEU cc_start: 0.9186 (mt) cc_final: 0.8910 (pp) REVERT: I 49 GLU cc_start: 0.9202 (tp30) cc_final: 0.8920 (tp30) REVERT: I 50 ILE cc_start: 0.9175 (mt) cc_final: 0.8876 (mm) REVERT: I 219 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7712 (mp0) REVERT: I 220 GLN cc_start: 0.8738 (pt0) cc_final: 0.8270 (tm-30) REVERT: I 221 GLN cc_start: 0.8935 (pt0) cc_final: 0.8405 (pp30) REVERT: I 222 LEU cc_start: 0.9274 (mt) cc_final: 0.9048 (mt) REVERT: I 226 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8221 (mm-30) REVERT: I 227 ILE cc_start: 0.9260 (mt) cc_final: 0.9024 (mt) REVERT: I 228 THR cc_start: 0.9162 (p) cc_final: 0.8928 (p) REVERT: I 229 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8780 (tp30) REVERT: I 267 VAL cc_start: 0.8892 (t) cc_final: 0.8690 (t) REVERT: I 332 PHE cc_start: 0.9057 (t80) cc_final: 0.8766 (t80) REVERT: I 335 ARG cc_start: 0.9150 (ttt180) cc_final: 0.8739 (ttm-80) REVERT: I 336 LEU cc_start: 0.9479 (mt) cc_final: 0.9185 (mt) REVERT: I 337 VAL cc_start: 0.9515 (t) cc_final: 0.9286 (t) REVERT: I 349 ASN cc_start: 0.7858 (p0) cc_final: 0.7494 (p0) REVERT: K 38 GLN cc_start: 0.9161 (mt0) cc_final: 0.8886 (mt0) REVERT: K 64 MET cc_start: 0.9208 (mtp) cc_final: 0.8493 (mmp) REVERT: K 65 LEU cc_start: 0.9581 (tp) cc_final: 0.9346 (tt) REVERT: K 77 LYS cc_start: 0.8798 (tttt) cc_final: 0.8529 (tttt) REVERT: K 87 GLN cc_start: 0.8380 (mm-40) cc_final: 0.6534 (pp30) REVERT: K 175 LEU cc_start: 0.8815 (tt) cc_final: 0.8321 (tt) REVERT: K 194 MET cc_start: 0.8801 (mmm) cc_final: 0.8356 (mmt) REVERT: K 201 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7741 (mm110) REVERT: K 223 TYR cc_start: 0.7686 (p90) cc_final: 0.7293 (p90) REVERT: M 14 LYS cc_start: 0.9309 (mttt) cc_final: 0.8915 (tptp) REVERT: M 24 LYS cc_start: 0.8030 (mttt) cc_final: 0.7575 (tptp) REVERT: M 46 TYR cc_start: 0.9195 (m-80) cc_final: 0.8953 (m-80) REVERT: M 49 THR cc_start: 0.9464 (p) cc_final: 0.9158 (p) REVERT: O 169 ASP cc_start: 0.9353 (t0) cc_final: 0.8965 (t0) REVERT: O 173 HIS cc_start: 0.8918 (m90) cc_final: 0.8479 (m90) REVERT: R 93 GLU cc_start: 0.9352 (tp30) cc_final: 0.9081 (tp30) REVERT: R 120 LEU cc_start: 0.9710 (mt) cc_final: 0.9356 (mt) REVERT: R 121 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8597 (mm-30) REVERT: R 126 MET cc_start: 0.6079 (ttp) cc_final: 0.5355 (tmm) outliers start: 4 outliers final: 0 residues processed: 802 average time/residue: 0.3152 time to fit residues: 380.8463 Evaluate side-chains 619 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 895 HIS ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 HIS ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 HIS G 758 HIS ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN H 352 GLN ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN H 414 ASN ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN R 56 GLN ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21657 Z= 0.270 Angle : 0.821 10.732 29446 Z= 0.427 Chirality : 0.047 0.363 3433 Planarity : 0.006 0.105 3798 Dihedral : 7.400 58.017 3036 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.37 % Favored : 87.55 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2465 helix: -0.40 (0.13), residues: 1302 sheet: -1.92 (0.34), residues: 226 loop : -3.79 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 696 HIS 0.010 0.002 HIS H 422 PHE 0.052 0.002 PHE I 262 TYR 0.029 0.002 TYR B 196 ARG 0.012 0.001 ARG B 966 *********************** 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 736 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 736 time to evaluate : 2.303 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: B 28 LEU cc_start: 0.8437 (mt) cc_final: 0.8211 (mt) REVERT: B 118 ASP cc_start: 0.9112 (m-30) cc_final: 0.8883 (m-30) REVERT: B 153 ASP cc_start: 0.8155 (p0) cc_final: 0.7878 (p0) REVERT: B 203 LYS cc_start: 0.8675 (tttt) cc_final: 0.8241 (tttp) REVERT: B 217 ASN cc_start: 0.8857 (m-40) cc_final: 0.8378 (m110) REVERT: B 262 MET cc_start: 0.8305 (tpt) cc_final: 0.7848 (tpt) REVERT: B 278 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8330 (mttt) REVERT: B 295 LEU cc_start: 0.8980 (mt) cc_final: 0.8779 (mt) REVERT: B 299 TYR cc_start: 0.8983 (t80) cc_final: 0.8499 (t80) REVERT: B 322 MET cc_start: 0.8212 (ttp) cc_final: 0.7889 (ppp) REVERT: B 355 PHE cc_start: 0.7805 (m-10) cc_final: 0.7552 (m-10) REVERT: B 358 PHE cc_start: 0.8838 (m-80) cc_final: 0.7873 (m-10) REVERT: B 362 MET cc_start: 0.6809 (tpt) cc_final: 0.6596 (tpp) REVERT: B 364 TRP cc_start: 0.8319 (t-100) cc_final: 0.7705 (t-100) REVERT: B 390 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8224 (tp30) REVERT: B 398 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7862 (tp30) REVERT: B 461 GLU cc_start: 0.7922 (tp30) cc_final: 0.7269 (tp30) REVERT: B 468 PHE cc_start: 0.9329 (m-10) cc_final: 0.9096 (m-80) REVERT: B 470 LEU cc_start: 0.8982 (mt) cc_final: 0.8754 (mt) REVERT: B 505 LYS cc_start: 0.9523 (mttt) cc_final: 0.9193 (mttt) REVERT: B 520 LYS cc_start: 0.9278 (mttt) cc_final: 0.9050 (tptt) REVERT: B 532 TYR cc_start: 0.6802 (m-10) cc_final: 0.6368 (m-80) REVERT: B 588 HIS cc_start: 0.7410 (m-70) cc_final: 0.7206 (m-70) REVERT: B 726 MET cc_start: 0.8421 (mtm) cc_final: 0.8198 (mtp) REVERT: B 794 TYR cc_start: 0.8353 (t80) cc_final: 0.7770 (t80) REVERT: B 797 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 827 ARG cc_start: 0.8894 (ttt180) cc_final: 0.8601 (mtp180) REVERT: B 833 ILE cc_start: 0.8883 (pt) cc_final: 0.8637 (pt) REVERT: B 837 LEU cc_start: 0.8909 (mt) cc_final: 0.8691 (mt) REVERT: B 846 TYR cc_start: 0.7460 (t80) cc_final: 0.7161 (t80) REVERT: B 854 CYS cc_start: 0.8564 (m) cc_final: 0.7689 (t) REVERT: B 859 ARG cc_start: 0.8761 (tpt170) cc_final: 0.8449 (tpt-90) REVERT: B 913 MET cc_start: 0.9113 (ttp) cc_final: 0.8903 (ttm) REVERT: B 914 ILE cc_start: 0.8702 (mt) cc_final: 0.8403 (mt) REVERT: B 916 ASN cc_start: 0.8873 (t0) cc_final: 0.8440 (p0) REVERT: B 952 GLN cc_start: 0.8697 (mt0) cc_final: 0.8363 (tt0) REVERT: E 889 HIS cc_start: 0.8073 (m-70) cc_final: 0.7735 (m-70) REVERT: E 904 HIS cc_start: 0.9588 (t70) cc_final: 0.9340 (t70) REVERT: E 916 LYS cc_start: 0.9442 (mmtt) cc_final: 0.9228 (mmmt) REVERT: E 922 GLN cc_start: 0.9424 (mm-40) cc_final: 0.9127 (mm-40) REVERT: G 223 HIS cc_start: 0.9535 (t70) cc_final: 0.9251 (t70) REVERT: G 329 ILE cc_start: 0.8769 (mt) cc_final: 0.8510 (mp) REVERT: G 342 PHE cc_start: 0.8084 (m-10) cc_final: 0.7552 (m-10) REVERT: G 559 LEU cc_start: 0.8637 (tp) cc_final: 0.7992 (tp) REVERT: G 563 GLU cc_start: 0.7563 (tt0) cc_final: 0.7266 (tt0) REVERT: G 566 THR cc_start: 0.7962 (t) cc_final: 0.7624 (m) REVERT: G 568 ARG cc_start: 0.7590 (mtt-85) cc_final: 0.7122 (mtt-85) REVERT: G 599 TYR cc_start: 0.8399 (m-80) cc_final: 0.7700 (m-80) REVERT: G 622 ILE cc_start: 0.9151 (tt) cc_final: 0.8457 (mm) REVERT: G 623 PHE cc_start: 0.8360 (m-80) cc_final: 0.6920 (m-10) REVERT: G 636 HIS cc_start: 0.7906 (t70) cc_final: 0.7515 (t-90) REVERT: G 640 ASN cc_start: 0.6968 (t0) cc_final: 0.6730 (t0) REVERT: G 649 ARG cc_start: 0.6849 (ptt180) cc_final: 0.6636 (ptt90) REVERT: G 654 TRP cc_start: 0.8104 (m100) cc_final: 0.6638 (m100) REVERT: G 696 TRP cc_start: 0.8696 (m100) cc_final: 0.6529 (m100) REVERT: G 703 MET cc_start: 0.7959 (pmm) cc_final: 0.7529 (pmm) REVERT: