Starting phenix.real_space_refine on Fri Jun 28 22:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsq_32764/06_2024/7wsq_32764_updated.pdb" } resolution = 3.8 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= 0.003 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 S 90 5.16 5 C 10438 2.51 5 N 2856 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391} Chain breaks: 1 Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500} Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "F" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1743 SG CYS A 226 56.402 34.924 73.094 1.00 11.67 S ATOM 1714 SG CYS A 222 54.539 31.327 76.966 1.00 16.07 S ATOM 1674 SG CYS A 216 56.131 28.347 72.238 1.00 12.67 S ATOM 9815 SG CYS D 226 49.725 95.575 73.082 1.00 12.69 S ATOM 9786 SG CYS D 222 51.584 99.211 76.969 1.00 16.63 S ATOM 9746 SG CYS D 216 50.012 102.154 72.238 1.00 15.48 S Time building chain proxies: 9.61, per 1000 atoms: 0.58 Number of scatterers: 16522 At special positions: 0 Unit cell: (106.14, 131.37, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 90 16.00 P 4 15.00 O 3122 8.00 N 2856 7.00 C 10438 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb=" F3S D 602 " pdb="FE1 F3S D 602 " - pdb=" SG CYS D 226 " pdb="FE4 F3S D 602 " - pdb=" SG CYS D 216 " pdb="FE3 F3S D 602 " - pdb=" SG CYS D 222 " Number of angles added : 18 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 14 sheets defined 33.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.565A pdb=" N SER A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.773A pdb=" N LYS A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.593A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 441 through 461 Processing helix chain 'A' and resid 523 through 541 removed outlier: 4.081A pdb=" N ASP A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 71 through 82 removed outlier: 4.441A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.007A pdb=" N SER B 87 " --> pdb=" O HIS B 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 89 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 4.041A pdb=" N ALA B 127 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 129 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 128 through 140 removed outlier: 4.021A pdb=" N SER C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.876A pdb=" N LYS C 168 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 265 through 273 removed outlier: 3.555A pdb=" N ILE C 271 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 272 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 273 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 409 through 422 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.972A pdb=" N LYS C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.540A pdb=" N LYS C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 470 removed outlier: 3.504A pdb=" N GLY C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 106 through 109 Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.789A pdb=" N LYS D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 153 Proline residue: D 144 - end of helix Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 356 through 359 removed outlier: 3.579A pdb=" N SER D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.764A pdb=" N MET D 379 " --> pdb=" O SER D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 400 removed outlier: 3.509A pdb=" N ILE D 395 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 398 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA D 400 " --> pdb=" O ARG D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 461 removed outlier: 3.852A pdb=" N ARG D 445 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D 447 " --> pdb=" O TYR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 513 No H-bonds generated for 'chain 'D' and resid 511 through 513' Processing helix chain 'D' and resid 523 through 541 removed outlier: 3.554A pdb=" N ALA D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 71 through 82 removed outlier: 4.436A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 4.008A pdb=" N SER E 87 " --> pdb=" O HIS E 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 89 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 94 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE E 97 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.993A pdb=" N ALA E 127 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 129 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.501A pdb=" N LEU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 55 No H-bonds generated for 'chain 'F' and resid 52 through 55' Processing helix chain 'F' and resid 96 through 103 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 128 through 