Starting phenix.real_space_refine on Wed Sep 25 14:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/09_2024/8fmx_29299.cif" } resolution = 3.37 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6504 2.51 5 N 1713 2.21 5 O 2058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10329 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.37, per 1000 atoms: 0.71 Number of scatterers: 10329 At special positions: 0 Unit cell: (109.375, 106.094, 112.656, 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 54 16.00 O 2058 8.00 N 1713 7.00 C 6504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 501 " - " ASN A 65 " " NAG B 501 " - " ASN B 65 " " NAG C 501 " - " ASN C 65 " " NAG D 1 " - " ASN A 459 " " NAG E 1 " - " ASN B 459 " " NAG F 1 " - " ASN C 459 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 40.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.667A pdb=" N LEU A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.649A pdb=" N GLU A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.758A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.662A pdb=" N ILE A 182 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.523A pdb=" N LEU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 353 No H-bonds generated for 'chain 'A' and resid 352 through 353' Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.648A pdb=" N LYS A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.242A pdb=" N THR A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.629A pdb=" N LEU B 28 " --> pdb=" O HIS B 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.654A pdb=" N GLU B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 179 through 182 removed outlier: 3.554A pdb=" N ILE B 182 " --> pdb=" O ILE B 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 186 through 215 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.546A pdb=" N LEU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.661A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.553A pdb=" N CYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 353 No H-bonds generated for 'chain 'B' and resid 352 through 353' Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N LYS B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 358 " --> pdb=" O THR B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 358' Processing helix chain 'B' and resid 447 through 465 removed outlier: 3.616A pdb=" N GLY B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.640A pdb=" N LEU C 28 " --> pdb=" O HIS C 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 94 removed outlier: 3.600A pdb=" N GLU C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 179 through 182 removed outlier: 3.588A pdb=" N ILE C 182 " --> pdb=" O ILE C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 186 through 215 Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.537A pdb=" N LEU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 removed outlier: 3.663A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 352 through 353 No H-bonds generated for 'chain 'C' and resid 352 through 353' Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N LYS C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 358 " --> pdb=" O THR C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 358' Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.676A pdb=" N GLY C 452 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157 removed outlier: 8.081A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 279 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 277 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 49 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 275 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 51 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 273 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 53 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 271 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222 removed outlier: 6.795A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 271 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 53 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 273 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 51 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 275 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 49 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 277 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 279 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.548A pdb=" N ALA A 108 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER C 423 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.901A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 407 removed outlier: 3.903A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.940A pdb=" N LEU A 421 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 157 removed outlier: 7.948A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 279 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 277 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 49 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 275 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 51 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 273 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 53 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 271 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.810A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 271 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 53 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 273 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 51 