G 774 MET cc_start: 0.6333 (mtt) cc_final: 0.6012 (mtp) REVERT: H 224 TYR cc_start: 0.8537 (t80) cc_final: 0.8118 (t80) REVERT: H 241 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8330 (tt0) REVERT: H 246 ILE cc_start: 0.8821 (mt) cc_final: 0.8587 (mm) REVERT: H 255 MET cc_start: 0.8585 (ppp) cc_final: 0.7889 (ppp) REVERT: H 256 LEU cc_start: 0.9298 (tp) cc_final: 0.8769 (tp) REVERT: H 259 PHE cc_start: 0.7990 (t80) cc_final: 0.7368 (t80) REVERT: H 279 LEU cc_start: 0.9067 (mt) cc_final: 0.8810 (mt) REVERT: H 282 LEU cc_start: 0.9601 (mt) cc_final: 0.9243 (mt) REVERT: H 285 MET cc_start: 0.8595 (ttt) cc_final: 0.8366 (mtp) REVERT: H 335 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8478 (ttp-110) REVERT: H 336 LEU cc_start: 0.9536 (mt) cc_final: 0.8918 (mm) REVERT: H 361 LYS cc_start: 0.9332 (mtmm) cc_final: 0.9129 (mttp) REVERT: H 363 TRP cc_start: 0.8447 (t60) cc_final: 0.8167 (t60) REVERT: H 370 TRP cc_start: 0.7875 (m100) cc_final: 0.7523 (m100) REVERT: H 421 ASP cc_start: 0.9135 (t0) cc_final: 0.8881 (m-30) REVERT: H 424 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8609 (tm-30) REVERT: H 427 LEU cc_start: 0.9545 (mt) cc_final: 0.9242 (mt) REVERT: H 428 LEU cc_start: 0.8776 (tp) cc_final: 0.8434 (mm) REVERT: H 435 LEU cc_start: 0.9185 (mt) cc_final: 0.8949 (pp) REVERT: I 49 GLU cc_start: 0.9169 (tp30) cc_final: 0.8912 (tp30) REVERT: I 68 THR cc_start: 0.8170 (p) cc_final: 0.7880 (p) REVERT: I 219 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7920 (mt-10) REVERT: I 220 GLN cc_start: 0.8799 (pt0) cc_final: 0.8449 (tm-30) REVERT: I 226 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8285 (mm-30) REVERT: I 227 ILE cc_start: 0.9268 (mt) cc_final: 0.9067 (mt) REVERT: I 229 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8881 (tp30) REVERT: I 309 MET cc_start: 0.9222 (mmm) cc_final: 0.8897 (mmp) REVERT: I 330 ARG cc_start: 0.8664 (mtt90) cc_final: 0.8357 (mtm-85) REVERT: I 332 PHE cc_start: 0.9049 (t80) cc_final: 0.8814 (t80) REVERT: I 335 ARG cc_start: 0.9062 (ttt180) cc_final: 0.8853 (ttm-80) REVERT: I 342 LYS cc_start: 0.9209 (mttt) cc_final: 0.9005 (pttm) REVERT: I 349 ASN cc_start: 0.7866 (p0) cc_final: 0.7353 (p0) REVERT: K 64 MET cc_start: 0.9057 (mtp) cc_final: 0.8414 (mmp) REVERT: K 77 LYS cc_start: 0.8865 (tttt) cc_final: 0.8023 (tttt) REVERT: K 87 GLN cc_start: 0.8284 (mm-40) cc_final: 0.6620 (pp30) REVERT: K 99 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8639 (mt-10) REVERT: K 176 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7595 (mmt90) REVERT: K 182 GLN cc_start: 0.8922 (tt0) cc_final: 0.8566 (pt0) REVERT: K 194 MET cc_start: 0.8576 (mmm) cc_final: 0.7980 (mmm) REVERT: K 201 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7862 (mm110) REVERT: M 14 LYS cc_start: 0.9311 (mttt) cc_final: 0.8789 (tptp) REVERT: M 19 MET cc_start: 0.7895 (mtp) cc_final: 0.6854 (ptp) REVERT: M 22 ILE cc_start: 0.8606 (mt) cc_final: 0.8338 (mt) REVERT: M 24 LYS cc_start: 0.8051 (mttt) cc_final: 0.7557 (tptp) REVERT: M 28 ILE cc_start: 0.8411 (tp) cc_final: 0.8023 (tp) REVERT: M 36 ILE cc_start: 0.8240 (mm) cc_final: 0.7690 (mm) REVERT: O 169 ASP cc_start: 0.9352 (t0) cc_final: 0.8937 (t0) REVERT: O 173 HIS cc_start: 0.8978 (m90) cc_final: 0.8438 (m90) REVERT: O 197 MET cc_start: 0.9047 (mmp) cc_final: 0.8766 (mmm) REVERT: R 76 LEU cc_start: 0.8679 (tp) cc_final: 0.8425 (tp) REVERT: R 93 GLU cc_start: 0.9347 (tp30) cc_final: 0.9071 (tp30) REVERT: R 126 MET cc_start: 0.6289 (ttp) cc_final: 0.5835 (tmm) outliers start: 0 outliers final: 0 residues processed: 736 average time/residue: 0.3356 time to fit residues: 371.3537 Evaluate side-chains 570 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN ** G 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 HIS ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 HIS H 414 ASN I 220 GLN O 122 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 21657 Z= 0.394 Angle : 0.920 12.074 29446 Z= 0.477 Chirality : 0.050 0.350 3433 Planarity : 0.007 0.104 3798 Dihedral : 7.507 60.871 3036 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.36 % Favored : 85.56 % Rotamer: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.16), residues: 2465 helix: -0.36 (0.14), residues: 1302 sheet: -2.04 (0.33), residues: 233 loop : -3.79 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 364 HIS 0.015 0.003 HIS B 924 PHE 0.055 0.003 PHE I 262 TYR 0.038 0.003 TYR M 46 ARG 0.009 0.001 ARG B 361 *********************** 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 672 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 670 time to evaluate : 2.441 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: 0.8487 (tptm) cc_final: 0.8077 (tptm) REVERT: B 28 LEU cc_start: 0.8446 (mt) cc_final: 0.8095 (mt) REVERT: B 145 LYS cc_start: 0.8181 (mttt) cc_final: 0.7832 (mmtm) REVERT: B 153 ASP cc_start: 0.8231 (p0) cc_final: 0.7816 (p0) REVERT: B 203 LYS cc_start: 0.8717 (tttt) cc_final: 0.8430 (tttp) REVERT: B 262 MET cc_start: 0.8238 (tpt) cc_final: 0.7800 (tpt) REVERT: B 278 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8426 (mttt) REVERT: B 322 MET cc_start: 0.8533 (ttp) cc_final: 0.8183 (ppp) REVERT: B 324 ILE cc_start: 0.8322 (mt) cc_final: 0.8042 (mt) REVERT: B 357 CYS cc_start: 0.7665 (m) cc_final: 0.7338 (t) REVERT: B 358 PHE cc_start: 0.9130 (m-80) cc_final: 0.8042 (m-80) REVERT: B 364 TRP cc_start: 0.8484 (t-100) cc_final: 0.7866 (t-100) REVERT: B 412 VAL cc_start: 0.9051 (t) cc_final: 0.8765 (t) REVERT: B 452 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7611 (ttmt) REVERT: B 463 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7574 (ttm170) REVERT: B 505 LYS cc_start: 0.9521 (mttt) cc_final: 0.9237 (mttt) REVERT: B 520 LYS cc_start: 0.9363 (mttt) cc_final: 0.9096 (tptt) REVERT: B 532 TYR cc_start: 0.6883 (m-10) cc_final: 0.6541 (m-10) REVERT: B 649 TRP cc_start: 0.7789 (m100) cc_final: 0.7043 (m100) REVERT: B 701 CYS cc_start: 0.7992 (m) cc_final: 0.7699 (m) REVERT: B 726 MET cc_start: 0.8446 (mtm) cc_final: 0.7916 (mtp) REVERT: B 753 MET cc_start: 0.8177 (ppp) cc_final: 0.7771 (ppp) REVERT: B 757 MET cc_start: 0.8483 (mtp) cc_final: 0.8239 (mtm) REVERT: B 797 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 913 MET cc_start: 0.9198 (ttp) cc_final: 0.8944 (ttm) REVERT: B 914 ILE cc_start: 0.8716 (mt) cc_final: 0.8478 (mt) REVERT: B 916 ASN cc_start: 0.8944 (t0) cc_final: 0.8523 (p0) REVERT: B 934 PRO cc_start: 0.8919 (Cg_endo) cc_final: 0.8691 (Cg_exo) REVERT: B 952 GLN cc_start: 0.8876 (mt0) cc_final: 0.8544 (tt0) REVERT: E 889 HIS cc_start: 0.8414 (m-70) cc_final: 0.7624 (m-70) REVERT: E 904 HIS cc_start: 0.9524 (t70) cc_final: 0.9234 (t-90) REVERT: E 916 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9215 (mmmm) REVERT: E 919 GLU cc_start: 0.9100 (mp0) cc_final: 0.8857 (mp0) REVERT: E 922 GLN cc_start: 0.9498 (mm-40) cc_final: 0.9217 (mm-40) REVERT: G 214 TYR cc_start: 0.8524 (m-10) cc_final: 0.8320 (m-80) REVERT: G 223 HIS cc_start: 0.9592 (t70) cc_final: 0.9288 (t70) REVERT: G 247 MET cc_start: 0.9138 (ptp) cc_final: 0.8887 (tmm) REVERT: G 248 TYR cc_start: 0.8911 (t80) cc_final: 0.8679 (t80) REVERT: G 251 LEU cc_start: 0.9605 (mt) cc_final: 0.9323 (mt) REVERT: G 563 GLU cc_start: 0.7841 (tt0) cc_final: 0.7437 (tm-30) REVERT: G 568 