140 removed outlier: 4.021A pdb=" N SER F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.750A pdb=" N LYS F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 196 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 246 through 255 Processing helix chain 'F' and resid 265 through 273 removed outlier: 3.547A pdb=" N ILE F 271 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU F 272 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS F 273 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 280 through 291 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 374 through 382 Processing helix chain 'F' and resid 409 through 422 Processing helix chain 'F' and resid 432 through 440 removed outlier: 3.972A pdb=" N LYS F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 removed outlier: 3.539A pdb=" N LYS F 449 " --> pdb=" O PRO F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 470 Processing sheet with id= A, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.604A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.598A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 256 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 329 through 332 removed outlier: 3.540A pdb=" N ILE A 405 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 70 through 73 removed outlier: 3.506A pdb=" N ILE C 71 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 78 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 385 through 388 Processing sheet with id= H, first strand: chain 'D' and resid 506 through 508 removed outlier: 6.632A pdb=" N PHE D 285 " --> pdb=" O PHE D 507 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS D 247 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= J, first strand: chain 'D' and resid 198 through 200 Processing sheet with id= K, first strand: chain 'D' and resid 277 through 281 removed outlier: 3.624A pdb=" N ALA D 256 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR D 271 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL D 254 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 329 through 332 removed outlier: 4.528A pdb=" N ASP D 404 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 70 through 73 removed outlier: 3.505A pdb=" N ILE F 71 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 78 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 385 through 388 431 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.83: 16930 1.83 - 2.45: 36 2.45 - 3.06: 0 3.06 - 3.68: 0 3.68 - 4.29: 6 Bond restraints: 16972 Sorted by residual: bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 4.268 -2.035 2.00e-02 2.50e+03 1.04e+04 bond pdb=" S4 F3S D 602 " pdb="FE1 F3S D 602 " ideal model delta sigma weight residual 2.233 4.268 -2.035 2.00e-02 2.50e+03 1.04e+04 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 4.291 -2.033 2.00e-02 2.50e+03 1.03e+04 bond pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " ideal model delta sigma weight residual 2.258 4.290 -2.032 2.00e-02 2.50e+03 1.03e+04 bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 4.248 -1.948 2.00e-02 2.50e+03 9.49e+03 ... (remaining 16967 not shown) Histogram of bond angle deviations from ideal: 37.34 - 65.68: 12 65.68 - 94.02: 40 94.02 - 122.36: 20398 122.36 - 150.70: 2740 150.70 - 179.04: 12 Bond angle restraints: 23202 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 37.34 77.41 3.00e+00 1.11e-01 6.66e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S3 F3S D 602 " ideal model delta sigma weight residual 114.75 37.36 77.39 3.00e+00 1.11e-01 6.65e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 38.05 74.54 3.00e+00 1.11e-01 6.17e+02 angle pdb=" S3 F3S D 602 " pdb="FE1 F3S D 602 " pdb=" S4 F3S D 602 " ideal model delta sigma weight residual 112.59 38.07 74.52 3.00e+00 1.11e-01 6.17e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S2 F3S D 602 " ideal model delta sigma weight residual 103.63 72.19 31.44 3.00e+00 1.11e-01 1.10e+02 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 9275 22.27 - 44.53: 609 44.53 - 66.80: 70 66.80 - 89.06: 26 89.06 - 111.33: 2 Dihedral angle restraints: 9982 sinusoidal: 3928 harmonic: 6054 Sorted by residual: dihedral pdb=" CA HIS E 118 " pdb=" C HIS E 118 " pdb=" N PRO E 119 " pdb=" CA PRO E 119 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA HIS B 118 " pdb=" C HIS B 118 " pdb=" N PRO B 119 " pdb=" CA PRO B 119 " ideal model delta harmonic sigma weight residual 180.00 134.44 45.56 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA PHE D 80 " pdb=" C PHE D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual -180.00 -140.76 -39.24 0 5.00e+00 4.00e-02 6.16e+01 ... (remaining 9979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.128: 2476 3.128 - 6.256: 0 6.256 - 9.384: 0 9.384 - 