Starting phenix.real_space_refine on Sat Mar 16 23:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/03_2024/7ljf_23392_neut_updated.pdb" } resolution = 4.0 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= 0.002 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 P 7 5.49 5 Mg 3 5.21 5 S 48 5.16 5 C 9926 2.51 5 N 2713 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 145": "OE1" <-> "OE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15742 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3551 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3551 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 5 Chain: "C" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3346 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3338 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.39, per 1000 atoms: 0.53 Number of scatterers: 15742 At special positions: 0 Unit cell: (133.812, 156.94, 128.856, 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) S 48 16.00 P 7 15.00 Mg 3 11.99 O 3045 8.00 N 2713 7.00 C 9926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 2.8 seconds 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 21 sheets defined 31.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.860A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.775A pdb=" N ALA A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 345 through 362 removed outlier: 4.092A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.706A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 517 through 537 removed outlier: 3.684A pdb=" N ARG A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.704A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 258 through 273 removed outlier: 4.315A pdb=" N LEU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 299 through 312 removed outlier: 4.492A pdb=" N ALA B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.942A pdb=" N ILE B 349 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.253A pdb=" N GLU B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 442 through 452 removed outlier: 4.001A pdb=" N GLN B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 removed outlier: 3.560A pdb=" N PHE B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 487 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 516 through 537 Processing helix chain 'B' and resid 544 through 560 removed outlier: 3.578A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.705A pdb=" N LEU C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 269 through 273' Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 299 through 312 removed outlier: 3.711A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 423 through 426 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 461 through 467 removed outlier: 4.332A pdb=" N ALA C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 467' Processing helix chain 'C' and resid 471 through 487 Processing helix chain 'C' and resid 491 through 493 No H-bonds generated for 'chain 'C' and resid 491 through 493' Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 516 through 537 Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.534A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.621A pdb=" N GLN F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 275 through 280 Processing helix chain 'F' and resid 299 through 312 Processing helix chain 'F' and resid 335 through 338 No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 345 through 360 removed outlier: 3.585A pdb=" N PHE F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 393 through 405 removed outlier: 4.797A pdb=" N GLY F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 426 Processing helix chain 'F' and resid 442 through 452 Processing helix chain 'F' and resid 461 through 466 removed outlier: 3.794A pdb=" N ALA F 465 " --> pdb=" O ALA F 461 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 461 through 466' Processing helix chain 'F' and resid 471 through 486 removed outlier: 4.269A pdb=" N LYS F 476 " --> pdb=" O SER F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing helix chain 'F' and resid 511 through 513 No H-bonds generated for 'chain 'F' and resid 511 through 513' Processing helix chain 'F' and resid 516 through 537 Processing helix chain 'F' and resid 544 through 556 Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.963A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 