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7623 (mtt-85) REVERT: G 599 TYR cc_start: 0.8289 (m-80) cc_final: 0.7718 (m-80) REVERT: G 636 HIS cc_start: 0.8085 (t70) cc_final: 0.7693 (t-90) REVERT: G 649 ARG cc_start: 0.7019 (ptt180) cc_final: 0.6616 (ptt90) REVERT: G 774 MET cc_start: 0.6348 (mtt) cc_final: 0.6095 (mtp) REVERT: H 224 TYR cc_start: 0.8572 (t80) cc_final: 0.8007 (t80) REVERT: H 241 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8550 (tt0) REVERT: H 322 ASP cc_start: 0.8653 (p0) cc_final: 0.8449 (p0) REVERT: H 324 ASP cc_start: 0.8040 (m-30) cc_final: 0.7505 (p0) REVERT: H 335 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8445 (ttp-110) REVERT: H 336 LEU cc_start: 0.9593 (mt) cc_final: 0.8874 (mm) REVERT: H 350 ASN cc_start: 0.7354 (t0) cc_final: 0.6869 (t0) REVERT: H 363 TRP cc_start: 0.8318 (t60) cc_final: 0.8099 (t60) REVERT: H 428 LEU cc_start: 0.8935 (tp) cc_final: 0.8580 (mm) REVERT: H 435 LEU cc_start: 0.9247 (mt) cc_final: 0.8944 (pp) REVERT: I 219 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8012 (mt-10) REVERT: I 226 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8433 (mm-30) REVERT: I 316 GLN cc_start: 0.7801 (mp10) cc_final: 0.7225 (mp10) REVERT: I 326 HIS cc_start: 0.9179 (m170) cc_final: 0.8820 (m170) REVERT: I 332 PHE cc_start: 0.9173 (t80) cc_final: 0.8950 (t80) REVERT: I 336 LEU cc_start: 0.9453 (mt) cc_final: 0.9206 (mt) REVERT: I 427 LEU cc_start: 0.9505 (mt) cc_final: 0.9201 (pp) REVERT: K 64 MET cc_start: 0.9087 (mtp) cc_final: 0.8443 (mmp) REVERT: K 65 LEU cc_start: 0.9653 (tp) cc_final: 0.9443 (tt) REVERT: K 87 GLN cc_start: 0.8347 (mm-40) cc_final: 0.6526 (pp30) REVERT: K 182 GLN cc_start: 0.9011 (tt0) cc_final: 0.8682 (pt0) REVERT: K 194 MET cc_start: 0.8532 (mmm) cc_final: 0.8233 (mmt) REVERT: M 14 LYS cc_start: 0.9157 (mttt) cc_final: 0.8903 (tptp) REVERT: M 19 MET cc_start: 0.7884 (mtp) cc_final: 0.7184 (ptp) REVERT: M 24 LYS cc_start: 0.8291 (mttt) cc_final: 0.7829 (tptp) REVERT: M 36 ILE cc_start: 0.8381 (mm) cc_final: 0.7580 (mm) REVERT: M 78 ARG cc_start: 0.9096 (tpt-90) cc_final: 0.8728 (tpt170) REVERT: O 169 ASP cc_start: 0.9362 (t0) cc_final: 0.8919 (t0) REVERT: O 173 HIS cc_start: 0.9002 (m90) cc_final: 0.8482 (m90) REVERT: O 197 MET cc_start: 0.9038 (mmp) cc_final: 0.8718 (mmm) REVERT: O 198 GLU cc_start: 0.9266 (tt0) cc_final: 0.9045 (tt0) REVERT: R 76 LEU cc_start: 0.8741 (tp) cc_final: 0.8534 (tp) REVERT: R 93 GLU cc_start: 0.9332 (tp30) cc_final: 0.9098 (tp30) REVERT: R 101 GLN cc_start: 0.9670 (mm110) cc_final: 0.9430 (mm-40) REVERT: R 111 LEU cc_start: 0.9215 (tt) cc_final: 0.8905 (tt) outliers start: 2 outliers final: 0 residues processed: 671 average time/residue: 0.3393 time to fit residues: 344.0491 Evaluate side-chains 522 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 272 GLN B 393 HIS ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** B 471 GLN ** 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 B 946 ASN ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 626 HIS ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN H 274 ASN H 414 ASN I 220 GLN I 270 ASN ** K 182 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5056 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= 0.243 Angle : 0.800 10.210 29446 Z= 0.412 Chirality : 0.047 0.400 3433 Planarity : 0.006 0.102 3798 Dihedral : 7.059 59.440 3036 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.45 % Favored : 87.46 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 3.81 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2465 helix: -0.02 (0.14), residues: 1302 sheet: -1.74 (0.34), residues: 222 loop : -3.69 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 627 HIS 0.012 0.002 HIS H 422 PHE 0.043 0.002 PHE I 262 TYR 0.027 0.002 TYR I 224 ARG 0.008 0.001 ARG B 392 *********************** 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 693 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 693 time to evaluate : 2.161 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 28 LEU cc_start: 0.8431 (mt) cc_final: 0.8211 (mt) REVERT: B 145 LYS cc_start: 0.8181 (mttt) cc_final: 0.7744 (mmtm) REVERT: B 148 ILE cc_start: 0.8739 (mp) cc_final: 0.8464 (mm) REVERT: B 153 ASP cc_start: 0.8164 (p0) cc_final: 0.7826 (p0) REVERT: B 262 MET cc_start: 0.8070 (tpt) cc_final: 0.7867 (tpt) REVERT: B 278 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8448 (mttt) REVERT: B 299 TYR cc_start: 0.8787 (t80) cc_final: 0.8067 (t80) REVERT: B 322 MET cc_start: 0.8562 (ttp) cc_final: 0.8204 (ppp) REVERT: B 358 PHE cc_start: 0.9110 (m-80) cc_final: 0.8323 (m-80) REVERT: B 364 TRP cc_start: 0.8532 (t-100) cc_final: 0.7983 (t-100) REVERT: B 452 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7659 (tttt) REVERT: B 457 MET cc_start: 0.8468 (mmp) cc_final: 0.8150 (mmp) REVERT: B 505 LYS cc_start: 0.9511 (mttt) cc_final: 0.9159 (mttt) REVERT: B 520 LYS cc_start: 0.9330 (mttt) cc_final: 0.9075 (tptt) REVERT: B 531 PHE cc_start: 0.8483 (m-80) cc_final: 0.8040 (m-80) REVERT: B 701 CYS cc_start: 0.7767 (m) cc_final: 0.7545 (m) REVERT: B 726 MET cc_start: 0.8352 (mtm) cc_final: 0.7987 (mtp) REVERT: B 753 MET cc_start: 0.8232 (ppp) cc_final: 0.7778 (ppp) REVERT: B 757 MET cc_start: 0.8404 (mtp) cc_final: 0.8033 (mtm) REVERT: B 797 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 832 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 837 LEU cc_start: 0.8748 (mt) cc_final: 0.8508 (mt) REVERT: B 846 TYR cc_start: 0.7717 (t80) cc_final: 0.7307 (t80) REVERT: B 854 CYS cc_start: 0.8406 (m) cc_final: 0.7748 (t) REVERT: B 914 ILE cc_start: 0.8764 (mt) cc_final: 0.8445 (mt) REVERT: B 916 ASN cc_start: 0.8858 (t0) cc_final: 0.8484 (p0) REVERT: B 934 PRO cc_start: 0.8819 (Cg_endo) cc_final: 0.8608 (Cg_exo) REVERT: B 952 GLN cc_start: 0.8793 (mt0) cc_final: 0.8508 (tt0) REVERT: E 889 HIS cc_start: 0.8133 (m-70) cc_final: 0.7671 (m-70) REVERT: E 904 HIS cc_start: 0.9587 (t70) cc_final: 0.9263 (t-90) REVERT: E 915 GLU cc_start: 0.9292 (pp20) cc_final: 0.9044 (pp20) REVERT: E 916 LYS cc_start: 0.9421 (mmtt) cc_final: 0.9127 (mmmm) REVERT: E 922 GLN cc_start: 0.9532 (mm-40) cc_final: 0.9255 (mm-40) REVERT: G 221 LEU cc_start: 0.9486 (mm) cc_final: 0.9162 (mm) REVERT: G 256 HIS cc_start: 0.8235 (m90) cc_final: 0.7932 (m-70) REVERT: G 559 LEU cc_start: 0.8503 (tp) cc_final: 0.7828 (tp) REVERT: G 568 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7230 (mtt-85) REVERT: G 599 TYR cc_start: 0.8179 (m-80) cc_final: 0.7661 (m-80) REVERT: G 623 PHE cc_start: 0.8357 (m-10) cc_final: 0.7920 (m-80) REVERT: G 636 HIS cc_start: 0.7954 (t70) cc_final: 0.7498 (t-90) REVERT: G 640 ASN cc_start: 0.7265 (t0) cc_final: 0.6941 (t0) REVERT: G 649 ARG cc_start: 0.6833 (ptt180) cc_final: 0.6602 (ptt90) REVERT: G 684 LEU cc_start: 0.8163 (tp) cc_final: 0.7873 (tp) REVERT: H 224 TYR cc_start: 0.8561 (t80) cc_final: 0.8073 (t80) REVERT: H 241 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8593 (tt0) REVERT: H 256 LEU cc_start: 0.9380 (tp) cc_final: 0.9153 (tt) REVERT: H 260 SER cc_start: 0.8989 (t) cc_final: 0.8774 (t) REVERT: H 279 LEU cc_start: 0.9127 (mt) cc_final: 0.8866 (mt) REVERT: H 282 LEU cc_start: 0.9563 (mt) cc_final: 0.9223 (mt) REVERT: H 283 MET cc_start: 0.9064 (mmp) cc_final: 0.8788 (mmm) REVERT: H 297 LEU cc_start: 0.9172 (tp) cc_final: 