12.512: 0 12.512 - 15.640: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" S2 F3S D 602 " pdb="FE1 F3S D 602 " pdb="FE3 F3S D 602 " pdb="FE4 F3S D 602 " both_signs ideal model delta sigma weight residual False 10.77 -4.87 15.64 2.00e-01 2.50e+01 6.12e+03 chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -4.87 15.64 2.00e-01 2.50e+01 6.11e+03 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2475 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC F 501 " -0.023 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" CGD HEC F 501 " 0.085 2.00e-02 2.50e+03 pdb=" O1D HEC F 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC F 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" CGD HEC C 501 " 0.085 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 111 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP A 111 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 111 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 111 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 111 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 111 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 111 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 111 " -0.001 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 11100 3.06 - 3.67: 26410 3.67 - 4.29: 38349 4.29 - 4.90: 61919 Nonbonded interactions: 137879 Sorted by model distance: nonbonded pdb=" SG CYS A 226 " pdb=" S1 F3S A 602 " model vdw 1.827 3.760 nonbonded pdb=" SG CYS D 226 " pdb=" S1 F3S D 602 " model vdw 1.850 3.760 nonbonded pdb=" CG ASN D 521 " pdb=" C4 FAD D 601 " model vdw 2.070 2.792 nonbonded pdb=" CG ASN A 521 " pdb=" C4 FAD A 601 " model vdw 2.079 2.792 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.112 2.440 ... (remaining 137874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.160 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 48.550 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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: 58.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.038 2.035 16972 Z= 2.423 Angle : 1.521 77.412 23202 Z= 0.562 Chirality : 0.446 15.640 2478 Planarity : 0.006 0.065 2986 Dihedral : 14.723 111.326 6122 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 2072 helix: 0.35 (0.21), residues: 646 sheet: 0.17 (0.43), residues: 176 loop : -0.96 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP A 111 HIS 0.006 0.001 HIS B 118 PHE 0.015 0.001 PHE B 144 TYR 0.032 0.001 TYR D 79 ARG 0.007 0.000 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5338 (ttmm) cc_final: 0.5090 (mtpp) REVERT: A 321 MET cc_start: 0.7044 (tpp) cc_final: 0.6784 (mmt) REVERT: C 130 ASP cc_start: 0.7306 (m-30) cc_final: 0.7101 (m-30) REVERT: C 352 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8002 (tppt) REVERT: D 321 MET cc_start: 0.7370 (tpp) cc_final: 0.7095 (mmt) REVERT: D 329 MET cc_start: 0.7587 (tpp) cc_final: 0.7208 (mtp) REVERT: F 130 ASP cc_start: 0.7282 (m-30) cc_final: 0.7078 (m-30) REVERT: F 352 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7964 (tppt) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2581 time to fit residues: 108.9994 Evaluate side-chains 213 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.7980 chunk 156 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 16972 Z= 0.255 Angle : 1.230 76.022 23202 Z= 0.461 Chirality : 0.051 0.947 2478 Planarity : 0.005 0.062 2986 Dihedral : 9.439 100.258 2432 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.53 % Allowed : 10.92 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 2072 helix: 0.54 (0.21), residues: 668 sheet: 0.01 (0.42), residues: 180 loop : -0.81 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 111 HIS 0.008 0.001 HIS A 110 PHE 0.014 0.001 PHE C 64 TYR 0.024 0.001 TYR D 79 ARG 0.006 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8166 (ttm) cc_final: 0.7932 (mtp) REVERT: A 310 ILE cc_start: 0.7218 (mm) cc_final: 0.6918 (tt) REVERT: A 497 TRP cc_start: 0.7189 (m100) cc_final: 0.6971 (m100) REVERT: C 187 ASP cc_start: 0.7326 (t70) cc_final: 0.6971 (t70) REVERT: C 352 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8056 (tppt) REVERT: D 156 MET cc_start: 0.8078 (ttm) cc_final: 0.7813 (mtp) REVERT: F 187 ASP cc_start: 0.7298 (t70) cc_final: 0.6966 (t70) REVERT: F 352 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8025 (tppt) outliers start: 9 outliers final: 7 residues processed: 248 average time/residue: 0.2591 time to fit residues: 99.3529 Evaluate side-chains 225 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 202 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 263 ASN D 503 HIS ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 16972 Z= 0.414 Angle : 1.202 90.758 23202 Z= 0.472 Chirality : 0.060 1.283 2478 Planarity : 0.006 0.061 2986 Dihedral : 9.786 110.952 2432 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.88 % Allowed : 15.67 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2072 helix: 0.31 (0.21), residues: 676 sheet: -0.10 (0.41), residues: 184 loop : -1.00 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 111 HIS 0.008 0.001 HIS A 110 PHE 0.025 0.002 PHE E 54 TYR 0.024 0.002 TYR D 79 ARG 0.004 0.001 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.8925 (t0) cc_final: 0.8500 (t0) REVERT: A 242 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 329 MET cc_start: 0.7793 (tpp) cc_final: 0.7567 (mmm) REVERT: C 124 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8471 (t0) REVERT: C 187 ASP cc_start: 0.7298 (t70) cc_final: 0.6901 (t70) REVERT: D 156 MET cc_start: 0.8251 (ttm) cc_final: 0.7970 (mtp) REVERT: D 211 ASP cc_start: 0.8146 (t0) cc_final: 0.7907 (t0) REVERT: D 221 ASN cc_start: 0.8965 (t0) cc_final: 0.8538 (t0) REVERT: D 242 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7416 (tm-30) REVERT: D 329 MET cc_start: 0.7529 (ttm) cc_final: 0.7172 (ttt) REVERT: D 352 PHE cc_start: 0.8364 (m-10) cc_final: 0.8054 (m-80) REVERT: F 124 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8562 (t0) REVERT: F 187 ASP cc_start: 0.7278 (t70) cc_final: 0.6881 (t70) outliers start: 32 outliers final: 21 residues processed: 254 average time/residue: 0.2467 time to fit residues: 98.0307 Evaluate side-chains 239 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 178 optimal weight: 0.0370 chunk 53 optimal weight: 10.0000 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN E 118 HIS ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 16972 Z= 0.217 Angle : 1.086 84.173 23202 Z= 0.413 Chirality : 0.060 1.446 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.474 106.813 2432 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.23 % Allowed : 16.78 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2072 helix: 0.66 (0.21), residues: 666 sheet: -0.24 (0.40), residues: 184 loop : -0.91 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 111 HIS 0.006 0.001 HIS A 110 PHE 0.013 0.001 PHE B 144 TYR 0.025 0.001 TYR D 79 ARG 0.008 0.000 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7874 (pp30) cc_final: 0.7660 (pp30) REVERT: A 221 ASN cc_start: 0.8799 (t0) cc_final: 0.8395 (t0) REVERT: B 55 MET cc_start: 0.7832 (tpp) cc_final: 0.7120 (mmt) REVERT: B 134 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: C 187 ASP cc_start: 0.7147 (t70) cc_final: 0.6762 (t70) REVERT: C 352 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8138 (tppt) REVERT: D 211 ASP cc_start: 0.8069 (t0) cc_final: 0.7772 (t0) REVERT: D 221 ASN cc_start: 0.8859 (t0) cc_final: 0.8416 (t0) REVERT: D 329 MET cc_start: 0.7368 (ttm) cc_final: 0.7115 (ttt) REVERT: E 134 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: F 187 ASP cc_start: 0.7124 (t70) cc_final: 0.6744 (t70) REVERT: F 352 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8105 (tppt) outliers start: 38 outliers final: 26 residues processed: 265 average time/residue: 0.2537 time to fit residues: 104.9536 Evaluate side-chains 244 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 178 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.211 Angle : 1.070 83.783 23202 Z= 0.408 Chirality : 0.059 1.445 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.343 103.149 2432 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.70 % Allowed : 18.96 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2072 helix: 0.72 (0.21), residues: 666 sheet: -0.24 (0.40), residues: 184 loop : -0.88 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 111 HIS 0.005 0.001 HIS D 110 PHE 0.017 0.001 PHE E 54 TYR 0.023 0.001 TYR D 79 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7954 (pp30) cc_final: 0.7745 (pp30) REVERT: A 156 MET cc_start: 0.8303 (ttm) cc_final: 0.7942 (mtp) REVERT: A 221 ASN cc_start: 0.8718 (t0) cc_final: 0.8349 (t0) REVERT: A 329 MET cc_start: 0.7561 (tpp) cc_final: 0.7211 (mtp) REVERT: B 55 MET cc_start: 0.7849 (tpp) cc_final: 0.7161 (mmt) REVERT: B 134 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: C 187 ASP cc_start: 0.7072 (t70) cc_final: 0.6787 (t70) REVERT: C 352 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8108 (tppt) REVERT: D 156 MET cc_start: 0.8256 (ttm) cc_final: 0.7889 (mtp) REVERT: D 211 ASP cc_start: 0.8067 (t0) cc_final: 0.7770 (t0) REVERT: D 221 ASN cc_start: 0.8753 (t0) cc_final: 0.8353 (t0) REVERT: D 321 MET cc_start: 0.7409 (tpp) cc_final: 0.7171 (mmt) REVERT: D 329 MET cc_start: 0.7335 (ttm) cc_final: 0.6990 (ttt) REVERT: E 134 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: F 187 ASP cc_start: 0.7045 (t70) cc_final: 0.6759 (t70) REVERT: F 225 