184 through 187 removed outlier: 5.934A pdb=" N VAL A 177 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 164 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP A 223 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 Processing sheet with id= D, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.153A pdb=" N LEU A 290 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 434 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 292 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS A 436 " --> pdb=" O TYR A 292 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= F, first strand: chain 'B' and resid 120 through 125 removed outlier: 5.778A pdb=" N PHE B 116 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 104 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 151 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.457A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 223 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 433 through 437 removed outlier: 3.563A pdb=" N ILE B 435 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL B 289 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 411 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 291 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 413 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N GLY B 293 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 366 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE B 412 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 368 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 507 through 509 removed outlier: 3.874A pdb=" N ARG B 585 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 499 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 583 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.660A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 219 through 222 removed outlier: 6.967A pdb=" N LEU C 175 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE C 167 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG C 173 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 328 through 332 removed outlier: 3.513A pdb=" N ILE C 410 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 289 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 413 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 290 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS C 434 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR C 292 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS C 436 " --> pdb=" O TYR C 292 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 505 through 509 Processing sheet with id= N, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.752A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR D 107 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR D 112 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 219 through 222 removed outlier: 3.655A pdb=" N THR D 163 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 175 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 140 through 142 removed outlier: 7.168A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR E 107 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR E 112 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.886A pdb=" N LEU E 175 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE E 167 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ARG E 173 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.668A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 184 through 187 removed outlier: 3.902A pdb=" N VAL F 186 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL F 177 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU F 164 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 231 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP F 223 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA F 229 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 433 through 437 removed outlier: 8.418A pdb=" N VAL F 289 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL F 411 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU F 291 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY F 413 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY F 293 " --> pdb=" O GLY F 413 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER F 415 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR F 328 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE F 369 " --> pdb=" O TYR F 328 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 505 through 509 removed outlier: 3.780A pdb=" N TYR F 583 " --> pdb=" O THR F 499 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1497 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: 4.61 Time building geometry restraints manager: 7.09 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: 5083 1.34 - 1.45: 1784 1.45 - 1.57: 9031 1.57 - 1.69: 11 1.69 - 1.81: 82 Bond restraints: 15991 Sorted by residual: bond pdb=" N VAL B 582 " pdb=" CA VAL B 582 " ideal model delta sigma weight residual 1.460 1.495 -0.035 8.60e-03 1.35e+04 1.68e+01 bond pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.23e-02 6.61e+03 8.26e+00 bond pdb=" N TYR F 228 " pdb=" CA TYR F 228 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.93e+00 bond pdb=" N TYR E 228 " pdb=" CA TYR E 228 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.35e+00 bond pdb=" N TYR B 228 " pdb=" CA TYR B 228 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 6.03e+00 ... (remaining 15986 not shown) Histogram of bond angle deviations from ideal: 98.34 - 106.60: 501 106.60 - 114.87: 9648 114.87 - 123.14: 10604 123.14 - 131.40: 860 131.40 - 139.67: 16 Bond angle restraints: 21629 Sorted by residual: angle pdb=" N VAL B 582 " pdb=" CA VAL B 582 " pdb=" C VAL B 582 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" CA ALA C 229 " pdb=" C ALA C 229 " pdb=" O ALA C 229 " ideal model delta sigma weight residual 121.47 117.07 4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" CA ALA D 229 " pdb=" C ALA D 229 " pdb=" O ALA D 229 " ideal model delta sigma weight residual 121.81 117.34 4.47 1.18e+00 7.18e-01 1.43e+01 angle pdb=" N PRO A 394 " pdb=" CA PRO A 394 " pdb=" C PRO A 394 " ideal model delta sigma weight residual 112.47 120.21 -7.74 2.06e+00 2.36e-01 1.41e+01 angle pdb=" CA ALA F 229 " pdb=" C ALA F 229 " pdb=" O ALA F 229 " ideal model delta sigma weight residual 121.16 117.29 3.87 1.12e+00 7.97e-01 1.19e+01 ... (remaining 21624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 9352 25.77 - 51.54: 435 51.54 - 77.31: 23 77.31 - 103.08: 10 103.08 - 128.85: 3 Dihedral angle restraints: 9823 sinusoidal: 4046 harmonic: 5777 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 68.84 -128.85 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 -176.46 116.46 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 52.73 -112.73 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 9820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1727 0.038 - 0.077: 479 0.077 - 0.115: 239 0.115 - 0.153: 37 0.153 - 0.191: 1 Chirality restraints: 2483 Sorted by residual: chirality pdb=" CA VAL B 582 " pdb=" N VAL B 582 " pdb=" C VAL B 582 " pdb=" CB VAL B 582 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA VAL A 392 " pdb=" N VAL A 392 " pdb=" C VAL A 392 " pdb=" CB VAL A 392 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA PRO A 394 " pdb=" N PRO A 394 " pdb=" C PRO A 394 " pdb=" CB PRO A 394 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2480 not shown) Planarity restraints: 2801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 334 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO F 335 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 335 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 335 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 570 " 0.012 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP A 570 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 570 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 570 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 570 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 570 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 570 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 334 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO C 335 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.024 5.00e-02 4.00e+02 ... (remaining 2798 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 264 2.57 - 3.15: 13402 3.15 - 3.73: 26053 3.73 - 4.32: 33389 4.32 - 4.90: 53379 Nonbonded interactions: 126487 Sorted by model distance: nonbonded pdb="MG MG A 701 " pdb=" O1A ATP A 702 " model vdw 1.987 2.170 nonbonded pdb=" O1B ADP B 701 " pdb="MG MG B 702 " model vdw 1.987 