Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:11:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/02_2023/6mzc_9298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/02_2023/6mzc_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_9298/02_2023/6mzc_9298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/02_2023/6mzc_9298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/02_2023/6mzc_9298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzc_9298/02_2023/6mzc_9298.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 11.97, per 1000 atoms: 0.56 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: 8.39 Conformation dependent library (CDL) restraints added in 3.0 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: 0.96 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: 6.25 Time building geometry restraints manager: 9.05 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 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. 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: 1.090 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: 0.030 Extract box with map and model: 6.640 Check model and map are aligned: 0.340 Process input model: 51.850 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 12.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.36 % Favored : 85.40 % Rotamer Outliers : 0.72 % 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 *********************** 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 : 2.405 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 outliers start: 15 outliers final: 5 residues processed: 951 average time/residue: 0.3580 time to fit residues: 503.1312 Evaluate side-chains 551 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 546 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3044 time to fit residues: 5.4786 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 HIS 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 316 GLN H 343 HIS ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN H 414 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 GLN ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 21657 Z= 0.245 Angle : 0.827 10.020 29446 Z= 0.434 Chirality : 0.047 0.372 3433 Planarity : 0.007 0.100 3798 Dihedral : 7.847 61.978 3036 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.81 % Favored : 88.11 % Rotamer Outliers : 0.34 % 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: -3.20 (0.15), residues: 2465 helix: -0.87 (0.13), residues: 1291 sheet: -2.10 (0.34), residues: 213 loop : -3.93 (0.18), residues: 961 *********************** 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 802 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 795 time to evaluate : 2.537 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 outliers start: 7 outliers final: 1 residues processed: 796 average time/residue: 0.3496 time to fit residues: 420.1972 Evaluate side-chains 565 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 564 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1878 time to fit residues: 3.6810 ------------------------------------------------------------------------------- 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: 2.9990 chunk 195 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 246 ASN B 353 GLN ** 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 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 256 HIS G 542 HIS G 605 HIS 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 302 HIS H 352 GLN ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN H 414 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN O 122 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 21657 Z= 0.306 Angle : 0.847 10.967 29446 Z= 0.443 Chirality : 0.048 0.399 3433 Planarity : 0.006 0.106 3798 Dihedral : 7.499 59.986 3036 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.35 % Favored : 86.57 % Rotamer Outliers : 0.05 % 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: -2.73 (0.16), residues: 2465 helix: -0.41 (0.13), residues: 1293 sheet: -1.95 (0.33), residues: 228 loop : -3.84 (0.19), residues: 944 *********************** 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 705 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 704 time to evaluate : 2.532 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 outliers start: 1 outliers final: 1 residues processed: 704 average time/residue: 0.3608 time to fit residues: 383.1045 Evaluate side-chains 532 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 531 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1919 time to fit residues: 3.7887 ------------------------------------------------------------------------------- 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: 7.9990 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 112 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 HIS ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS B 946 ASN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** G 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 302 HIS H 414 ASN I 220 GLN K 201 GLN O 122 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: 0.7366 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 21657 Z= 0.263 Angle : 0.803 10.262 29446 Z= 0.418 Chirality : 0.046 0.304 3433 Planarity : 0.006 0.102 3798 Dihedral : 7.203 59.107 3036 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 3.81 % 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: -2.27 (0.17), residues: 2465 helix: -0.05 (0.14), residues: 1302 sheet: -1.66 (0.35), residues: 219 loop : -3.65 (0.19), residues: 944 *********************** 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 701 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 700 time to evaluate : 2.238 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 outliers start: 1 outliers final: 1 residues processed: 700 average time/residue: 0.3512 time to fit residues: 370.3520 Evaluate side-chains 524 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1866 time to fit residues: 3.4725 ------------------------------------------------------------------------------- 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: 30.0000 chunk 142 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 183 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** 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 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 302 HIS H 414 ASN I 220 GLN O 122 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 21657 Z= 0.239 Angle : 0.792 11.071 29446 Z= 0.410 Chirality : 0.046 0.344 3433 Planarity : 0.006 0.102 3798 Dihedral : 6.963 60.301 3036 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer Outliers : 0.00 % 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: -2.09 (0.17), residues: 2465 helix: 0.10 (0.14), residues: 1307 sheet: -1.57 (0.35), residues: 222 loop : -3.60 (0.19), residues: 936 *********************** 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 680 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 2.587 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 outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.3366 time to fit residues: 349.9581 Evaluate side-chains 510 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1799 ------------------------------------------------------------------------------- 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: 4.9990 chunk 225 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 430 HIS ** 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 848 HIS ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN I 220 GLN O 122 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 21657 Z= 0.312 Angle : 0.850 10.839 29446 Z= 0.442 Chirality : 0.048 0.320 3433 Planarity : 0.006 0.101 3798 Dihedral : 7.027 60.181 3036 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 3.81 % 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: -2.13 (0.17), residues: 2465 helix: 0.06 (0.14), residues: 1299 sheet: -1.55 (0.35), residues: 228 loop : -3.59 (0.19), residues: 938 *********************** 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 656 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 655 time to evaluate : 2.568 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 outliers start: 1 outliers final: 0 residues processed: 655 average time/residue: 0.3499 time to fit residues: 349.1026 Evaluate side-chains 494 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3296 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** 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 848 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN I 220 GLN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 21657 Z= 0.338 Angle : 0.881 11.232 29446 Z= 0.456 Chirality : 0.049 0.373 3433 Planarity : 0.006 0.102 3798 Dihedral : 7.064 59.776 3036 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 26.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer Outliers : 0.05 % 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: -2.16 (0.17), residues: 2465 helix: 0.01 (0.14), residues: 1308 sheet: -1.44 (0.36), residues: 220 loop : -3.62 (0.19), residues: 937 *********************** 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 643 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 642 time to evaluate : 2.569 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 outliers start: 1 outliers final: 1 residues processed: 642 average time/residue: 0.3416 time to fit residues: 336.2234 Evaluate side-chains 507 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 2.321 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2705 time to fit residues: 3.6016 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** 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 687 GLN B 750 GLN B 908 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN B 952 GLN E 875 GLN E 889 HIS E 923 GLN ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN I 220 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 21657 Z= 0.238 Angle : 0.824 11.353 29446 Z= 0.427 Chirality : 0.048 0.354 3433 Planarity : 0.006 0.100 3798 Dihedral : 6.765 57.289 3036 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.09 % Favored : 87.87 % Rotamer Outliers : 0.00 % 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: -1.90 (0.17), residues: 2465 helix: 0.21 (0.14), residues: 1310 sheet: -1.14 (0.37), residues: 211 loop : -3.54 (0.20), residues: 944 *********************** 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 642 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 642 time to evaluate : 2.370 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 outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 0.3560 time to fit residues: 348.8581 Evaluate side-chains 508 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9328 ------------------------------------------------------------------------------- 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: 10.0000 chunk 239 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 232 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 220 optimal weight: 0.1980 chunk 231 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS ** B 430 HIS ** 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 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 924 HIS ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN E 889 HIS G 232 HIS G 276 GLN ** G 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN I 220 GLN ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 GLN ** O 122 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 21657 Z= 0.495 Angle : 1.021 13.536 29446 Z= 0.535 Chirality : 0.055 0.529 3433 Planarity : 0.007 0.104 3798 Dihedral : 7.352 62.719 3036 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 32.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -2.40 (0.17), residues: 2465 helix: -0.19 (0.14), residues: 1307 sheet: -1.72 (0.35), residues: 221 loop : -3.66 (0.19), residues: 937 *********************** 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 605 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 2.528 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 outliers start: 0 outliers final: 0 residues processed: 605 average time/residue: 0.3492 time to fit residues: 322.0164 Evaluate side-chains 479 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3120 ------------------------------------------------------------------------------- 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: 0.8980 chunk 245 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS ** B 430 HIS ** 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 912 ASN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN E 889 HIS E 923 GLN ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 HIS ** H 385 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: 0.7397 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 21657 Z= 0.297 Angle : 0.903 17.513 29446 Z= 0.467 Chirality : 0.050 0.435 3433 Planarity : 0.006 0.099 3798 Dihedral : 7.015 60.569 3036 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer Outliers : 0.00 % 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: -2.13 (0.17), residues: 2465 helix: 0.05 (0.14), residues: 1305 sheet: -1.37 (0.37), residues: 206 loop : -3.63 (0.19), residues: 954 ********************** 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 615 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 2.757 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 outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.3394 time to fit residues: 321.4468 Evaluate side-chains 494 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1260 ------------------------------------------------------------------------------- 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: 1.9990 chunk 218 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 189 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 211 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 285 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN ** B 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 631 ASN G 673 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.111552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089248 restraints weight = 72800.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092090 restraints weight = 45998.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094096 restraints weight = 29812.593| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6612 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= 0.228 Angle : 0.847 12.046 29446 Z= 0.438 Chirality : 0.049 0.422 3433 Planarity : 0.006 0.100 3798 Dihedral : 6.605 56.404 3036 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 3.81 % 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: -1.78 (0.17), residues: 2465 helix: 0.38 (0.14), residues: 1297 sheet: -1.14 (0.38), residues: 205 loop : -3.51 (0.19), residues: 963 =============================================================================== Job complete usr+sys time: 5929.76 seconds wall clock time: 107 minutes 10.56 seconds (6430.56 seconds total)