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 275 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 49 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 277 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 279 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.904A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.923A pdb=" N LEU B 421 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 157 removed outlier: 7.952A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN C 279 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE C 277 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 49 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 275 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 51 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU C 273 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 53 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 271 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.813A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 271 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 53 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU C 273 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 51 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 275 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 49 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE C 277 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN C 279 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL C 333 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 471 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3399 1.34 - 1.46: 1207 1.46 - 1.57: 5778 1.57 - 1.69: 2 1.69 - 1.81: 78 Bond restraints: 10464 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.600 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.467 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 12939 1.52 - 3.04: 1064 3.04 - 4.56: 192 4.56 - 6.08: 33 6.08 - 7.60: 7 Bond angle restraints: 14235 Sorted by residual: angle pdb=" N ILE C 446 " pdb=" CA ILE C 446 " pdb=" C ILE C 446 " ideal model delta sigma weight residual 107.75 112.97 -5.22 1.46e+00 4.69e-01 1.28e+01 angle pdb=" N ILE B 446 " pdb=" CA ILE B 446 " pdb=" C ILE B 446 " ideal model delta sigma weight residual 107.75 112.94 -5.19 1.46e+00 4.69e-01 1.26e+01 angle pdb=" N THR C 169 " pdb=" CA THR C 169 " pdb=" C THR C 169 " ideal model delta sigma weight residual 111.11 115.08 -3.97 1.20e+00 6.94e-01 1.09e+01 angle pdb=" N THR B 169 " pdb=" CA THR B 169 " pdb=" C THR B 169 " ideal model delta sigma weight residual 111.11 115.04 -3.93 1.20e+00 6.94e-01 1.07e+01 angle pdb=" N CYS C 66 " pdb=" CA CYS C 66 " pdb=" C CYS C 66 " ideal model delta sigma weight residual 113.41 117.27 -3.86 1.22e+00 6.72e-01 1.00e+01 ... (remaining 14230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 6232 21.35 - 42.69: 258 42.69 - 64.04: 36 64.04 - 85.39: 35 85.39 - 106.73: 15 Dihedral angle restraints: 6576 sinusoidal: 2700 harmonic: 3876 Sorted by residual: dihedral pdb=" CA LYS A 161 " pdb=" C LYS A 161 " pdb=" N GLN A 162 " pdb=" CA GLN A 162 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -133.35 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ILE A 451 " pdb=" CA ILE A 451 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 6573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1486 0.072 - 0.143: 252 0.143 - 0.215: 28 0.215 - 0.286: 6 0.286 - 0.358: 4 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 459 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 459 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 459 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1773 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 206 " -0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C LEU C 206 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU C 206 " -0.029 2.00e-02 2.50e+03 pdb=" N THR C 207 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 459 " -0.027 2.00e-02 2.50e+03 2.63e-02 8.67e+00 pdb=" CG ASN A 459 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 459 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 459 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 296 " -0.008 2.00e-02 2.50e+03 1.91e-02 7.27e+00 pdb=" CG TYR B 296 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 296 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 296 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 296 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 296 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 296 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR B 296 " -0.029 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4103 2.90 - 3.40: 9866 3.40 - 3.90: 16690 3.90 - 4.40: 18183 4.40 - 4.90: 31375 Nonbonded interactions: 80217 Sorted by model distance: nonbonded pdb=" O THR A 315 " pdb=" OG1 THR A 316 " model vdw 2.404 3.040 nonbonded pdb=" O THR C 315 " pdb=" OG1 THR C 316 " model vdw 2.431 3.040 nonbonded pdb=" O THR B 315 " pdb=" OG1 THR B 316 " model vdw 2.436 3.040 nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.499 3.040 nonbonded pdb=" N ASP A 436 " pdb=" OD1 ASP A 436 " model vdw 2.500 3.120 ... (remaining 80212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 2.010 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: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.880 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.005 0.081 10464 Z= 0.322 Angle : 0.930 7.599 14235 Z= 0.549 Chirality : 0.056 0.358 1776 Planarity : 0.006 0.059 1812 Dihedral : 14.518 106.735 4041 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.06 (0.21), residues: 1329 helix: -0.60 (0.22), residues: 453 