2.170 nonbonded pdb="MG MG A 701 " pdb=" O3B ATP A 702 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR A 300 " pdb="MG MG A 701 " model vdw 2.049 2.170 nonbonded pdb=" O1A ADP B 701 " pdb="MG MG B 702 " model vdw 2.059 2.170 ... (remaining 126482 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' and (resid 97 through 557 or resid 580 through 587)) selection = (chain 'B' and (resid 97 through 557 or resid 580 through 587)) selection = (chain 'C' and (resid 97 through 557 or resid 580 through 587)) selection = (chain 'F' and (resid 97 through 557 or resid 580 through 587)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.910 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: 4.490 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 43.130 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.003 0.037 15991 Z= 0.185 Angle : 0.619 8.775 21629 Z= 0.324 Chirality : 0.044 0.191 2483 Planarity : 0.004 0.047 2801 Dihedral : 13.984 128.847 6081 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.41 % Allowed : 0.18 % Favored : 99.41 % 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: 0.00 (0.20), residues: 1951 helix: 0.57 (0.22), residues: 573 sheet: -0.93 (0.24), residues: 450 loop : 0.35 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 570 HIS 0.003 0.001 HIS B 274 PHE 0.018 0.001 PHE A 370 TYR 0.020 0.001 TYR F 583 ARG 0.008 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 219 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 372 GLU cc_start: 0.6715 (mp0) cc_final: 0.6512 (mp0) REVERT: B 508 MET cc_start: 0.6751 (mpp) cc_final: 0.6525 (mpp) REVERT: C 328 TYR cc_start: 0.6577 (m-10) cc_final: 0.5987 (m-10) REVERT: E 131 ASP cc_start: 0.9109 (t70) cc_final: 0.8834 (t70) REVERT: F 448 ILE cc_start: 0.8281 (mm) cc_final: 0.8046 (mm) outliers start: 7 outliers final: 2 residues processed: 226 average time/residue: 0.2228 time to fit residues: 80.2921 Evaluate side-chains 164 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain B residue 582 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 0.0970 chunk 179 optimal weight: 4.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15991 Z= 0.308 Angle : 0.642 9.831 21629 Z= 0.325 Chirality : 0.044 0.169 2483 Planarity : 0.005 0.044 2801 Dihedral : 7.955 120.884 2227 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.42 % Allowed : 11.35 % Favored : 87.23 % 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: -0.18 (0.20), residues: 1951 helix: 0.43 (0.21), residues: 578 sheet: -1.03 (0.23), residues: 476 loop : 0.26 (0.23), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 570 HIS 0.010 0.001 HIS C 179 PHE 0.025 0.002 PHE A 272 TYR 0.015 0.002 TYR F 583 ARG 0.014 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8276 (tp30) cc_final: 0.7941 (tp30) REVERT: A 406 LEU cc_start: 0.8607 (mt) cc_final: 0.8371 (mt) REVERT: A 557 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: C 328 TYR cc_start: 0.6451 (m-10) cc_final: 0.6047 (m-80) REVERT: E 131 ASP cc_start: 0.9185 (t70) cc_final: 0.8917 (t70) REVERT: E 182 GLU cc_start: 0.8042 (pm20) cc_final: 0.7547 (pm20) REVERT: F 448 ILE cc_start: 0.8087 (mm) cc_final: 0.7847 (mm) REVERT: F 506 GLU cc_start: 0.8077 (tt0) cc_final: 0.7555 (mm-30) REVERT: F 529 ASN cc_start: 0.9166 (m-40) cc_final: 0.8879 (m-40) REVERT: F 555 PHE cc_start: 0.7559 (m-80) cc_final: 0.7347 (m-80) outliers start: 24 outliers final: 17 residues processed: 189 average time/residue: 0.2285 time to fit residues: 68.0476 Evaluate side-chains 172 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15991 Z= 0.372 Angle : 0.679 10.135 21629 Z= 0.344 Chirality : 0.044 0.190 2483 Planarity : 0.005 0.050 2801 Dihedral : 8.068 126.149 2225 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 15.61 % Favored : 81.73 % 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: -0.54 (0.19), residues: 1951 helix: 0.19 (0.21), residues: 576 sheet: -1.26 (0.22), residues: 475 loop : 0.02 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 570 HIS 0.008 0.001 HIS C 179 PHE 0.025 0.002 PHE A 272 TYR 0.013 0.002 TYR F 101 ARG 0.009 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.4854 (t70) REVERT: A 478 MET cc_start: 0.8344 (tpp) cc_final: 0.8132 (tpp) REVERT: C 269 GLU cc_start: 0.8694 (tt0) cc_final: 0.8461 (tm-30) REVERT: C 328 TYR cc_start: 0.6431 (m-10) cc_final: 0.6021 (m-80) REVERT: E 104 