Starting phenix.real_space_refine (version: dev) on Tue Dec 13 15:21:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/12_2022/7ljf_23392_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/12_2022/7ljf_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_23392/12_2022/7ljf_23392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/12_2022/7ljf_23392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/12_2022/7ljf_23392_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljf_23392/12_2022/7ljf_23392_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral 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-4807/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: 8.77, per 1000 atoms: 0.56 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: 6.26 Conformation dependent library (CDL) restraints added in 2.4 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: 1.67 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: 5.86 Time building geometry restraints manager: 6.81 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: 9344 25.77 - 51.54: 414 51.54 - 77.31: 22 77.31 - 103.08: 9 103.08 - 128.85: 3 Dihedral angle restraints: 9792 sinusoidal: 4015 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 9789 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.630 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.140 Process input model: 43.080 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 13.737 128.847 6050 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 % 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 *********************** 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 : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 226 average time/residue: 0.2196 time to fit residues: 79.1282 Evaluate side-chains 164 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1307 time to fit residues: 3.1381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 15991 Z= 0.303 Angle : 0.640 9.780 21629 Z= 0.324 Chirality : 0.044 0.168 2483 Planarity : 0.005 0.044 2801 Dihedral : 6.785 120.812 2194 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.36 % 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: 0.42 (0.21), residues: 578 sheet: -1.02 (0.23), residues: 482 loop : 0.27 (0.23), residues: 891 *********************** 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 199 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 191 average time/residue: 0.2394 time to fit residues: 72.7250 Evaluate side-chains 169 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1395 time to fit residues: 6.9584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 149 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** 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: 0.8192 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 15991 Z= 0.454 Angle : 0.733 9.428 21629 Z= 0.376 Chirality : 0.046 0.201 2483 Planarity : 0.005 0.051 2801 Dihedral : 7.173 127.660 2194 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 1.77 % 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: -0.74 (0.19), residues: 1951 helix: -0.01 (0.21), residues: 574 sheet: -1.33 (0.22), residues: 481 loop : -0.10 (0.22), residues: 896 *********************** 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 188 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 182 average time/residue: 0.2138 time to fit residues: 63.8746 Evaluate side-chains 165 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1386 time to fit residues: 8.1426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0170 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 40.0000 chunk 94 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.0026 ------------------------------------------------------------------------------- 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 263 GLN F 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1368 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= 0.167 Angle : 0.619 10.460 21629 Z= 0.304 Chirality : 0.043 0.158 2483 Planarity : 0.004 0.051 2801 Dihedral : 6.644 122.937 2194 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.95 % 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: -0.12 (0.20), residues: 1951 helix: 0.49 (0.22), residues: 576 sheet: -1.00 (0.23), residues: 478 loop : 0.30 (0.23), residues: 897 *********************** 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 196 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 190 average time/residue: 0.2287 time to fit residues: 70.3098 Evaluate side-chains 168 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1553 time to fit residues: 5.4091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 5.1186 ------------------------------------------------------------------------------- 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 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 15991 Z= 0.336 Angle : 0.657 8.815 21629 Z= 0.330 Chirality : 0.044 0.201 2483 Planarity : 0.005 0.050 2801 Dihedral : 6.887 121.912 2194 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 2.01 % 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: -0.39 (0.19), residues: 1951 helix: 0.30 (0.21), residues: 574 sheet: -1.12 (0.23), residues: 482 loop : 0.09 (0.22), residues: 895 *********************** 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 197 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 189 average time/residue: 0.2206 time to fit residues: 68.6605 Evaluate side-chains 177 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1732 time to fit residues: 11.0627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 15991 Z= 0.261 Angle : 0.624 8.901 21629 Z= 0.313 Chirality : 0.043 0.185 2483 Planarity : 0.004 0.050 2801 Dihedral : 6.810 123.288 2194 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.42 % 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: -0.28 (0.20), residues: 1951 helix: 0.42 (0.22), residues: 573 sheet: -1.07 (0.23), residues: 480 loop : 0.14 (0.22), residues: 898 *********************** 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 193 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 189 average time/residue: 0.2196 time to fit residues: 67.7455 Evaluate side-chains 165 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1437 time to fit residues: 4.9006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15991 Z= 0.265 Angle : 0.647 9.002 21629 Z= 0.323 Chirality : 0.043 0.184 2483 Planarity : 0.004 0.050 2801 Dihedral : 6.811 122.596 2194 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 1.06 % 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: -0.31 (0.20), residues: 1951 helix: 0.40 (0.21), residues: 574 sheet: -1.10 (0.23), residues: 481 loop : 0.13 (0.22), residues: 896 *********************** 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 181 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 176 average time/residue: 0.2276 time to fit residues: 66.1214 Evaluate side-chains 166 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2109 time to fit residues: 7.9234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15991 Z= 0.221 Angle : 0.636 9.052 21629 Z= 0.316 Chirality : 0.043 0.189 2483 Planarity : 0.004 0.053 2801 Dihedral : 6.733 121.557 2194 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 1.06 % 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: -0.24 (0.20), residues: 1951 helix: 0.45 (0.22), residues: 582 sheet: -1.03 (0.23), residues: 482 loop : 0.16 (0.23), residues: 887 *********************** 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 185 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.2240 time to fit residues: 65.8043 Evaluate side-chains 166 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1408 time to fit residues: 4.9988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 chunk 160 optimal weight: 9.9990 chunk 168 optimal weight: 0.0070 chunk 116 optimal weight: 8.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15991 Z= 0.197 Angle : 0.634 10.052 21629 Z= 0.312 Chirality : 0.043 0.203 2483 Planarity : 0.004 0.059 2801 Dihedral : 6.631 119.743 2194 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.41 % 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: -0.17 (0.20), residues: 1951 helix: 0.51 (0.22), residues: 580 sheet: -0.98 (0.23), residues: 482 loop : 0.20 (0.23), residues: 889 *********************** 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 176 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 173 average time/residue: 0.2274 time to fit residues: 63.8845 Evaluate side-chains 156 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1354 time to fit residues: 2.7854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 197 optimal weight: 30.0000 chunk 181 optimal weight: 0.0010 chunk 157 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 5.5994 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 15991 Z= 0.364 Angle : 0.710 10.579 21629 Z= 0.355 Chirality : 0.045 0.212 2483 Planarity : 0.005 0.053 2801 Dihedral : 6.891 121.422 2194 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.65 % 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: 0.23 (0.21), residues: 580 sheet: -1.11 (0.23), residues: 480 loop : -0.02 (0.22), residues: 891 ********************** 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 166 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.2556 time to fit residues: 68.9810 Evaluate side-chains 162 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1532 time to fit residues: 4.9376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3710 r_free = 0.3710 target = 0.083464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063810 restraints weight = 66491.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065315 restraints weight = 42062.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065635 restraints weight = 30512.217| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 15991 Z= 0.405 Angle : 0.745 9.932 21629 Z= 0.374 Chirality : 0.046 0.211 2483 Planarity : 0.005 0.052 2801 Dihedral : 7.130 125.860 2194 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 0.35 % 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: -0.76 (0.19), residues: 1951 helix: 0.11 (0.21), residues: 573 sheet: -1.31 (0.23), residues: 477 loop : -0.25 (0.22), residues: 901 =============================================================================== Job complete usr+sys time: 2410.69 seconds wall clock time: 45 minutes 36.10 seconds (2736.10 seconds total)