Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 19:51:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2023/5oaf_3773_neut_updated.pdb" } resolution = 4.06 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 C 12342 2.51 5 N 3434 2.21 5 O 3868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ARG 438": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 19748 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3357 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3232 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3253 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 16, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3187 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "E" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3400 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3157 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.22, per 1000 atoms: 0.47 Number of scatterers: 19748 At special positions: 0 Unit cell: (131.44, 127.2, 132.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 12 15.00 O 3868 8.00 N 3434 7.00 C 12342 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: 7.45 Conformation dependent library (CDL) restraints added in 3.0 seconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 23 sheets defined 39.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.746A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 257 through 262 removed outlier: 4.114A pdb=" N GLY A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.809A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 368 through 382 removed outlier: 4.382A pdb=" N LYS A 372 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 375 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 380 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.387A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.957A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.768A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.760A pdb=" N ASN B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.552A pdb=" N ARG B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 377 removed outlier: 3.859A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 399 through 415 removed outlier: 3.673A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 Processing helix chain 'B' and resid 436 through 445 removed outlier: 4.480A pdb=" N GLN B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.032A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 108 through 119 removed outlier: 4.104A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.088A pdb=" N LYS C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.939A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 320 removed outlier: 4.144A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.886A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.559A pdb=" N LYS C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.660A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.824A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 108 No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.712A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 removed outlier: 3.713A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.675A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.636A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 Processing helix chain 'D' and resid 399 through 415 Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 445 removed outlier: 4.987A pdb=" N LYS D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.917A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL E 53 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 4.545A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.726A pdb=" N LEU E 180 " --> pdb=" O PHE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 248 Processing helix chain 'E' and resid 256 through 262 removed outlier: 3.652A pdb=" N MET E 259 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 262 " --> pdb=" O MET E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 removed outlier: 3.516A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 319 removed outlier: 3.681A pdb=" N THR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.998A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 removed outlier: 3.881A pdb=" N ILE E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 410 through 420 Processing helix chain 'E' and resid 427 through 436 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 115 through 125 removed outlier: 3.782A pdb=" N LEU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 removed outlier: 4.029A pdb=" N SER F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.668A pdb=" N ILE F 250 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN F 251 " --> pdb=" O ASP F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.764A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 removed outlier: 3.611A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.729A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.974A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 364 through 376 removed outlier: 3.818A pdb=" N LYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.709A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.726A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.507A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 removed outlier: 3.984A pdb=" N GLN F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.768A pdb=" N VAL A 327 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU A 68 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLY A 70 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER A 331 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 300 " --> pdb=" O CYS A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 239 Processing sheet with id= C, first strand: chain 'A' and resid 166 through 172 removed outlier: 3.602A pdb=" N GLU A 134 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 189 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.758A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 324 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 75 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET B 326 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY B 77 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR B 328 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 239 through 243 Processing sheet with id= F, first strand: chain 'B' and resid 162 through 164 Processing sheet with id= G, first strand: chain 'B' and resid 193 through 195 removed outlier: 4.044A pdb=" N ILE B 202 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.668A pdb=" N VAL C 327 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU C 68 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE C 329 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 229 through 239 Processing sheet with id= J, first strand: chain 'C' and resid 134 through 137 Processing sheet with id= K, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= L, first strand: chain 'D' and resid 355 through 359 removed outlier: 3.838A pdb=" N LEU D 355 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 324 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE D 75 