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8400 (pt) REVERT: F 352 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8080 (tppt) outliers start: 29 outliers final: 24 residues processed: 249 average time/residue: 0.2503 time to fit residues: 97.1355 Evaluate side-chains 248 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.216 Angle : 1.064 83.735 23202 Z= 0.404 Chirality : 0.059 1.456 2478 Planarity : 0.005 0.059 2986 Dihedral : 9.294 102.434 2432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.58 % Allowed : 19.07 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 2072 helix: 0.68 (0.20), residues: 690 sheet: -0.26 (0.40), residues: 184 loop : -0.93 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 497 HIS 0.004 0.001 HIS A 110 PHE 0.014 0.001 PHE E 54 TYR 0.023 0.001 TYR D 79 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 228 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7975 (pp30) cc_final: 0.7630 (pp30) REVERT: A 156 MET cc_start: 0.8308 (ttm) cc_final: 0.7845 (mtp) REVERT: A 221 ASN cc_start: 0.8701 (t0) cc_final: 0.8297 (t0) REVERT: A 321 MET cc_start: 0.7240 (tpp) cc_final: 0.6984 (mmt) REVERT: A 329 MET cc_start: 0.7628 (tpp) cc_final: 0.7306 (mtp) REVERT: B 134 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: C 187 ASP cc_start: 0.7006 (t70) cc_final: 0.6793 (t70) REVERT: C 352 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8118 (tppt) REVERT: D 156 MET cc_start: 0.8294 (ttm) cc_final: 0.7867 (mtp) REVERT: D 211 ASP cc_start: 0.8071 (t0) cc_final: 0.7777 (t0) REVERT: D 221 ASN cc_start: 0.8747 (t0) cc_final: 0.8332 (t0) REVERT: D 321 MET cc_start: 0.7349 (tpp) cc_final: 0.7094 (mmt) REVERT: D 329 MET cc_start: 0.7337 (ttm) cc_final: 0.6961 (ttt) REVERT: F 187 ASP cc_start: 0.6963 (t70) cc_final: 0.6745 (t70) REVERT: F 352 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8113 (tppt) outliers start: 44 outliers final: 34 residues processed: 263 average time/residue: 0.2459 time to fit residues: 100.1783 Evaluate side-chains 254 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 chunk 145 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 198 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.198 Angle : 1.054 83.694 23202 Z= 0.399 Chirality : 0.059 1.443 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.161 100.239 2432 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.11 % Allowed : 19.89 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 2072 helix: 0.74 (0.20), residues: 690 sheet: -0.31 (0.40), residues: 184 loop : -0.88 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 497 HIS 0.005 0.001 HIS D 110 PHE 0.012 0.001 PHE F 64 TYR 0.035 0.001 TYR A 79 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7365 (t) cc_final: 0.6982 (p) REVERT: A 156 MET cc_start: 0.8283 (ttm) cc_final: 0.7807 (mtp) REVERT: A 221 ASN cc_start: 0.8637 (t0) cc_final: 0.8411 (t0) REVERT: A 321 MET cc_start: 0.7203 (tpp) cc_final: 0.6929 (mmt) REVERT: A 329 MET cc_start: 0.7567 (tpp) cc_final: 0.7254 (mtp) REVERT: C 352 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8080 (tppt) REVERT: D 156 MET cc_start: 0.8268 (ttm) cc_final: 0.7882 (mtp) REVERT: D 211 ASP cc_start: 0.8104 (t0) cc_final: 0.7776 (t0) REVERT: D 221 ASN cc_start: 0.8705 (t0) cc_final: 0.8293 (t0) REVERT: D 321 MET cc_start: 0.7249 (tpp) cc_final: 0.6989 (mmt) REVERT: F 352 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8058 (tppt) outliers start: 36 outliers final: 28 residues processed: 264 average time/residue: 0.2676 time to fit residues: 111.3634 Evaluate side-chains 248 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 0.0050 chunk 126 optimal weight: 0.0270 chunk 135 optimal weight: 0.0270 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 215 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 16972 Z= 0.190 Angle : 1.053 83.644 23202 Z= 0.400 Chirality : 0.059 1.445 2478 Planarity : 0.004 0.058 2986 Dihedral : 9.063 97.185 2432 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.11 % Allowed : 20.60 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 2072 helix: 0.77 (0.20), residues: 692 sheet: -0.49 (0.39), residues: 184 loop : -0.84 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 497 HIS 0.006 0.001 HIS F 308 PHE 0.013 0.001 PHE C 64 TYR 0.032 0.001 TYR A 79 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7250 (t) cc_final: 0.6868 (p) REVERT: A 156 MET cc_start: 0.8236 (ttm) cc_final: 0.7744 (mtp) REVERT: A 221 ASN cc_start: 0.8589 (t0) cc_final: 0.8342 (t0) REVERT: A 329 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7102 (mtp) REVERT: B 134 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: C 352 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8147 (tppt) REVERT: D 70 SER cc_start: 0.7302 (t) cc_final: 