0.8725 (tt) REVERT: H 324 ASP cc_start: 0.8114 (m-30) cc_final: 0.7782 (p0) REVERT: H 327 TRP cc_start: 0.7550 (m100) cc_final: 0.6263 (m100) REVERT: H 335 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8526 (ttp-110) REVERT: H 336 LEU cc_start: 0.9596 (mt) cc_final: 0.9115 (mt) REVERT: H 373 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8549 (mtm180) REVERT: H 428 LEU cc_start: 0.8907 (tp) cc_final: 0.8562 (mm) REVERT: H 435 LEU cc_start: 0.9182 (mt) cc_final: 0.8904 (pp) REVERT: I 49 GLU cc_start: 0.9163 (tp30) cc_final: 0.8933 (tp30) REVERT: I 219 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7826 (mt-10) REVERT: I 221 GLN cc_start: 0.8687 (pt0) cc_final: 0.8260 (pt0) REVERT: I 226 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8299 (mm-30) REVERT: I 227 ILE cc_start: 0.9272 (mt) cc_final: 0.8975 (mt) REVERT: I 259 PHE cc_start: 0.7318 (t80) cc_final: 0.7019 (t80) REVERT: I 309 MET cc_start: 0.9199 (mmm) cc_final: 0.8936 (mmp) REVERT: I 316 GLN cc_start: 0.7745 (mp10) cc_final: 0.7370 (mp10) REVERT: I 326 HIS cc_start: 0.9124 (m170) cc_final: 0.8887 (m170) REVERT: I 332 PHE cc_start: 0.9155 (t80) cc_final: 0.8831 (t80) REVERT: I 336 LEU cc_start: 0.9397 (mt) cc_final: 0.9189 (mt) REVERT: I 342 LYS cc_start: 0.8473 (pttt) cc_final: 0.8179 (pttm) REVERT: K 54 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8985 (mt-10) REVERT: K 64 MET cc_start: 0.9081 (mtp) cc_final: 0.8449 (mmp) REVERT: K 65 LEU cc_start: 0.9676 (tp) cc_final: 0.9438 (tt) REVERT: K 77 LYS cc_start: 0.8868 (tttt) cc_final: 0.7906 (ttmt) REVERT: K 87 GLN cc_start: 0.8271 (mm-40) cc_final: 0.6465 (pp30) REVERT: K 182 GLN cc_start: 0.8946 (tt0) cc_final: 0.8600 (pt0) REVERT: K 194 MET cc_start: 0.8516 (mmm) cc_final: 0.8051 (mmm) REVERT: K 196 LYS cc_start: 0.6366 (mppt) cc_final: 0.6149 (mppt) REVERT: M 14 LYS cc_start: 0.9141 (mttt) cc_final: 0.8897 (tptp) REVERT: M 24 LYS cc_start: 0.8391 (mttt) cc_final: 0.8070 (tptp) REVERT: M 28 ILE cc_start: 0.8465 (tp) cc_final: 0.8108 (tp) REVERT: M 36 ILE cc_start: 0.8299 (mm) cc_final: 0.7966 (mm) REVERT: M 57 TYR cc_start: 0.9535 (m-10) cc_final: 0.9289 (m-10) REVERT: O 126 TYR cc_start: 0.8061 (m-10) cc_final: 0.7764 (m-80) REVERT: O 169 ASP cc_start: 0.9337 (t0) cc_final: 0.8859 (t0) REVERT: O 173 HIS cc_start: 0.8975 (m90) cc_final: 0.8606 (m90) REVERT: O 197 MET cc_start: 0.9098 (mmp) cc_final: 0.8671 (mmm) REVERT: O 198 GLU cc_start: 0.9205 (tt0) cc_final: 0.8992 (pt0) REVERT: R 56 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7963 (tm-30) REVERT: R 76 LEU cc_start: 0.8770 (tp) cc_final: 0.8543 (tp) REVERT: R 86 GLN cc_start: 0.9471 (mp10) cc_final: 0.9236 (mp10) REVERT: R 93 GLU cc_start: 0.9277 (tp30) cc_final: 0.9027 (tp30) outliers start: 0 outliers final: 0 residues processed: 693 average time/residue: 0.3534 time to fit residues: 372.7992 Evaluate side-chains 547 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 924 HIS B 946 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 HIS G 631 ASN ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 414 ASN I 220 GLN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 21657 Z= 0.329 Angle : 0.861 11.276 29446 Z= 0.445 Chirality : 0.049 0.422 3433 Planarity : 0.006 0.102 3798 Dihedral : 7.117 61.169 3036 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.91 % Favored : 86.00 % Rotamer: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2465 helix: -0.05 (0.14), residues: 1304 sheet: -1.74 (0.34), residues: 238 loop : -3.70 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 649 HIS 0.015 0.002 HIS H 430 PHE 0.050 0.003 PHE I 262 TYR 0.042 0.003 TYR B 794 ARG 0.007 0.001 ARG H 239 *********************** 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 663 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 662 time to evaluate : 2.460 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: B 27 LYS cc_start: 0.8559 (tptm) cc_final: 0.8017 (tppt) REVERT: B 28 LEU cc_start: 0.8494 (mt) cc_final: 0.8109 (mt) REVERT: B 145 LYS cc_start: 0.8288 (mttt) cc_final: 0.7877 (mmtm) REVERT: B 278 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8523 (mttt) REVERT: B 322 MET cc_start: 0.8555 (ttp) cc_final: 0.8204 (ppp) REVERT: B 324 ILE cc_start: 0.8331 (mt) cc_final: 0.8119 (mt) REVERT: B 358 PHE cc_start: 0.9048 (m-80) cc_final: 0.8582 (m-80) REVERT: B 412 VAL cc_start: 0.9075 (t) cc_final: 0.8821 (t) REVERT: B 452 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7572 (ttmt) REVERT: B 456 VAL cc_start: 0.9080 (m) cc_final: 0.8835 (m) REVERT: B 505 LYS cc_start: 0.9442 (mttt) cc_final: 0.9187 (mttt) REVERT: B 520 LYS cc_start: 0.9338 (mttt) cc_final: 0.9103 (tptt) REVERT: B 531 PHE cc_start: 0.8761 (m-80) cc_final: 0.8265 (m-80) REVERT: B 588 HIS cc_start: 0.7868 (m-70) cc_final: 0.7474 (m-70) REVERT: B 599 ASN cc_start: 0.9041 (p0) cc_final: 0.8751 (m-40) REVERT: B 614 MET cc_start: 0.7558 (mmm) cc_final: 0.7282 (mmm) REVERT: B 701 CYS cc_start: 0.7989 (m) cc_final: 0.7632 (m) REVERT: B 753 MET cc_start: 0.8285 (ppp) cc_final: 0.8038 (ppp) REVERT: B 757 MET cc_start: 0.8549 (mtp) cc_final: 0.8271 (ttt) REVERT: B 771 VAL cc_start: 0.9442 (t) cc_final: 0.9241 (t) REVERT: B 774 PHE cc_start: 0.9090 (t80) cc_final: 0.8835 (t80) REVERT: B 797 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 854 CYS cc_start: 0.8682 (m) cc_final: 0.7809 (t) REVERT: B 913 MET cc_start: 0.9248 (mtt) cc_final: 0.8807 (mtt) REVERT: B 914 ILE cc_start: 0.8981 (mt) cc_final: 0.8751 (mt) REVERT: B 916 ASN cc_start: 0.8986 (t0) cc_final: 0.8566 (p0) REVERT: B 955 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8821 (mttt) REVERT: B 964 ASP cc_start: 0.6807 (m-30) cc_final: 0.5383 (m-30) REVERT: E 870 GLU cc_start: 0.8166 (pp20) cc_final: 0.7907 (pp20) REVERT: E 885 ILE cc_start: 0.8380 (mm) cc_final: 0.8169 (mm) REVERT: E 889 HIS cc_start: 0.8423 (m-70) cc_final: 0.8072 (m-70) REVERT: E 904 HIS cc_start: 0.9618 (t70) cc_final: 0.9263 (t70) REVERT: E 915 GLU cc_start: 0.9473 (pp20) cc_final: 0.9145 (pp20) REVERT: E 916 LYS cc_start: 0.9428 (mmtt) cc_final: 0.9196 (mmmt) REVERT: E 919 GLU cc_start: 0.8993 (pm20) cc_final: 0.8605 (pm20) REVERT: E 922 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9294 (mm-40) REVERT: G 221 LEU cc_start: 0.9505 (mm) cc_final: 0.9262 (mm) REVERT: G 224 PHE cc_start: 0.9289 (t80) cc_final: 0.9037 (t80) REVERT: G 256 HIS cc_start: 0.8281 (m90) cc_final: 0.8004 (m-70) REVERT: G 589 TRP cc_start: 0.7948 (m-90) cc_final: 0.7423 (m-90) REVERT: G 599 TYR cc_start: 0.8247 (m-80) cc_final: 0.7754 (m-80) REVERT: G 636 HIS cc_start: 0.8055 (t70) cc_final: 0.7594 (t-90) REVERT: G 640 ASN cc_start: 0.7176 (t0) cc_final: 0.6934 (t0) REVERT: G 649 ARG cc_start: 0.6929 (ptt180) cc_final: 0.6417 (ptt90) REVERT: G 654 TRP cc_start: 0.8190 (m100) cc_final: 0.7332 (m100) REVERT: H 224 TYR cc_start: 0.8560 (t80) cc_final: 0.8064 (t80) REVERT: H 241 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8711 (tt0) REVERT: H 244 GLN cc_start: 0.8563 (tp40) cc_final: 0.8202 (tp-100) REVERT: H 260 SER cc_start: 0.8962 (t) cc_final: 0.8689 (t) REVERT: H 282 LEU cc_start: 0.9666 (mt) cc_final: 0.9436 (mt) REVERT: H 335 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8449 (ttp-110) REVERT: H 336 LEU cc_start: 0.9604 (mt) cc_final: 0.8733 (mm) REVERT: H 398 