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET D 326 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY D 77 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR D 328 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 240 through 243 removed outlier: 3.562A pdb=" N ILE D 131 " --> pdb=" O HIS D 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 134 through 136 Processing sheet with id= O, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.685A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 161 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR D 172 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.895A pdb=" N ILE D 202 " --> pdb=" O THR D 194 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 359 through 362 removed outlier: 3.526A pdb=" N MET E 359 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL E 327 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU E 68 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE E 329 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS E 94 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 300 " --> pdb=" O CYS E 94 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 229 through 239 Processing sheet with id= S, first strand: chain 'E' and resid 157 through 163 removed outlier: 3.688A pdb=" N VAL E 157 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 355 through 358 removed outlier: 6.077A pdb=" N LEU F 324 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE F 75 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET F 326 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP F 299 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 289 through 292 removed outlier: 3.589A pdb=" N VAL F 238 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 137 through 140 Processing sheet with id= W, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.582A pdb=" N LYS F 160 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6639 1.34 - 1.46: 3384 1.46 - 1.58: 9789 1.58 - 1.69: 18 1.69 - 1.81: 160 Bond restraints: 19990 Sorted by residual: bond pdb=" C CYS D 227 " pdb=" N PRO D 228 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C ASP E 273 " pdb=" N LYS E 274 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.31e+00 bond pdb=" N GLN E 251 " pdb=" CA GLN E 251 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C GLY A 198 " pdb=" N ALA A 199 " ideal model delta sigma weight residual 1.331 1.319 0.013 1.29e-02 6.01e+03 1.01e+00 ... (remaining 19985 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.59: 581 107.59 - 114.75: 12558 114.75 - 121.90: 9560 121.90 - 129.05: 4181 129.05 - 136.21: 70 Bond angle restraints: 26950 Sorted by residual: angle pdb=" N LEU E 315 " pdb=" CA LEU E 315 " pdb=" C LEU E 315 " ideal model delta sigma weight residual 111.28 106.26 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" CA LEU B 232 " pdb=" CB LEU B 232 " pdb=" CG LEU B 232 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.81e+00 angle pdb=" C ASP A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.09e+00 angle pdb=" N ALA F 198 " pdb=" CA ALA F 198 " pdb=" C ALA F 198 " ideal model delta sigma weight residual 113.19 109.84 3.35 1.19e+00 7.06e-01 7.92e+00 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 110.87 114.69 -3.82 1.54e+00 4.22e-01 6.15e+00 ... (remaining 26945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.58: 12275 30.58 - 61.16: 71 61.16 - 91.73: 0 91.73 - 122.31: 4 122.31 - 152.89: 10 Dihedral angle restraints: 12360 sinusoidal: 5113 harmonic: 7247 Sorted by residual: dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 92.89 -152.89 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 89.33 -149.32 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PA ADP B 501 " pdb=" PB ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 72.88 -132.88 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 12357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2172 0.031 - 0.061: 635 0.061 - 0.092: 136 0.092 - 0.123: 215 0.123 - 0.153: 12 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA TYR E 314 " pdb=" N TYR E 314 " pdb=" C TYR E 314 " pdb=" CB TYR E 314 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE E 350 " pdb=" N ILE E 350 " pdb=" C ILE E 350 " pdb=" CB ILE E 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3167 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 139 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 140 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 295 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 296 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 98 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO F 99 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 99 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 99 " -0.021 5.00e-02 4.00e+02 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 500 2.71 - 3.26: 20111 3.26 - 3.81: 28730 3.81 - 4.35: 37932 4.35 - 4.90: 61567 Nonbonded interactions: 148840 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" OE1 GLU A 370 " model vdw 2.165 2.440 nonbonded pdb=" O TYR B 387 " pdb=" OG1 THR B 391 " model vdw 2.201 2.440 nonbonded pdb=" O TYR D 387 " pdb=" OG1 THR D 391 " model vdw 2.209 2.440 nonbonded pdb=" NH1 ARG F 400 " pdb=" O2A ADP F 501 " model vdw 2.212 2.520 nonbonded pdb=" OG SER E 99 " pdb=" OG SER F 310 " model vdw 2.235 2.440 ... (remaining 148835 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 11 through 205 or resid 224 through 452 or resid 501)) selection = (chain 'C' and (resid 11 through 144 or resid 151 through 452 or resid 501)) selection = (chain 'E' and (resid 11 through 144 or resid 151 through 205 or resid 224 throu \ gh 452 or resid 501)) } ncs_group { reference = (chain 'B' and (resid 16 through 146 or resid 159 through 210 or resid 228 throu \ gh 449 or resid 501)) selection = (chain 'D' and (resid 16 through 210 or resid 228 through 449 or resid 501)) selection = (chain 'F' and (resid 16 through 449 or resid 501)) } 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=0.01 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: 1.960 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: 0.020 Extract box with map and model: 6.330 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 47.600 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.001 0.038 19990 Z= 0.100 Angle : 0.475 10.387 26950 Z= 0.255 Chirality : 0.040 0.153 3170 Planarity : 0.003 0.052 3434 Dihedral : 9.128 152.889 7692 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.28 % 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: -2.75 (0.13), residues: 2512 helix: -2.78 (0.11), residues: 1006 sheet: -0.45 (0.20), residues: 428 loop : -1.20 (0.16), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 759 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 761 average time/residue: 0.3581 time to fit residues: 394.1984 Evaluate side-chains 396 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1956 time to fit residues: 3.4644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 146 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 393 HIS A 408 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 245 HIS B 251 ASN B 329 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 414 ASN E 34 GLN E 305 HIS F 78 GLN F 302 