LEU cc_start: 0.9102 (tp) cc_final: 0.8891 (tp) REVERT: E 131 ASP cc_start: 0.9205 (t70) cc_final: 0.8918 (t70) REVERT: E 190 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: F 448 ILE cc_start: 0.8167 (mm) cc_final: 0.7920 (mm) REVERT: F 506 GLU cc_start: 0.8065 (tt0) cc_final: 0.7619 (mm-30) REVERT: F 529 ASN cc_start: 0.9148 (m-40) cc_final: 0.8881 (m-40) outliers start: 45 outliers final: 33 residues processed: 200 average time/residue: 0.2247 time to fit residues: 72.1869 Evaluate side-chains 185 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 9.9990 chunk 135 optimal weight: 0.0040 chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 191 optimal weight: 40.0000 chunk 94 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN F 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15991 Z= 0.169 Angle : 0.607 9.171 21629 Z= 0.299 Chirality : 0.043 0.153 2483 Planarity : 0.004 0.048 2801 Dihedral : 7.584 122.491 2225 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.77 % Allowed : 18.39 % Favored : 79.83 % 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: -0.10 (0.20), residues: 1951 helix: 0.53 (0.22), residues: 576 sheet: -1.00 (0.23), residues: 474 loop : 0.29 (0.23), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 570 HIS 0.007 0.001 HIS F 546 PHE 0.018 0.001 PHE A 272 TYR 0.012 0.001 TYR A 328 ARG 0.006 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8316 (tp30) cc_final: 0.8087 (tp30) REVERT: C 328 TYR cc_start: 0.6383 (m-10) cc_final: 0.6022 (m-80) REVERT: D 160 GLU cc_start: 0.6593 (tm-30) cc_final: 0.5839 (tm-30) REVERT: D 162 SER cc_start: 0.8803 (p) cc_final: 0.8571 (m) REVERT: E 131 ASP cc_start: 0.9089 (t70) cc_final: 0.8816 (t70) REVERT: E 166 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: F 448 ILE cc_start: 0.8116 (mm) cc_final: 0.7865 (mm) REVERT: F 506 GLU cc_start: 0.8020 (tt0) cc_final: 0.7597 (mm-30) REVERT: F 529 ASN cc_start: 0.9099 (m-40) cc_final: 0.8813 (m-40) outliers start: 30 outliers final: 22 residues processed: 196 average time/residue: 0.2185 time to fit residues: 69.4831 Evaluate side-chains 184 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0970 chunk 108 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 48 optimal weight: 0.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15991 Z= 0.181 Angle : 0.577 8.904 21629 Z= 0.285 Chirality : 0.042 0.163 2483 Planarity : 0.004 0.050 2801 Dihedral : 7.459 120.839 2225 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 19.46 % Favored : 78.30 % 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: -0.02 (0.20), residues: 1951 helix: 0.64 (0.22), residues: 579 sheet: -0.95 (0.23), residues: 486 loop : 0.33 (0.23), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 570 HIS 0.009 0.001 HIS F 546 PHE 0.017 0.001 PHE A 272 TYR 0.016 0.001 TYR F 583 ARG 0.005 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.4964 (p0) REVERT: A 262 GLU cc_start: 0.8297 (tp30) cc_final: 0.8084 (tp30) REVERT: A 406 LEU cc_start: 0.8488 (mt) cc_final: 0.8192 (mt) REVERT: A 557 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (pp20) REVERT: B 372 GLU cc_start: 0.6854 (mp0) cc_final: 0.6523 (mp0) REVERT: C 328 TYR cc_start: 0.6385 (m-10) cc_final: 0.6009 (m-10) REVERT: D 160 GLU cc_start: 0.6699 (tm-30) cc_final: 0.5957 (tm-30) REVERT: D 162 SER cc_start: 0.8830 (p) cc_final: 0.8592 (m) REVERT: E 131 ASP cc_start: 0.9090 (t70) cc_final: 0.8805 (t70) REVERT: F 506 GLU cc_start: 0.8066 (tt0) cc_final: 0.7604 (mm-30) REVERT: F 529 ASN cc_start: 0.9111 (m-40) cc_final: 0.8793 (m-40) outliers start: 38 outliers final: 30 residues processed: 195 average time/residue: 0.2120 time to fit residues: 66.6065 Evaluate side-chains 191 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 40.0000 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15991 Z= 0.354 Angle : 0.665 9.657 21629 Z= 0.335 Chirality : 0.044 0.216 2483 Planarity : 0.005 0.049 2801 Dihedral : 7.803 122.110 2225 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.31 % Allowed : 19.87 % Favored : 76.82 % 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: -0.36 (0.19), residues: 1951 helix: 0.35 (0.21), residues: 579 sheet: -1.04 (0.23), residues: 477 loop : 0.05 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 570 HIS 0.007 0.001 HIS F 546 PHE 0.023 0.002 PHE A 272 TYR 0.012 0.002 TYR F 101 ARG 0.008 