GLN cc_start: 0.8966 (mp10) cc_final: 0.8427 (mp10) REVERT: H 428 LEU cc_start: 0.8900 (tp) cc_final: 0.8571 (mm) REVERT: H 435 LEU cc_start: 0.9196 (mt) cc_final: 0.8929 (pp) REVERT: I 219 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8060 (mt-10) REVERT: I 221 GLN cc_start: 0.8743 (pt0) cc_final: 0.8487 (pt0) REVERT: I 226 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8329 (mm-30) REVERT: I 227 ILE cc_start: 0.9295 (mt) cc_final: 0.8912 (mt) REVERT: I 259 PHE cc_start: 0.7337 (t80) cc_final: 0.6932 (t80) REVERT: I 285 MET cc_start: 0.8953 (tmm) cc_final: 0.8654 (tmm) REVERT: I 316 GLN cc_start: 0.7729 (mp10) cc_final: 0.7183 (mp10) REVERT: I 325 ASN cc_start: 0.8978 (m110) cc_final: 0.8717 (p0) REVERT: I 326 HIS cc_start: 0.9122 (m170) cc_final: 0.8076 (m170) REVERT: I 332 PHE cc_start: 0.9139 (t80) cc_final: 0.8845 (t80) REVERT: I 336 LEU cc_start: 0.9441 (mt) cc_final: 0.9185 (mt) REVERT: I 342 LYS cc_start: 0.8549 (pttt) cc_final: 0.8077 (pttm) REVERT: I 427 LEU cc_start: 0.9517 (mt) cc_final: 0.9207 (pp) REVERT: K 54 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9009 (mt-10) REVERT: K 64 MET cc_start: 0.9076 (mtp) cc_final: 0.8457 (mmp) REVERT: K 65 LEU cc_start: 0.9693 (tp) cc_final: 0.9487 (tt) REVERT: K 77 LYS cc_start: 0.8578 (tttt) cc_final: 0.8062 (tppt) REVERT: K 81 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8044 (mm-30) REVERT: K 87 GLN cc_start: 0.8302 (mm-40) cc_final: 0.6455 (pp30) REVERT: K 182 GLN cc_start: 0.8846 (tt0) cc_final: 0.8608 (pt0) REVERT: M 14 LYS cc_start: 0.9137 (mttt) cc_final: 0.8883 (tptp) REVERT: M 24 LYS cc_start: 0.8396 (mttt) cc_final: 0.8046 (tptp) REVERT: M 28 ILE cc_start: 0.8662 (tp) cc_final: 0.8270 (tp) REVERT: M 57 TYR cc_start: 0.9516 (m-10) cc_final: 0.9260 (m-10) REVERT: M 78 ARG cc_start: 0.9108 (tpt-90) cc_final: 0.8713 (tpt170) REVERT: O 126 TYR cc_start: 0.8061 (m-10) cc_final: 0.7721 (m-80) REVERT: O 169 ASP cc_start: 0.9338 (t0) cc_final: 0.8841 (t0) REVERT: O 173 HIS cc_start: 0.8978 (m90) cc_final: 0.8602 (m90) REVERT: O 197 MET cc_start: 0.9107 (mmp) cc_final: 0.8659 (mmm) REVERT: R 56 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7830 (tm-30) REVERT: R 76 LEU cc_start: 0.8796 (tp) cc_final: 0.8555 (tp) REVERT: R 85 LEU cc_start: 0.9498 (mt) cc_final: 0.9269 (mt) REVERT: R 93 GLU cc_start: 0.9292 (tp30) cc_final: 0.9047 (tp30) outliers start: 1 outliers final: 1 residues processed: 663 average time/residue: 0.3387 time to fit residues: 341.5307 Evaluate side-chains 521 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 142 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN E 889 HIS E 923 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN H 302 HIS H 414 ASN I 220 GLN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 GLN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 21657 Z= 0.477 Angle : 1.015 13.437 29446 Z= 0.527 Chirality : 0.054 0.493 3433 Planarity : 0.007 0.105 3798 Dihedral : 7.668 65.393 3036 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.38 % Favored : 84.54 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 5.71 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.16), residues: 2465 helix: -0.48 (0.14), residues: 1304 sheet: -1.82 (0.34), residues: 228 loop : -3.87 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 443 HIS 0.035 0.003 HIS G 782 PHE 0.050 0.003 PHE I 262 TYR 0.032 0.003 TYR B 283 ARG 0.008 0.001 ARG B 678 *********************** 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 632 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 632 time to evaluate : 2.481 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: B 145 LYS cc_start: 0.8305 (mttt) cc_final: 0.7991 (mmtm) REVERT: B 217 ASN cc_start: 0.9016 (m-40) cc_final: 0.8645 (m110) REVERT: B 278 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8488 (mtmt) REVERT: B 290 PHE cc_start: 0.8758 (t80) cc_final: 0.8451 (t80) REVERT: B 295 LEU cc_start: 0.8807 (mm) cc_final: 0.8568 (mm) REVERT: B 299 TYR cc_start: 0.8947 (t80) cc_final: 0.8375 (t80) REVERT: B 322 MET cc_start: 0.8546 (ttp) cc_final: 0.8227 (ppp) REVERT: B 324 ILE cc_start: 0.8654 (mt) cc_final: 0.8275 (mt) REVERT: B 358 PHE cc_start: 0.9068 (m-80) cc_final: 0.8775 (m-80) REVERT: B 364 TRP cc_start: 0.8728 (t-100) cc_final: 0.8262 (t-100) REVERT: B 376 TYR cc_start: 0.8003 (t80) cc_final: 0.7795 (t80) REVERT: B 452 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7646 (tttt) REVERT: B 505 LYS cc_start: 0.9422 (mttt) cc_final: 0.9104 (mttt) REVERT: B 531 PHE cc_start: 0.8536 (m-80) cc_final: 0.8177 (m-80) REVERT: B 588 HIS cc_start: 0.7614 (m-70) cc_final: 0.7215 (m-70) REVERT: B 614 MET cc_start: 0.7247 (mmm) cc_final: 0.6966 (mmm) REVERT: B 701 CYS cc_start: 0.8141 (m) cc_final: 0.7586 (m) REVERT: B 726 MET cc_start: 0.8397 (mtm) cc_final: 0.8164 (mtp) REVERT: B 771 VAL cc_start: 0.9492 (t) cc_final: 0.9212 (t) REVERT: B 797 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 823 ASN cc_start: 0.8535 (p0) cc_final: 0.8334 (p0) REVERT: B 833 ILE cc_start: 0.9040 (pt) cc_final: 0.8833 (pt) REVERT: B 854 CYS cc_start: 0.8872 (m) cc_final: 0.8649 (m) REVERT: B 916 ASN cc_start: 0.9051 (t0) cc_final: 0.8585 (p0) REVERT: B 955 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8958 (mttt) REVERT: B 964 ASP cc_start: 0.6818 (m-30) cc_final: 0.5810 (m-30) REVERT: E 870 GLU cc_start: 0.8320 (pp20) cc_final: 0.8079 (pp20) REVERT: E 889 HIS cc_start: 0.8341 (m90) cc_final: 0.7888 (m-70) REVERT: E 904 HIS cc_start: 0.9591 (t70) cc_final: 0.9144 (t-90) REVERT: E 908 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9053 (mm110) REVERT: E 912 ASN cc_start: 0.9495 (t0) cc_final: 0.9192 (t0) REVERT: E 919 GLU cc_start: 0.8943 (pm20) cc_final: 0.8644 (mp0) REVERT: E 922 GLN cc_start: 0.9628 (mm-40) cc_final: 0.9397 (mm-40) REVERT: G 221 LEU cc_start: 0.9604 (mm) cc_final: 0.9364 (mm) REVERT: G 224 PHE cc_start: 0.9347 (t80) cc_final: 0.9113 (t80) REVERT: G 256 HIS cc_start: 0.8267 (m90) cc_final: 0.8048 (m-70) REVERT: G 261 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9107 (ptpp) REVERT: G 301 ARG cc_start: 0.7989 (tpt170) cc_final: 0.7758 (tpt90) REVERT: G 563 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7210 (tm-30) REVERT: G 568 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7050 (mtt-85) REVERT: G 599 TYR cc_start: 0.8163 (m-80) cc_final: 0.7558 (m-80) REVERT: G 636 HIS cc_start: 0.8032 (t70) cc_final: 0.7568 (t-90) REVERT: G 640 ASN cc_start: 0.7538 (t0) cc_final: 0.7328 (t0) REVERT: G 649 ARG cc_start: 0.6974 (ptt180) cc_final: 0.6603 (ptt90) REVERT: G 654 TRP cc_start: 0.8325 (m100) cc_final: 0.7303 (m100) REVERT: H 224 TYR cc_start: 0.8735 (t80) cc_final: 0.8038 (t80) REVERT: H 241 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8608 (tt0) REVERT: H 244 GLN cc_start: 0.8511 (tp40) cc_final: 0.8309 (tp-100) REVERT: H 275 ASN cc_start: 0.9269 (t0) cc_final: 0.8979 (t0) REVERT: H 282 LEU cc_start: 0.9680 (mt) cc_final: 0.9474 (mt) REVERT: H 285 MET cc_start: 0.8848 (ttt) cc_final: 0.8632 (mtp) REVERT: H 295 LEU cc_start: 0.8515 (mt) cc_final: 0.8308 (mt) REVERT: H 336 LEU cc_start: 0.9602 (mt) cc_final: 0.8898 (mm) REVERT: H 423 VAL cc_start: 0.9658 (t) cc_final: 0.8948 (t) REVERT: H 435 LEU cc_start: 0.9277 (mt) cc_final: 0.8987 (pp) REVERT: I 68 THR cc_start: 0.8459 (p) cc_final: 0.7793 (t) REVERT: I 219 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8079 (mt-10) REVERT: I 226 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8440 (mm-30) REVERT: I 227 ILE cc_start: 0.9358 (mt) cc_final: 0.8979 (mt) REVERT: I 259 PHE cc_start: 0.7387 (t80) cc_final: 0.6859 (t80) REVERT: I 309 MET cc_start: 0.9087 (mmm) cc_final: 0.8832 (mmm) REVERT: I 316 GLN cc_start: 0.7405 (mp10) cc_final: 0.7084 (mp10) REVERT: I 332 PHE cc_start: 0.9190 (t80) cc_final: 0.8883 (t80) REVERT: I 336 LEU cc_start: 0.9445 (mt) cc_final: 0.9215 (mt) REVERT: I 342 LYS cc_start: 0.8586 (pttt) cc_final: 0.8168 (pttm) REVERT: K 64 MET cc_start: 0.9189 (mtp) cc_final: 0.8545 (mmp) REVERT: K 65 LEU cc_start: 0.9689 (tp) cc_final: 0.9461 (tt) REVERT: K 77 LYS cc_start: 0.8701 (tttt) cc_final: 0.8414 (tttt) REVERT: K 221 ILE cc_start: 0.8349 (tp) cc_final: 0.8090 (mm) REVERT: M 14 LYS cc_start: 0.9127 (mttt) cc_final: 0.8889 (tptp) REVERT: M 21 GLN cc_start: 0.8782 (tp40) cc_final: 0.8528 (tp40) REVERT: M 24 LYS cc_start: 0.8570 (mttt) cc_final: 0.8227 (tptp) REVERT: M 28 ILE cc_start: 0.8658 (tp) cc_final: 0.8305 (tp) REVERT: M 32 GLU cc_start: 0.8149 (tt0) cc_final: 0.7736 (tm-30) REVERT: M 36 ILE cc_start: 0.8132 (mm) cc_final: 0.7684 (mm) REVERT: M 57 TYR cc_start: 0.9495 (m-10) cc_final: 0.9218 (m-10) REVERT: M 78 ARG cc_start: 0.9195 (tpt-90) cc_final: 0.8775 (tpt170) REVERT: O 126 TYR cc_start: 0.8081 (m-10) cc_final: 0.7802 (m-80) REVERT: O 169 ASP cc_start: 0.9315 (t0) cc_final: 0.8843 (t0) REVERT: O 173 HIS cc_start: 0.8993 (m90) cc_final: 0.8639 (m90) REVERT: O 197 MET cc_start: 0.9065 (mmp) cc_final: 0.8703 (mmm) REVERT: R 56 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7600 (tm-30) REVERT: R 59 THR cc_start: 0.8847 (t) cc_final: 0.8600 (t) REVERT: R 76 LEU cc_start: 0.8704 (tp) cc_final: 0.8438 (tp) REVERT: R 124 TRP cc_start: 0.8100 (m100) cc_final: 0.7892 (m100) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.3312 time to fit residues: 321.1893 Evaluate side-chains 492 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS ** B 430 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 750 GLN B 946 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 HIS H 414 ASN I 220 GLN I 221 GLN K 182 GLN O 122 GLN O 160 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21657 Z= 0.235 Angle : 0.831 11.796 29446 Z= 0.427 Chirality : 0.048 0.433 3433 Planarity : 0.006 0.099 3798 Dihedral : 6.935 58.094 3036 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.29 % Favored : 87.63 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2465 helix: 0.08 (0.14), residues: 1290 sheet: -1.70 (0.34), residues: 236 loop : -3.66 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 589 HIS 0.013 0.002 HIS G 782 PHE 0.028 0.002 PHE I 262 TYR 0.049 0.002 TYR B 794 ARG 0.015 0.001 ARG H 330 *********************** 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 682 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 2.349 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: B 27 LYS cc_start: 0.8409 (tptm) cc_final: 0.7898 (tppt) REVERT: B 28 LEU cc_start: 0.8364 (mt) cc_final: 0.7875 (mt) REVERT: B 145 LYS cc_start: 0.8313 (mttt) cc_final: 0.8067 (mmtm) REVERT: B 270 LEU cc_start: 0.8455 (mm) cc_final: 0.8235 (mm) REVERT: B 272 GLN cc_start: 0.8625 (pm20) cc_final: 0.8151 (pm20) REVERT: B 278 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8384 (mtmt) REVERT: B 289 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 324 ILE cc_start: 0.8346 (mt) cc_final: 0.8112 (mt) REVERT: B 355 PHE cc_start: 0.8224 (m-10) cc_final: 0.7923 (m-80) REVERT: B 358 PHE cc_start: 0.9078 (m-80) cc_final: 0.8837 (m-80) REVERT: B 364 TRP cc_start: 0.8639 (t-100) cc_final: 0.8200 (t-100) REVERT: B 505 LYS cc_start: 0.9416 (mttt) cc_final: 0.9167 (mttt) REVERT: B 531 PHE cc_start: 0.8688 (m-80) cc_final: 0.8344 (m-80) REVERT: B 588 HIS cc_start: 0.7955 (m-70) cc_final: 0.7466 (m-70) REVERT: B 614 MET cc_start: 0.7471 (mmm) cc_final: 0.7217 (mmm) REVERT: B 701 CYS cc_start: 0.7961 (m) cc_final: 0.7686 (m) REVERT: B 774 PHE cc_start: 0.9056 (t80) cc_final: 0.8855 (t80) REVERT: B 797 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 823 ASN cc_start: 0.8269 (p0) cc_final: 0.7963 (m110) REVERT: B 837 LEU cc_start: 0.8811 (mt) cc_final: 0.8592 (mt) REVERT: B 850 ILE cc_start: 0.9098 (mp) cc_final: 0.8892 (mp) REVERT: B 854 CYS cc_start: 0.8428 (m) cc_final: 0.7788 (t) REVERT: B 873 LEU cc_start: 0.7309 (tp) cc_final: 0.7102 (tp) REVERT: B 912 ASN cc_start: 0.8367 (t0) cc_final: 0.8114 (t0) REVERT: B 916 ASN cc_start: 0.9111 (t0) cc_final: 0.8510 (p0) REVERT: B 955 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8787 (mttt) REVERT: E 870 GLU cc_start: 0.8325 (pp20) cc_final: 0.8058 (pp20) REVERT: E 885 ILE cc_start: 0.7847 (mp) cc_final: 0.7387 (mp) REVERT: E 889 HIS cc_start: 0.8133 (m90) cc_final: 0.7745 (m-70) REVERT: E 904 HIS cc_start: 0.9543 (t70) cc_final: 0.9220 (t-90) REVERT: E 915 GLU cc_start: 0.9412 (pp20) cc_final: 0.8937 (pp20) REVERT: E 916 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9128 (mmmt) REVERT: E 919 GLU cc_start: 0.8894 (pm20) cc_final: 0.8607 (mp0) REVERT: E 922 GLN cc_start: 0.9618 (mm-40) cc_final: 0.9387 (mm-40) REVERT: G 216 GLU cc_start: 0.9581 (mp0) cc_final: 0.9374 (mp0) REVERT: G 256 HIS cc_start: 0.8273 (m90) cc_final: 0.8044 (m-70) REVERT: G 559 LEU cc_start: 0.8652 (tp) cc_final: 0.8127 (tp) REVERT: G 590 ASP cc_start: 0.7487 (t0) cc_final: 0.6948 (p0) REVERT: G 591 THR cc_start: 0.9095 (p) cc_final: 0.8702 (p) REVERT: G 599 TYR cc_start: 0.8231 (m-80) cc_final: 0.7629 (m-80) REVERT: G 623 PHE cc_start: 0.8323 (m-10) cc_final: 0.7862 (m-80) REVERT: G 649 ARG cc_start: 0.6735 (ptt180) cc_final: 0.6157 (ptt90) REVERT: G 684 LEU cc_start: 0.8333 (tp) cc_final: 0.7932 (tp) REVERT: G 774 MET cc_start: 0.6181 (mtt) cc_final: 0.5946 (mtp) REVERT: H 224 TYR cc_start: 0.8538 (t80) cc_final: 0.8008 (t80) REVERT: H 256 LEU cc_start: 0.9409 (tp) cc_final: 0.9176 (tp) REVERT: H 260 SER cc_start: 0.9043 (t) cc_final: 0.8817 (t) REVERT: H 282 LEU cc_start: 0.9584 (mt) cc_final: 0.9335 (mt) REVERT: H 297 LEU cc_start: 0.9100 (tp) cc_final: 0.8771 (tt) REVERT: H 327 TRP cc_start: 0.7618 (m100) cc_final: 0.6852 (m100) REVERT: H 335 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8346 (ttp-110) REVERT: H 336 LEU cc_start: 0.9590 (mt) cc_final: 0.8727 (mm) REVERT: H 339 GLN cc_start: 0.7552 (mt0) cc_final: 0.7249 (mt0) REVERT: H 428 LEU cc_start: 0.8545 (tt) cc_final: 0.8311 (mm) REVERT: H 435 LEU cc_start: 0.9173 (mt) cc_final: 0.8916 (pp) REVERT: I 59 HIS cc_start: 0.8277 (m-70) cc_final: 0.7996 (m-70) REVERT: I 72 ASP cc_start: 0.8629 (m-30) cc_final: 0.8356 (m-30) REVERT: I 219 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7939 (mt-10) REVERT: I 226 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8298 (mm-30) REVERT: I 227 ILE cc_start: 0.9175 (mt) cc_final: 0.8671 (mt) REVERT: I 228 THR cc_start: 0.8931 (p) cc_final: 0.8714 (p) REVERT: I 309 MET cc_start: 0.9001 (mmm) cc_final: 0.8673 (mmp) REVERT: I 332 PHE cc_start: 0.9111 (t80) cc_final: 0.8815 (t80) REVERT: I 342 LYS cc_start: 0.8525 (pttt) cc_final: 0.8302 (pttm) REVERT: K 60 THR cc_start: 0.9233 (m) cc_final: 0.8935 (p) REVERT: K 64 MET cc_start: 0.9033 (mtp) cc_final: 