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19990 Z= 0.175 Angle : 0.589 7.389 26950 Z= 0.287 Chirality : 0.043 0.177 3170 Planarity : 0.004 0.108 3434 Dihedral : 9.313 159.773 2788 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 2512 helix: -1.29 (0.14), residues: 1020 sheet: 0.02 (0.21), residues: 443 loop : -0.85 (0.17), residues: 1049 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.3344 time to fit residues: 236.1289 Evaluate side-chains 317 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 155 optimal weight: 0.0170 chunk 62 optimal weight: 20.0000 chunk 228 optimal weight: 0.2980 chunk 246 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 245 HIS B 341 GLN C 229 HIS C 247 ASN C 414 ASN D 146 GLN E 196 ASN F 27 HIS F 245 HIS F 344 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19990 Z= 0.157 Angle : 0.581 7.476 26950 Z= 0.282 Chirality : 0.043 0.191 3170 Planarity : 0.004 0.051 3434 Dihedral : 8.789 152.430 2788 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer Outliers : 0.09 % 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: -0.83 (0.15), residues: 2512 helix: -0.53 (0.15), residues: 1025 sheet: 0.29 (0.21), residues: 446 loop : -0.79 (0.17), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 437 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 439 average time/residue: 0.3080 time to fit residues: 207.4498 Evaluate side-chains 324 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS F 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 19990 Z= 0.224 Angle : 0.626 8.320 26950 Z= 0.305 Chirality : 0.044 0.164 3170 Planarity : 0.004 0.031 3434 Dihedral : 8.561 152.432 2788 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Rotamer Outliers : 0.00 % 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: -0.56 (0.16), residues: 2512 helix: -0.26 (0.16), residues: 1007 sheet: 0.37 (0.22), residues: 480 loop : -0.69 (0.18), residues: 1025 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3154 time to fit residues: 194.5006 Evaluate side-chains 303 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 0.0270 chunk 137 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 207 optimal weight: 0.0770 chunk 167 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 316 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 19990 Z= 0.201 Angle : 0.612 7.594 26950 Z= 0.296 Chirality : 0.044 0.163 3170 Planarity : 0.003 0.040 3434 Dihedral : 8.213 148.094 2788 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer Outliers : 0.00 % 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: -0.43 (0.16), residues: 2512 helix: -0.05 (0.16), residues: 1005 sheet: 0.37 (0.22), residues: 478 loop : -0.70 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3214 time to fit residues: 193.4064 Evaluate side-chains 289 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 59 optimal weight: 0.0060 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19990 Z= 0.150 Angle : 0.589 9.329 26950 Z= 0.281 Chirality : 0.043 0.162 3170 Planarity : 0.003 0.067 3434 Dihedral : 7.691 138.715 2788 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer Outliers : 0.00 % 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 (0.16), residues: 2512 helix: 0.14 (0.16), residues: 1001 sheet: 0.36 (0.23), residues: 461 loop : -0.68 (0.18), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3107 time to fit residues: 187.3680 Evaluate side-chains 285 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS D 25 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 19990 Z= 0.215 Angle : 0.635 8.918 26950 Z= 0.307 Chirality : 0.044 0.165 3170 Planarity : 0.004 0.039 3434 Dihedral : 7.413 128.509 2788 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer Outliers : 0.00 % 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: -0.35 (0.16), residues: 2512 helix: 0.07 (0.16), residues: 1007 sheet: 0.29 (0.23), residues: 478 loop : -0.65 (0.18), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.3092 time to fit residues: 173.0147 Evaluate side-chains 268 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.343 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.0170 chunk 153 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 HIS C 18 HIS C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 19990 Z= 0.163 Angle : 0.610 9.497 26950 Z= 0.293 Chirality : 0.043 0.161 3170 Planarity : 0.003 0.047 3434 Dihedral : 7.065 122.664 2788 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer Outliers : 0.00 % 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: -0.32 (0.16), residues: 2512 helix: 0.13 (0.16), residues: 1016 sheet: 0.35 (0.23), residues: 474 loop : -0.71 (0.18), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3055 time to fit residues: 175.5966 Evaluate side-chains 275 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.4980 chunk 231 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 177 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 19990 Z= 0.157 Angle : 0.608 8.632 26950 Z= 0.293 Chirality : 0.043 0.161 3170 Planarity : 0.003 0.034 3434 Dihedral : 6.865 122.471 2788 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer Outliers : 0.00 % 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: -0.25 (0.16), residues: 2512 helix: 0.25 (0.16), residues: 1010 sheet: 0.33 (0.23), residues: 472 loop : -0.70 (0.18), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3108 time to fit residues: 170.1590 Evaluate side-chains 268 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 165 optimal weight: 0.0770 chunk 250 optimal weight: 0.4980 chunk 230 optimal weight: 0.7980 chunk 199 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19990 Z= 0.157 Angle : 0.608 11.187 26950 Z= 0.291 Chirality : 0.043 0.217 3170 Planarity : 0.003 0.034 3434 Dihedral : 6.714 122.724 2788 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer Outliers : 0.00 % 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 (0.16), residues: 2512 helix: 0.25 (0.16), residues: 1017 sheet: 0.29 (0.23), residues: 464 loop : -0.66 (0.18), residues: 1031 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2967 time to fit residues: 161.3408 Evaluate side-chains 268 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 4.9990 chunk 212 optimal weight: 0.0370 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 199 optimal weight: 0.0000 chunk 83 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112069 restraints weight = 45266.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114373 restraints weight = 27858.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115952 restraints weight = 19015.478| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 19990 Z= 0.222 Angle : 0.646 8.633 26950 Z= 0.315 Chirality : 0.045 0.180 3170 Planarity : 0.004 0.055 3434 Dihedral : 6.949 126.698 2788 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer Outliers : 0.00 % 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: -0.37 (0.16), residues: 2512 helix: 0.15 (0.16), residues: 1014 sheet: 0.25 (0.23), residues: 467 loop : -0.75 (0.19), residues: 1031 =============================================================================== Job complete usr+sys time: 4229.45 seconds wall clock time: 77 minutes 43.04 seconds (4663.04 seconds total)