0.6951 (p) REVERT: D 156 MET cc_start: 0.8229 (ttm) cc_final: 0.7774 (mtp) REVERT: D 211 ASP cc_start: 0.8128 (t0) cc_final: 0.7794 (t0) REVERT: D 221 ASN cc_start: 0.8658 (t0) cc_final: 0.8241 (t0) REVERT: F 352 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8090 (tppt) outliers start: 36 outliers final: 23 residues processed: 270 average time/residue: 0.2605 time to fit residues: 108.3428 Evaluate side-chains 246 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16972 Z= 0.279 Angle : 1.087 83.838 23202 Z= 0.417 Chirality : 0.061 1.474 2478 Planarity : 0.005 0.057 2986 Dihedral : 9.142 102.070 2432 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.93 % Allowed : 20.07 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2072 helix: 0.61 (0.20), residues: 698 sheet: -0.40 (0.40), residues: 180 loop : -0.88 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 497 HIS 0.009 0.001 HIS A 110 PHE 0.028 0.002 PHE A 507 TYR 0.033 0.002 TYR A 79 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7390 (t) cc_final: 0.6931 (p) REVERT: A 156 MET cc_start: 0.8403 (ttm) cc_final: 0.8001 (mtp) REVERT: A 221 ASN cc_start: 0.8739 (t0) cc_final: 0.8339 (t0) REVERT: A 329 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7325 (mtp) REVERT: B 84 HIS cc_start: 0.5616 (OUTLIER) cc_final: 0.5119 (t70) REVERT: B 134 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7100 (pt0) REVERT: C 352 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8159 (tppt) REVERT: D 70 SER cc_start: 0.7530 (t) cc_final: 0.7001 (p) REVERT: D 156 MET cc_start: 0.8385 (ttm) cc_final: 0.8021 (mtp) REVERT: D 211 ASP cc_start: 0.8117 (t0) cc_final: 0.7812 (t0) REVERT: D 221 ASN cc_start: 0.8792 (t0) cc_final: 0.8410 (t0) REVERT: F 352 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8148 (tppt) outliers start: 50 outliers final: 41 residues processed: 265 average time/residue: 0.2576 time to fit residues: 106.5027 Evaluate side-chains 264 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 136 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 126 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 345 GLN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 374 ASN ** F 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.197 Angle : 1.063 83.657 23202 Z= 0.403 Chirality : 0.059 1.451 2478 Planarity : 0.005 0.057 2986 Dihedral : 9.126 99.822 2432 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.88 % Allowed : 21.19 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2072 helix: 0.71 (0.20), residues: 692 sheet: -0.55 (0.39), residues: 184 loop : -0.84 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 497 HIS 0.005 0.001 HIS D 110 PHE 0.025 0.001 PHE A 507 TYR 0.039 0.001 TYR D 79 ARG 0.004 0.000 ARG A 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.7209 (t) cc_final: 0.6841 (p) REVERT: A 156 MET cc_start: 0.8151 (ttm) cc_final: 0.7650 (mtp) REVERT: A 221 ASN cc_start: 0.8637 (t0) cc_final: 0.8415 (t0) REVERT: A 329 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: B 134 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: C 282 ASP cc_start: 0.6244 (m-30) cc_final: 0.5906 (t0) REVERT: C 352 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8104 (tppt) REVERT: D 70 SER cc_start: 0.7356 (t) cc_final: 0.7001 (p) REVERT: D 156 MET cc_start: 0.8139 (ttm) cc_final: 0.7711 (mtp) REVERT: D 211 ASP cc_start: 0.8090 (t0) cc_final: 0.7756 (t0) REVERT: D 221 ASN cc_start: 0.8702 (t0) cc_final: 0.8345 (t0) REVERT: E 94 ARG cc_start: 0.5312 (mtt90) cc_final: 0.5016 (mtt90) REVERT: F 352 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8088 (tppt) outliers start: 32 outliers final: 24 residues processed: 251 average time/residue: 0.2561 time to fit residues: 100.0795 Evaluate side-chains 243 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 168 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147753 restraints weight = 25654.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147771 restraints weight = 29757.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.149007 restraints weight = 23518.788| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 16972 Z= 0.288 Angle : 1.094 83.891 23202 Z= 0.420 Chirality : 0.061 1.463 2478 Planarity : 0.005 0.057 2986 Dihedral : 9.040 103.111 2432 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.23 % Allowed : 20.48 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 2072 helix: 0.61 (0.20), residues: 694 sheet: -0.44 (0.40), residues: 180 loop : -0.91 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 497 HIS 0.009 0.001 HIS D 110 PHE 0.030 0.002 PHE A 507 TYR 0.040 0.002 TYR D 79 ARG 0.004 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.86 seconds wall clock time: 56 minutes 55.64 seconds (3415.64 seconds total)