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.4800 (t70) REVERT: A 262 GLU cc_start: 0.8346 (tp30) cc_final: 0.7992 (tp30) REVERT: A 406 LEU cc_start: 0.8606 (mt) cc_final: 0.8359 (mt) REVERT: A 557 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: C 151 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: C 244 GLU cc_start: 0.4783 (tt0) cc_final: 0.4400 (tt0) REVERT: C 328 TYR cc_start: 0.6424 (m-10) cc_final: 0.5988 (m-10) REVERT: D 160 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6124 (tm-30) REVERT: D 162 SER cc_start: 0.8823 (p) cc_final: 0.8552 (m) REVERT: E 131 ASP cc_start: 0.9200 (t70) cc_final: 0.8882 (t70) REVERT: F 506 GLU cc_start: 0.8152 (tt0) cc_final: 0.7794 (mm-30) REVERT: F 529 ASN cc_start: 0.9124 (m-40) cc_final: 0.8823 (m-40) outliers start: 56 outliers final: 41 residues processed: 209 average time/residue: 0.2439 time to fit residues: 83.4435 Evaluate side-chains 199 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15991 Z= 0.339 Angle : 0.668 9.177 21629 Z= 0.336 Chirality : 0.044 0.202 2483 Planarity : 0.004 0.049 2801 Dihedral : 7.870 124.742 2225 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.43 % Allowed : 21.23 % Favored : 75.34 % 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: -0.49 (0.19), residues: 1951 helix: 0.26 (0.21), residues: 579 sheet: -1.11 (0.23), residues: 472 loop : -0.07 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 570 HIS 0.005 0.001 HIS F 546 PHE 0.025 0.002 PHE F 369 TYR 0.012 0.002 TYR B 328 ARG 0.007 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5498 (OUTLIER) cc_final: 0.4656 (t70) REVERT: A 557 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: B 372 GLU cc_start: 0.6843 (mp0) cc_final: 0.6593 (mp0) REVERT: C 151 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: C 244 GLU cc_start: 0.4773 (tt0) cc_final: 0.4363 (tt0) REVERT: C 328 TYR cc_start: 0.6500 (m-10) cc_final: 0.6075 (m-10) REVERT: D 160 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6113 (tm-30) REVERT: D 162 SER cc_start: 0.8740 (p) cc_final: 0.8406 (m) REVERT: E 131 ASP cc_start: 0.9185 (t70) cc_final: 0.8896 (t70) REVERT: E 166 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: F 506 GLU cc_start: 0.7984 (tt0) cc_final: 0.7676 (mm-30) REVERT: F 529 ASN cc_start: 0.9106 (m-40) cc_final: 0.8804 (m-40) outliers start: 58 outliers final: 42 residues processed: 209 average time/residue: 0.2221 time to fit residues: 74.9117 Evaluate side-chains 200 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15991 Z= 0.247 Angle : 0.639 8.887 21629 Z= 0.318 Chirality : 0.043 0.185 2483 Planarity : 0.004 0.052 2801 Dihedral : 7.684 122.916 2225 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.02 % Allowed : 21.88 % Favored : 75.10 % 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: -0.34 (0.19), residues: 1951 helix: 0.41 (0.22), residues: 577 sheet: -1.06 (0.23), residues: 477 loop : 0.03 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 570 HIS 0.004 0.001 HIS F 546 PHE 0.021 0.001 PHE A 272 TYR 0.019 0.001 TYR F 583 ARG 0.007 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.5027 (p0) REVERT: A 557 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: B 372 GLU cc_start: 0.6870 (mp0) cc_final: 0.6584 (mp0) REVERT: C 151 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: C 244 GLU cc_start: 0.4753 (tt0) cc_final: 0.4345 (tt0) REVERT: C 328 TYR cc_start: 0.6451 (m-10) cc_final: 0.6030 (m-10) REVERT: D 160 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6082 (tm-30) REVERT: D 162 SER cc_start: 0.8755 (p) cc_final: 0.8413 (m) REVERT: E 131 ASP cc_start: 0.9165 (t70) cc_final: 0.8866 (t70) REVERT: E 166 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: F 506 GLU cc_start: 0.8099 (tt0) cc_final: 0.7764 (mt-10) REVERT: F 529 ASN cc_start: 0.9103 (m-40) cc_final: 0.8800 (m-40) outliers start: 51 outliers final: 41 residues processed: 211 average time/residue: 0.2109 time to fit residues: 71.1451 Evaluate side-chains 203 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.0670 chunk 182 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15991 Z= 0.186 Angle : 0.629 9.300 21629 Z= 0.308 Chirality : 0.043 0.238 2483 Planarity : 0.004 0.055 2801 Dihedral : 7.411 120.387 2225 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.60 % Allowed : 22.35 % Favored : 75.04 % 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: -0.14 (0.20), residues: 1951 helix: 0.56 (0.22), residues: 575 sheet: -0.95 (0.23), residues: 481 loop : 0.18 (0.23), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 570 HIS 0.003 0.001 HIS F 546 PHE 0.021 0.001 PHE A 272 TYR 0.014 0.001 TYR B 583 ARG 0.011 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5049 (p0) REVERT: A 557 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: B 372 GLU cc_start: 0.6850 (mp0) cc_final: 0.6555 (mp0) REVERT: C 244 GLU cc_start: 0.4732 (tt0) cc_final: 0.4319 (tt0) REVERT: C 328 TYR cc_start: 0.6351 (m-10) cc_final: 0.5940 (m-10) REVERT: C 354 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8973 (mp10) REVERT: D 160 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6022 (tm-30) REVERT: D 162 SER cc_start: 0.8693 (p) cc_final: 0.8391 (m) REVERT: E 131 ASP cc_start: 0.9163 (t70) cc_final: 0.8854 (t70) REVERT: E 166 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: F 506 GLU cc_start: 0.8159 (tt0) cc_final: 0.7785 (mt-10) REVERT: F 529 ASN cc_start: 0.9044 (m-40) cc_final: 0.8748 (m-40) outliers start: 44 outliers final: 36 residues processed: 208 average time/residue: 0.2247 time to fit residues: 75.3523 Evaluate side-chains 201 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.0980 chunk 114 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 197 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15991 Z= 0.234 Angle : 0.650 10.473 21629 Z= 0.320 Chirality : 0.044 0.250 2483 Planarity : 0.004 0.055 2801 Dihedral : 7.427 119.289 2225 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.78 % Allowed : 22.35 % Favored : 74.87 % 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: -0.19 (0.20), residues: 1951 helix: 0.50 (0.22), residues: 575 sheet: -0.98 (0.23), residues: 482 loop : 0.18 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 570 HIS 0.003 0.001 HIS F 179 PHE 0.017 0.001 PHE F 369 TYR 0.009 0.001 TYR A 328 ARG 0.008 0.000 ARG D 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.5601 (OUTLIER) cc_final: 0.5098 (p0) REVERT: A 406 LEU cc_start: 0.8465 (mt) cc_final: 0.8179 (mt) REVERT: A 531 ILE cc_start: 0.9214 (tp) cc_final: 0.8967 (tp) REVERT: A 557 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: B 372 GLU cc_start: 0.6878 (mp0) cc_final: 0.6571 (mp0) REVERT: C 244 GLU cc_start: 0.4798 (tt0) cc_final: 0.4390 (tt0) REVERT: C 328 TYR cc_start: 0.6374 (m-10) cc_final: 0.5954 (m-10) REVERT: D 123 ARG cc_start: 0.6785 (ptt-90) cc_final: 0.6283 (ptt90) REVERT: D 160 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6004 (tm-30) REVERT: D 162 SER cc_start: 0.8767 (p) cc_final: 0.8389 (m) REVERT: E 131 ASP cc_start: 0.9156 (t70) cc_final: 0.8852 (t70) REVERT: E 166 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: F 506 GLU cc_start: 0.8163 (tt0) cc_final: 0.7797 (mt-10) REVERT: F 529 ASN cc_start: 0.9066 (m-40) cc_final: 0.8769 (m-40) REVERT: F 545 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9015 (pm20) outliers start: 47 outliers final: 41 residues processed: 199 average time/residue: 0.2158 time to fit residues: 69.5286 Evaluate side-chains 208 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 545 GLN Chi-restraints excluded: chain F residue 546 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 10.0000 chunk 48 optimal weight: 0.0770 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.086114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065418 restraints weight = 64874.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067138 restraints weight = 40959.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067504 restraints weight = 27680.375| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15991 Z= 0.208 Angle : 0.647 11.320 21629 Z= 0.316 Chirality : 0.044 0.248 2483 Planarity : 0.004 0.052 2801 Dihedral : 7.383 118.392 2225 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.84 % Allowed : 22.47 % Favored : 74.69 % 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: -0.18 (0.20), residues: 1951 helix: 0.47 (0.22), residues: 575 sheet: -0.96 (0.23), residues: 482 loop : 0.19 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 570 HIS 0.012 0.001 HIS F 546 PHE 0.017 0.001 PHE A 272 TYR 0.015 0.001 TYR C 228 ARG 0.007 0.000 ARG D 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.89 seconds wall clock time: 48 minutes 14.21 seconds (2894.21 seconds total)