0.8466 (mmp) REVERT: K 87 GLN cc_start: 0.8066 (mm-40) cc_final: 0.6427 (pp30) REVERT: K 182 GLN cc_start: 0.9066 (tt0) cc_final: 0.8740 (pt0) REVERT: K 194 MET cc_start: 0.8464 (mmm) cc_final: 0.8150 (mmm) REVERT: K 221 ILE cc_start: 0.8403 (tp) cc_final: 0.7949 (mm) REVERT: M 14 LYS cc_start: 0.9023 (mttt) cc_final: 0.8809 (tptp) REVERT: M 21 GLN cc_start: 0.8725 (tp40) cc_final: 0.8201 (tp40) REVERT: M 22 ILE cc_start: 0.8395 (mt) cc_final: 0.8173 (mt) REVERT: M 24 LYS cc_start: 0.8676 (mttt) cc_final: 0.8280 (tptp) REVERT: M 25 ASP cc_start: 0.8186 (m-30) cc_final: 0.7902 (m-30) REVERT: M 28 ILE cc_start: 0.8495 (tp) cc_final: 0.8046 (tp) REVERT: M 32 GLU cc_start: 0.8139 (tt0) cc_final: 0.7548 (tm-30) REVERT: M 78 ARG cc_start: 0.9102 (tpt-90) cc_final: 0.8614 (tpt170) REVERT: O 126 TYR cc_start: 0.8025 (m-10) cc_final: 0.7751 (m-80) REVERT: O 169 ASP cc_start: 0.9308 (t0) cc_final: 0.8768 (t0) REVERT: O 173 HIS cc_start: 0.8945 (m90) cc_final: 0.8527 (m90) REVERT: O 197 MET cc_start: 0.9077 (mmp) cc_final: 0.8771 (mmm) REVERT: R 56 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7442 (tm-30) REVERT: R 76 LEU cc_start: 0.8630 (tp) cc_final: 0.8404 (tp) REVERT: R 93 GLU cc_start: 0.9194 (tp30) cc_final: 0.8962 (tp30) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.3472 time to fit residues: 360.9827 Evaluate side-chains 526 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 235 HIS B 246 ASN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN H 414 ASN I 220 GLN I 270 ASN ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN O 160 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21657 Z= 0.279 Angle : 0.857 13.284 29446 Z= 0.441 Chirality : 0.048 0.383 3433 Planarity : 0.006 0.102 3798 Dihedral : 6.841 57.819 3036 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.14 % Favored : 86.73 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2465 helix: 0.12 (0.14), residues: 1302 sheet: -1.64 (0.34), residues: 233 loop : -3.66 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 368 HIS 0.019 0.002 HIS G 782 PHE 0.029 0.002 PHE I 262 TYR 0.061 0.002 TYR B 846 ARG 0.019 0.001 ARG H 330 *********************** 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 651 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 649 time to evaluate : 2.264 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 27 LYS cc_start: 0.8416 (tptm) cc_final: 0.7900 (tppt) REVERT: B 28 LEU cc_start: 0.8055 (mt) cc_final: 0.7627 (mt) REVERT: B 145 LYS cc_start: 0.8331 (mttt) cc_final: 0.8098 (mmtm) REVERT: B 270 LEU cc_start: 0.8371 (mm) cc_final: 0.8087 (mm) REVERT: B 278 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8473 (mttt) REVERT: B 289 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 290 PHE cc_start: 0.8387 (t80) cc_final: 0.8171 (t80) REVERT: B 301 TYR cc_start: 0.8082 (m-80) cc_final: 0.7770 (m-80) REVERT: B 355 PHE cc_start: 0.8184 (m-10) cc_final: 0.7597 (m-80) REVERT: B 358 PHE cc_start: 0.9138 (m-80) cc_final: 0.8927 (m-10) REVERT: B 406 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7748 (tt0) REVERT: B 412 VAL cc_start: 0.9226 (t) cc_final: 0.8893 (t) REVERT: B 452 LYS cc_start: 0.8026 (tttt) cc_final: 0.7573 (ttmt) REVERT: B 459 LEU cc_start: 0.8819 (mt) cc_final: 0.7528 (mt) REVERT: B 505 LYS cc_start: 0.9405 (mttt) cc_final: 0.9172 (mttt) REVERT: B 531 PHE cc_start: 0.8643 (m-80) cc_final: 0.8384 (m-80) REVERT: B 588 HIS cc_start: 0.7837 (m-70) cc_final: 0.7326 (m-70) REVERT: B 614 MET cc_start: 0.7389 (mmm) cc_final: 0.7088 (mmm) REVERT: B 701 CYS cc_start: 0.8047 (m) cc_final: 0.7796 (m) REVERT: B 797 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 823 ASN cc_start: 0.8142 (p0) cc_final: 0.7074 (p0) REVERT: B 833 ILE cc_start: 0.9054 (pt) cc_final: 0.8443 (pt) REVERT: B 837 LEU cc_start: 0.8892 (mt) cc_final: 0.8666 (mt) REVERT: B 850 ILE cc_start: 0.9039 (mp) cc_final: 0.8831 (mp) REVERT: B 854 CYS cc_start: 0.8636 (m) cc_final: 0.7687 (t) REVERT: B 912 ASN cc_start: 0.8367 (t0) cc_final: 0.8122 (t0) REVERT: B 916 ASN cc_start: 0.9139 (t0) cc_final: 0.8590 (p0) REVERT: B 955 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8789 (mttt) REVERT: B 964 ASP cc_start: 0.7074 (m-30) cc_final: 0.5778 (m-30) REVERT: E 885 ILE cc_start: 0.7881 (mp) cc_final: 0.7395 (mp) REVERT: E 889 HIS cc_start: 0.8134 (m90) cc_final: 0.7792 (m-70) REVERT: E 904 HIS cc_start: 0.9559 (t70) cc_final: 0.9247 (t-90) REVERT: E 919 GLU cc_start: 0.9166 (pm20) cc_final: 0.8933 (pm20) REVERT: E 922 GLN cc_start: 0.9613 (mm-40) cc_final: 0.9411 (mm-40) REVERT: G 559 LEU cc_start: 0.8713 (tp) cc_final: 0.8083 (tp) REVERT: G 590 ASP cc_start: 0.7585 (t0) cc_final: 0.6963 (p0) REVERT: G 591 THR cc_start: 0.9114 (p) cc_final: 0.8490 (p) REVERT: G 599 TYR cc_start: 0.8150 (m-80) cc_final: 0.7576 (m-80) REVERT: G 633 THR cc_start: 0.6978 (t) cc_final: 0.5780 (t) REVERT: G 640 ASN cc_start: 0.7578 (t0) cc_final: 0.7216 (t0) REVERT: G 649 ARG cc_start: 0.6804 (ptt180) cc_final: 0.6195 (ptt90) REVERT: G 684 LEU cc_start: 0.8401 (tp) cc_final: 0.8051 (tp) REVERT: H 224 TYR cc_start: 0.8535 (t80) cc_final: 0.7973 (t80) REVERT: H 241 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8559 (tt0) REVERT: H 260 SER cc_start: 0.8964 (t) cc_final: 0.8690 (t) REVERT: H 275 ASN cc_start: 0.9206 (t0) cc_final: 0.8856 (t0) REVERT: H 282 LEU cc_start: 0.9597 (mt) cc_final: 0.9363 (mt) REVERT: H 327 TRP cc_start: 0.7525 (m100) cc_final: 0.7209 (m100) REVERT: H 335 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.7850 (ttp-110) REVERT: H 387 VAL cc_start: 0.9081 (t) cc_final: 0.8848 (t) REVERT: H 398 GLN cc_start: 0.8607 (mp10) cc_final: 0.8240 (mp10) REVERT: H 423 VAL cc_start: 0.9624 (t) cc_final: 0.9240 (t) REVERT: H 435 LEU cc_start: 0.9221 (mt) cc_final: 0.8913 (pp) REVERT: I 72 ASP cc_start: 0.8641 (m-30) cc_final: 0.8397 (m-30) REVERT: I 219 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7963 (mt-10) REVERT: I 226 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8289 (mm-30) REVERT: I 227 ILE cc_start: 0.9216 (mt) cc_final: 0.8837 (mt) REVERT: I 270 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.7917 (t0) REVERT: I 278 LEU cc_start: 0.9084 (mt) cc_final: 0.8752 (pp) REVERT: I 309 MET cc_start: 0.9055 (mmm) cc_final: 0.8703 (mmp) REVERT: I 332 PHE cc_start: 0.9085 (t80) cc_final: 0.8824 (t80) REVERT: I 336 LEU cc_start: 0.9515 (mt) cc_final: 0.9309 (mt) REVERT: I 342 LYS cc_start: 0.8545 (pttt) cc_final: 0.8306 (pttm) REVERT: K 60 THR cc_start: 0.9247 (m) cc_final: 0.8933 (p) REVERT: K 64 MET cc_start: 0.9103 (mtp) cc_final: 0.8501 (mmp) REVERT: K 87 GLN cc_start: 0.8040 (mm-40) cc_final: 0.6415 (pp30) REVERT: K 176 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7420 (mmt180) REVERT: K 194 MET cc_start: 0.8445 (mmm) cc_final: 0.8149 (mmm) REVERT: K 221 ILE cc_start: 0.8392 (tp) cc_final: 0.7890 (mm) REVERT: M 14 LYS cc_start: 0.9021 (mttt) cc_final: 0.8800 (tptp) REVERT: M 21 GLN cc_start: 0.8615 (tp40) cc_final: 0.8148 (tp40) REVERT: M 24 LYS cc_start: 0.8708 (mttt) cc_final: 0.8422 (tptp) REVERT: M 25 ASP cc_start: 0.8165 (m-30) cc_final: 0.7884 (m-30) REVERT: M 28 ILE cc_start: 0.8521 (tp) cc_final: 0.7924 (tp) REVERT: M 32 GLU cc_start: 0.8100 (tt0) cc_final: 0.7628 (tm-30) REVERT: M 57 TYR cc_start: 0.9492 (m-10) cc_final: 0.9244 (m-10) REVERT: M 78 ARG cc_start: 0.9297 (tpt170) cc_final: 0.8754 (tpt170) REVERT: O 126 TYR cc_start: 0.8033 (m-10) cc_final: 0.7687 (m-80) REVERT: O 169 ASP cc_start: 0.9317 (t0) cc_final: 0.8629 (t0) REVERT: O 173 HIS cc_start: 0.8901 (m90) cc_final: 0.8493 (m90) REVERT: O 197 MET cc_start: 0.9096 (mmp) cc_final: 0.8831 (mmm) REVERT: R 56 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7404 (tm-30) REVERT: R 76 LEU cc_start: 0.8663 (tp) cc_final: 0.8399 (tp) REVERT: R 93 GLU cc_start: 0.9186 (tp30) cc_final: 0.8948 (tp30) REVERT: R 124 TRP cc_start: 0.8024 (m100) cc_final: 0.7738 (m100) outliers start: 2 outliers final: 0 residues processed: 650 average time/residue: 0.3271 time to fit residues: 325.4986 Evaluate side-chains 517 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 171 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 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 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 HIS ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN O 160 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 21657 Z= 0.468 Angle : 1.006 14.130 29446 Z= 0.522 Chirality : 0.054 0.425 3433 Planarity : 0.007 0.103 3798 Dihedral : 7.321 62.192 3036 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.29 % Favored : 84.58 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.17), residues: 2465 helix: -0.31 (0.14), residues: 1306 sheet: -1.86 (0.34), residues: 239 loop : -3.82 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 368 HIS 0.027 0.003 HIS G 782 PHE 0.055 0.003 PHE I 262 TYR 0.058 0.003 TYR B 846 ARG 0.015 0.001 ARG H 330 ********************** 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 611 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 2.243 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: B 27 LYS cc_start: 0.8516 (tptm) cc_final: 0.8036 (tppt) REVERT: B 28 LEU cc_start: 0.8234 (mt) cc_final: 0.7863 (mt) REVERT: B 145 LYS cc_start: 0.8442 (mttt) cc_final: 0.8165 (mmtm) REVERT: B 261 TYR cc_start: 0.7536 (m-10) cc_final: 0.7275 (m-80) REVERT: B 278 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8626 (mttt) REVERT: B 289 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 299 TYR cc_start: 0.8859 (t80) cc_final: 0.7748 (t80) REVERT: B 313 TYR cc_start: 0.7371 (t80) cc_final: 0.6761 (t80) REVERT: B 457 MET cc_start: 0.8553 (mmp) cc_final: 0.8335 (mmp) REVERT: B 459 LEU cc_start: 0.8708 (mt) cc_final: 0.8238 (mt) REVERT: B 505 LYS cc_start: 0.9429 (mttt) cc_final: 0.9128 (mttt) REVERT: B 531 PHE cc_start: 0.8431 (m-80) cc_final: 0.8191 (m-80) REVERT: B 588 HIS cc_start: 0.7631 (m-70) cc_final: 0.7163 (m-70) REVERT: B 614 MET cc_start: 0.7286 (mmm) cc_final: 0.7018 (mmm) REVERT: B 797 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 833 ILE cc_start: 0.9076 (pt) cc_final: 0.8689 (tp) REVERT: B 854 CYS cc_start: 0.8866 (m) cc_final: 0.8449 (m) REVERT: B 916 ASN cc_start: 0.9206 (t0) cc_final: 0.8633 (p0) REVERT: B 955 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8913 (mttt) REVERT: B 964 ASP cc_start: 0.7170 (m-30) cc_final: 0.6032 (m-30) REVERT: E 904 HIS cc_start: 0.9548 (t70) cc_final: 0.9174 (t-90) REVERT: E 908 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8971 (mm110) REVERT: E 919 GLU cc_start: 0.9216 (pm20) cc_final: 0.8913 (mp0) REVERT: E 922 GLN cc_start: 0.9655 (mm-40) cc_final: 0.9443 (mm-40) REVERT: G 559 LEU cc_start: 0.8620 (tp) cc_final: 0.8331 (tp) REVERT: G 568 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7458 (mmm-85) REVERT: G 599 TYR cc_start: 0.8042 (m-80) cc_final: 0.7459 (m-80) REVERT: G 640 ASN cc_start: 0.7828 (t0) cc_final: 0.7429 (t0) REVERT: G 649 ARG cc_start: 0.6771 (ptt180) cc_final: 0.6356 (ptt90) REVERT: G 654 TRP cc_start: 0.8289 (m100) cc_final: 0.7226 (m100) REVERT: G 684 LEU cc_start: 0.8591 (tp) cc_final: 0.8218 (tp) REVERT: H 224 TYR cc_start: 0.8699 (t80) cc_final: 0.8010 (t80) REVERT: H 241 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8653 (tt0) REVERT: H 275 ASN cc_start: 0.9257 (t0) cc_final: 0.8877 (t0) REVERT: H 291 ASP cc_start: 0.8974 (m-30) cc_final: 0.8649 (m-30) REVERT: H 327 TRP cc_start: 0.7545 (m100) cc_final: 0.7205 (m100) REVERT: H 336 LEU cc_start: 0.9569 (tt) cc_final: 0.9223 (tt) REVERT: H 423 VAL cc_start: 0.9661 (t) cc_final: 0.9196 (t) REVERT: H 435 LEU cc_start: 0.9260 (mt) cc_final: 0.8934 (pp) REVERT: I 68 THR cc_start: 0.8367 (p) cc_final: 0.7648 (t) REVERT: I 72 ASP cc_start: 0.8817 (m-30) cc_final: 0.8390 (m-30) REVERT: I 219 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7948 (mt-10) REVERT: I 226 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8446 (mm-30) REVERT: I 270 ASN cc_start: 0.9170 (m-40) cc_final: 0.8770 (p0) REVERT: I 309 MET cc_start: 0.9071 (mmm) cc_final: 0.8766 (mmp) REVERT: I 332 PHE cc_start: 0.9157 (t80) cc_final: 0.8875 (t80) REVERT: I 336 LEU cc_start: 0.9466 (mt) cc_final: 0.9192 (mt) REVERT: I 342 LYS cc_start: 0.8529 (pttt) cc_final: 0.8296 (pttm) REVERT: K 64 MET cc_start: 0.9070 (mtp) cc_final: 0.8492 (mmp) REVERT: K 70 SER cc_start: 0.9382 (m) cc_final: 0.9069 (p) REVERT: K 77 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8403 (tppt) REVERT: K 221 ILE cc_start: 0.8379 (tp) cc_final: 0.8009 (mm) REVERT: M 22 ILE cc_start: 0.8706 (mt) cc_final: 0.8405 (mt) REVERT: M 57 TYR cc_start: 0.9475 (m-10) cc_final: 0.9260 (m-10) REVERT: O 122 GLN cc_start: 0.9521 (tp-100) cc_final: 0.9297 (pt0) REVERT: O 169 ASP cc_start: 0.9333 (t0) cc_final: 0.8673 (t0) REVERT: O 173 HIS cc_start: 0.8903 (m90) cc_final: 0.8509 (m90) REVERT: O 197 MET cc_start: 0.9097 (mmp) cc_final: 0.8850 (mmm) REVERT: R 59 THR cc_start: 0.8733 (t) cc_final: 0.8533 (t) REVERT: R 76 LEU cc_start: 0.8620 (tp) cc_final: 0.8363 (tp) REVERT: R 93 GLU cc_start: 0.9200 (tp30) cc_final: 0.8997 (tp30) REVERT: R 124 TRP cc_start: 0.8001 (m100) cc_final: 0.7488 (m100) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.3466 time to fit residues: 324.8512 Evaluate side-chains 474 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 189 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 211 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 331 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN H 302 HIS I 220 GLN I 221 GLN ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.109014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086532 restraints weight = 73154.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.089115 restraints weight = 46792.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.090937 restraints weight = 31074.235| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21657 Z= 0.226 Angle : 0.843 11.713 29446 Z= 0.434 Chirality : 0.048 0.319 3433 Planarity : 0.006 0.099 3798 Dihedral : 6.753 56.448 3036 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.13 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 3.81 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2465 helix: 0.05 (0.14), residues: 1310 sheet: -1.64 (0.35), residues: 230 loop : -3.65 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 368 HIS 0.011 0.002 HIS G 782 PHE 0.032 0.002 PHE B 503 TYR 0.030 0.002 TYR B 846 ARG 0.010 0.001 ARG B 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6016.92 seconds wall clock time: 108 minutes 29.23 seconds (6509.23 seconds total)