sheet: -0.18 (0.32), residues: 261 loop : -0.89 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 303 HIS 0.005 0.002 HIS C 130 PHE 0.023 0.003 PHE C 234 TYR 0.030 0.006 TYR B 201 ARG 0.012 0.002 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.217 Fit side-chains REVERT: A 235 ASP cc_start: 0.8391 (t70) cc_final: 0.8179 (t70) REVERT: A 454 GLN cc_start: 0.8696 (mt0) cc_final: 0.8485 (mt0) REVERT: B 92 MET cc_start: 0.9215 (tpp) cc_final: 0.8997 (tpp) REVERT: C 92 MET cc_start: 0.9220 (tpp) cc_final: 0.8851 (tpp) REVERT: C 448 LYS cc_start: 0.9166 (mttt) cc_final: 0.8919 (tppp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3002 time to fit residues: 36.7025 Evaluate side-chains 44 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 384 ASN A 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10464 Z= 0.472 Angle : 0.752 7.596 14235 Z= 0.381 Chirality : 0.049 0.380 1776 Planarity : 0.004 0.056 1812 Dihedral : 10.283 77.412 1671 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.87 % Allowed : 4.43 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.01 (0.22), residues: 1329 helix: 0.92 (0.24), residues: 456 sheet: 0.18 (0.32), residues: 261 loop : -0.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.006 0.002 HIS A 130 PHE 0.020 0.002 PHE C 105 TYR 0.014 0.002 TYR A 41 ARG 0.005 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 1.638 Fit side-chains REVERT: A 454 GLN cc_start: 0.8834 (mt0) cc_final: 0.8595 (mt0) REVERT: C 92 MET cc_start: 0.9334 (tpp) cc_final: 0.8916 (tpp) REVERT: C 448 LYS cc_start: 0.9234 (mttt) cc_final: 0.8954 (tppp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.2733 time to fit residues: 22.9995 Evaluate side-chains 45 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0070 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10464 Z= 0.154 Angle : 0.553 7.059 14235 Z= 0.288 Chirality : 0.045 0.247 1776 Planarity : 0.003 0.035 1812 Dihedral : 7.485 51.519 1671 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.87 % Allowed : 5.56 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.23), residues: 1329 helix: 1.63 (0.25), residues: 456 sheet: 0.31 (0.33), residues: 258 loop : -0.55 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.000 HIS A 130 PHE 0.012 0.001 PHE B 277 TYR 0.008 0.001 TYR C 415 ARG 0.003 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 1.272 Fit side-chains REVERT: A 454 GLN cc_start: 0.8715 (mt0) cc_final: 0.8505 (mt0) REVERT: B 110 MET cc_start: 0.8156 (tpp) cc_final: 0.7776 (tpp) REVERT: C 92 MET cc_start: 0.9244 (tpp) cc_final: 0.8968 (tpp) REVERT: C 110 MET cc_start: 0.8071 (tpp) cc_final: 0.7762 (tpt) REVERT: C 343 MET cc_start: 0.8100 (mtm) cc_final: 0.7859 (mpp) REVERT: C 448 LYS cc_start: 0.9186 (mttt) cc_final: 0.8899 (tppp) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.1884 time to fit residues: 17.6690 Evaluate side-chains 46 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10464 Z= 0.185 Angle : 0.528 7.078 14235 Z= 0.272 Chirality : 0.044 0.214 1776 Planarity : 0.003 0.036 1812 Dihedral : 5.973 50.625 1671 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.22 % Allowed : 6.16 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.68 (0.23), residues: 1329 helix: 1.88 (0.25), residues: 456 sheet: 0.23 (0.32), residues: 258 loop : -0.52 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.003 0.001 HIS C 130 PHE 0.010 0.001 PHE A 277 TYR 0.007 0.001 TYR C 249 ARG 0.003 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 1.172 Fit side-chains REVERT: A 92 MET cc_start: 0.9016 (tpp) cc_final: 0.8775 (tpp) REVERT: B 92 MET cc_start: 0.9184 (tpp) cc_final: 0.8982 (tpp) REVERT: B 110 MET cc_start: 0.8143 (tpp) cc_final: 0.7844 (tpp) REVERT: B 448 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8863 (mmtt) REVERT: C 92 MET cc_start: 0.9254 (tpp) cc_final: 0.8978 (tpp) REVERT: C 110 MET cc_start: 0.8079 (tpp) cc_final: 0.7784 (tpt) REVERT: C 448 LYS cc_start: 0.9200 (mttt) cc_final: 0.8980 (tppp) outliers start: 14 outliers final: 2 residues processed: 56 average time/residue: 0.1915 time to fit residues: 17.0084 Evaluate side-chains 43 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain B residue 257 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10464 Z= 0.182 Angle : 0.514 8.399 14235 Z= 0.265 Chirality : 0.043 0.191 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.606 50.697 1671 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.52 % Allowed : 6.94 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.73 (0.23), residues: 1329 helix: 1.98 (0.26), residues: 456 sheet: 0.16 (0.32), residues: 261 loop : -0.49 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.002 0.001 HIS C 130 PHE 0.012 0.001 PHE B 277 TYR 0.007 0.001 TYR C 249 ARG 0.002 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 1.128 Fit side-chains REVERT: A 92 MET cc_start: 0.9105 (tpp) cc_final: 0.8801 (tpp) REVERT: A 453 ASN cc_start: 0.8952 (m-40) cc_final: 0.8749 (m110) REVERT: B 92 MET cc_start: 0.9232 (tpp) cc_final: 0.9007 (tpp) REVERT: B 448 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8732 (tppt) REVERT: C 92 MET cc_start: 0.9252 (tpp) cc_final: 0.8979 (tpp) REVERT: C 448 LYS cc_start: 0.9168 (mttt) cc_final: 0.8942 (tppp) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.2063 time to fit residues: 16.1884 Evaluate side-chains 44 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10464 Z= 0.124 Angle : 0.492 9.894 14235 Z= 0.253 Chirality : 0.043 0.175 1776 Planarity : 0.003 0.034 1812 Dihedral : 5.307 51.776 1671 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.43 % Allowed : 7.73 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.81 (0.24), residues: 1329 helix: 2.02 (0.26), residues: 459 sheet: 0.22 (0.32), residues: 261 loop : -0.45 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.001 0.000 HIS A 130 PHE 0.020 0.001 PHE A 105 TYR 0.016 0.001 TYR A 345 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9165 (tpp) cc_final: 0.8884 (tpp) REVERT: A 390 MET cc_start: 0.8578 (mmm) cc_final: 0.8337 (mmm) REVERT: A 453 ASN cc_start: 0.8976 (m-40) cc_final: 0.8767 (m110) REVERT: B 92 MET cc_start: 0.9257 (tpp) cc_final: 0.9046 (tpp) REVERT: C 448 LYS cc_start: 0.9152 (mttt) cc_final: 0.8888 (tppt) outliers start: 5 outliers final: 0 residues processed: 55 average time/residue: 0.1959 time to fit residues: 17.0929 Evaluate side-chains 43 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10464 Z= 0.145 Angle : 0.496 11.236 14235 Z= 0.254 Chirality : 0.042 0.167 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.233 51.493 1671 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.43 % Allowed : 8.07 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.88 (0.24), residues: 1329 helix: 2.12 (0.26), residues: 456 sheet: 0.29 (0.32), residues: 261 loop : -0.43 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.002 0.001 HIS C 130 PHE 0.011 0.001 PHE A 105 TYR 0.015 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 1.218 Fit side-chains REVERT: A 92 MET cc_start: 0.9201 (tpp) cc_final: 0.8902 (tpp) REVERT: A 453 ASN cc_start: 0.8953 (m-40) cc_final: 0.8740 (m110) REVERT: A 454 GLN cc_start: 0.9166 (pt0) cc_final: 0.8954 (pt0) REVERT: B 92 MET cc_start: 0.9286 (tpp) cc_final: 0.9069 (tpp) REVERT: B 448 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8866 (tppt) REVERT: C 448 LYS cc_start: 0.9158 (mttt) cc_final: 0.8870 (tppp) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.2044 time to fit residues: 15.0343 Evaluate side-chains 44 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10464 Z= 0.133 Angle : 0.479 9.884 14235 Z= 0.245 Chirality : 0.042 0.161 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.112 51.729 1671 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.35 % Allowed : 8.16 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.94 (0.24), residues: 1329 helix: 2.18 (0.26), residues: 456 sheet: 0.34 (0.32), residues: 261 loop : -0.41 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.002 0.001 HIS C 130 PHE 0.011 0.001 PHE A 105 TYR 0.018 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.120 Fit side-chains REVERT: A 92 MET cc_start: 0.9198 (tpp) cc_final: 0.8935 (tpp) REVERT: A 343 MET cc_start: 0.6222 (ptp) cc_final: 0.5947 (ptp) REVERT: A 453 ASN cc_start: 0.8968 (m-40) cc_final: 0.8737 (m110) REVERT: A 454 GLN cc_start: 0.9170 (pt0) cc_final: 0.8949 (pt0) REVERT: B 448 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8707 (tppt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.2060 time to fit residues: 14.4761 Evaluate side-chains 43 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10464 Z= 0.197 Angle : 0.514 9.172 14235 Z= 0.258 Chirality : 0.042 0.154 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.106 51.013 1671 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.35 % Allowed : 8.16 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.96 (0.24), residues: 1329 helix: 2.23 (0.26), residues: 456 sheet: 0.33 (0.32), residues: 261 loop : -0.42 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE A 105 TYR 0.016 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.286 Fit side-chains REVERT: A 92 MET cc_start: 0.9215 (tpp) cc_final: 0.8903 (tpp) REVERT: A 454 GLN cc_start: 0.9163 (pt0) cc_final: 0.8926 (pt0) REVERT: B 448 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8809 (tppt) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.2127 time to fit residues: 14.8263 Evaluate side-chains 42 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN C 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10464 Z= 0.184 Angle : 0.510 8.756 14235 Z= 0.259 Chirality : 0.042 0.153 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.102 51.083 1671 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.94 (0.24), residues: 1329 helix: 2.22 (0.26), residues: 459 sheet: 0.35 (0.32), residues: 261 loop : -0.47 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.003 0.001 HIS A 130 PHE 0.009 0.001 PHE A 105 TYR 0.021 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.350 Fit side-chains REVERT: A 92 MET cc_start: 0.9227 (tpp) cc_final: 0.8917 (tpp) REVERT: A 454 GLN cc_start: 0.9062 (pt0) cc_final: 0.8755 (pt0) REVERT: B 448 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8781 (tppt) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.2064 time to fit residues: 14.2292 Evaluate side-chains 43 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.047167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.036151 restraints weight = 44792.734| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.42 r_work: 0.2408 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10464 Z= 0.143 Angle : 0.501 10.363 14235 Z= 0.255 Chirality : 0.043 0.241 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.024 51.462 1671 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.35 % Allowed : 8.33 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.98 (0.24), residues: 1329 helix: 2.27 (0.26), residues: 459 sheet: 0.38 (0.32), residues: 261 loop : -0.47 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.002 0.001 HIS B 130 PHE 0.009 0.001 PHE A 105 TYR 0.019 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.39 seconds wall clock time: 35 minutes 8.68 seconds (2108.68 seconds total)