Starting phenix.real_space_refine on Wed Apr 10 14:44:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/04_2024/5oaf_3773_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/04_2024/5oaf_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_3773/04_2024/5oaf_3773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/04_2024/5oaf_3773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/04_2024/5oaf_3773_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/04_2024/5oaf_3773_neut_updated.pdb" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-dev-5288/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: 10.82, per 1000 atoms: 0.55 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: 7.57 Conformation dependent library (CDL) restraints added in 3.6 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: 4.46 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: 5.66 Time building geometry restraints manager: 8.21 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: 1.660 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: 5.720 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 52.170 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.110 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.710 ------------------------------------------------------------------------------- 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 % Allowed : 0.05 % Favored : 99.67 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 283 HIS 0.002 0.000 HIS A 316 PHE 0.007 0.001 PHE D 224 TYR 0.007 0.001 TYR E 314 ARG 0.004 0.000 ARG F 400 *********************** 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 : 2.323 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: A 184 ARG cc_start: 0.7324 (mpt180) cc_final: 0.6510 (mtp180) REVERT: A 215 LEU cc_start: 0.6942 (mt) cc_final: 0.6441 (tt) REVERT: A 260 MET cc_start: 0.6668 (ptm) cc_final: 0.6126 (ppp) REVERT: A 298 VAL cc_start: 0.6472 (t) cc_final: 0.6113 (t) REVERT: B 117 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 141 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6725 (pp20) REVERT: B 168 MET cc_start: 0.4892 (mmm) cc_final: 0.4655 (ttt) REVERT: B 174 LEU cc_start: 0.7024 (mt) cc_final: 0.6550 (mt) REVERT: B 199 THR cc_start: 0.7066 (p) cc_final: 0.6809 (m) REVERT: B 232 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6750 (pp) REVERT: C 271 ILE cc_start: 0.8453 (mm) cc_final: 0.8242 (mm) REVERT: C 332 ASN cc_start: 0.8119 (t0) cc_final: 0.7834 (t0) REVERT: C 359 MET cc_start: 0.7115 (mtp) cc_final: 0.6752 (mtt) REVERT: C 380 GLN cc_start: 0.8255 (tt0) cc_final: 0.8008 (mt0) REVERT: D 176 THR cc_start: 0.7392 (p) cc_final: 0.6800 (t) REVERT: E 274 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7713 (tmtt) REVERT: E 303 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6564 (mm-30) REVERT: E 308 ASP cc_start: 0.7439 (t0) cc_final: 0.6736 (t0) REVERT: E 380 GLN cc_start: 0.8415 (tt0) cc_final: 0.8198 (tp-100) REVERT: F 135 THR cc_start: 0.8509 (p) cc_final: 0.7695 (p) REVERT: F 277 ASN cc_start: 0.7195 (m-40) cc_final: 0.6611 (m110) REVERT: F 313 ASN cc_start: 0.6645 (t0) cc_final: 0.5792 (t0) outliers start: 6 outliers final: 1 residues processed: 761 average time/residue: 0.3861 time to fit residues: 427.4363 Evaluate side-chains 405 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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: 0.2980 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: 3.9990 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 146 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.6952 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19990 Z= 0.167 Angle : 0.591 7.795 26950 Z= 0.289 Chirality : 0.043 0.177 3170 Planarity : 0.004 0.110 3434 Dihedral : 9.279 158.366 2788 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -1.41 (0.15), residues: 2512 helix: -1.25 (0.14), residues: 1023 sheet: 0.04 (0.21), residues: 443 loop : -0.83 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 283 HIS 0.013 0.001 HIS B 245 PHE 0.016 0.001 PHE D 224 TYR 0.014 0.001 TYR C 314 ARG 0.008 0.001 ARG B 130 *********************** 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 483 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.266 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 REVERT: A 184 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6493 (mtp180) REVERT: A 215 LEU cc_start: 0.7290 (mt) cc_final: 0.6711 (mt) REVERT: A 259 MET cc_start: 0.3364 (mtt) cc_final: 0.2907 (mtm) REVERT: A 260 MET cc_start: 0.6562 (ptm) cc_final: 0.5998 (ppp) REVERT: B 46 MET cc_start: 0.8350 (mmm) cc_final: 0.7946 (mmm) REVERT: B 117 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 141 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6740 (pp20) REVERT: B 401 TYR cc_start: 0.7338 (t80) cc_final: 0.6972 (t80) REVERT: C 28 GLU cc_start: 0.7676 (tp30) cc_final: 0.7399 (tp30) REVERT: C 323 ILE cc_start: 0.7291 (pt) cc_final: 0.7084 (mm) REVERT: D 141 GLU cc_start: 0.8387 (tt0) cc_final: 0.7987 (tp30) REVERT: D 176 THR cc_start: 0.6859 (p) cc_final: 0.6371 (t) REVERT: D 261 PHE cc_start: 0.6513 (p90) cc_final: 0.6258 (p90) REVERT: E 47 GLU cc_start: 0.7426 (pt0) cc_final: 0.7080 (pt0) REVERT: E 249 ARG cc_start: 0.6480 (mpp80) cc_final: 0.5851 (mtt90) REVERT: E 308 ASP cc_start: 0.7405 (t0) cc_final: 0.6954 (t0) REVERT: E 380 GLN cc_start: 0.8495 (tt0) cc_final: 0.8221 (tp-100) REVERT: F 168 MET cc_start: 0.5701 (ptp) cc_final: 0.5476 (ptm) REVERT: F 368 LYS cc_start: 0.7705 (tttt) cc_final: 0.7278 (tttt) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.3356 time to fit residues: 240.0618 Evaluate side-chains 328 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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: 7.9990 chunk 70 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 228 optimal weight: 0.0370 chunk 246 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 348 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 247 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 302 HIS E 196 ASN E 305 HIS ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS F 277 ASN 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: 0.7092 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19990 Z= 0.188 Angle : 0.600 7.093 26950 Z= 0.294 Chirality : 0.043 0.167 3170 Planarity : 0.004 0.050 3434 Dihedral : 8.802 155.188 2788 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Rotamer: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % 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: -0.80 (0.15), residues: 2512 helix: -0.49 (0.15), residues: 1006 sheet: 0.26 (0.21), residues: 458 loop : -0.77 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 283 HIS 0.015 0.002 HIS E 316 PHE 0.019 0.002 PHE F 123 TYR 0.019 0.002 TYR E 314 ARG 0.006 0.001 ARG A 276 *********************** 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: 3 poor density : 436 time to evaluate : 2.435 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 REVERT: A 184 ARG cc_start: 0.7008 (mpt180) cc_final: 0.6496 (mtp180) REVERT: A 203 GLN cc_start: 0.5950 (tp-100) cc_final: 0.5734 (tp40) REVERT: A 259 MET cc_start: 0.3757 (mtt) cc_final: 0.3379 (mtm) REVERT: A 260 MET cc_start: 0.6811 (ptm) cc_final: 0.6228 (ppp) REVERT: B 46 MET cc_start: 0.8330 (mmm) cc_final: 0.7922 (mmm) REVERT: B 178 MET cc_start: 0.7707 (ppp) cc_final: 0.7432 (ppp) REVERT: B 401 TYR cc_start: 0.7842 (t80) cc_final: 0.7473 (t80) REVERT: C 28 GLU cc_start: 0.7989 (tp30) cc_final: 0.7668 (tp30) REVERT: C 134 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7128 (tm-30) REVERT: C 271 ILE cc_start: 0.8384 (mm) cc_final: 0.8054 (mm) REVERT: D 141 GLU cc_start: 0.8432 (tt0) cc_final: 0.7837 (tp30) REVERT: D 176 THR cc_start: 0.6923 (p) cc_final: 0.6416 (t) REVERT: D 254 THR cc_start: 0.7851 (p) cc_final: 0.7648 (p) REVERT: D 262 SER cc_start: 0.6566 (p) cc_final: 0.6205 (t) REVERT: E 47 GLU cc_start: 0.7519 (pt0) cc_final: 0.7190 (pt0) REVERT: E 308 ASP cc_start: 0.7525 (t0) cc_final: 0.7077 (t0) REVERT: E 380 GLN cc_start: 0.8425 (tt0) cc_final: 0.8202 (tp-100) REVERT: F 139 GLU cc_start: 0.7818 (pm20) cc_final: 0.7579 (pm20) REVERT: F 168 MET cc_start: 0.5495 (ptp) cc_final: 0.5173 (ptm) REVERT: F 301 VAL cc_start: 0.8352 (t) cc_final: 0.8086 (t) REVERT: F 313 ASN cc_start: 0.6811 (t0) cc_final: 0.6596 (t0) REVERT: F 375 CYS cc_start: 0.7174 (m) cc_final: 0.6929 (m) outliers start: 3 outliers final: 0 residues processed: 439 average time/residue: 0.3192 time to fit residues: 212.8504 Evaluate side-chains 320 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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: 7.9990 chunk 171 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 302 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS D 146 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 19990 Z= 0.470 Angle : 0.861 10.326 26950 Z= 0.433 Chirality : 0.051 0.212 3170 Planarity : 0.006 0.062 3434 Dihedral : 9.601 179.945 2788 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % 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: -1.47 (0.15), residues: 2512 helix: -1.00 (0.15), residues: 1018 sheet: -0.15 (0.22), residues: 492 loop : -1.19 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 283 HIS 0.014 0.003 HIS B 302 PHE 0.025 0.003 PHE B 123 TYR 0.029 0.003 TYR A 286 ARG 0.016 0.001 ARG A 64 *********************** 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 361 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 359 time to evaluate : 2.435 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: A 180 LEU cc_start: 0.8424 (mm) cc_final: 0.7874 (mm) REVERT: A 259 MET cc_start: 0.4981 (mtt) cc_final: 0.4667 (mtt) REVERT: A 260 MET cc_start: 0.7255 (ptm) cc_final: 0.4412 (ppp) REVERT: A 316 HIS cc_start: 0.8039 (p90) cc_final: 0.7784 (p90) REVERT: B 178 MET cc_start: 0.7962 (ppp) cc_final: 0.7668 (ppp) REVERT: B 261 PHE cc_start: 0.7373 (p90) cc_final: 0.7082 (p90) REVERT: D 141 GLU cc_start: 0.8693 (tt0) cc_final: 0.8036 (tp30) REVERT: D 196 ASP cc_start: 0.8771 (m-30) cc_final: 0.8269 (p0) REVERT: D 205 LEU cc_start: 0.7426 (mt) cc_final: 0.7206 (mt) REVERT: D 305 ASP cc_start: 0.7470 (t0) cc_final: 0.7252 (t0) REVERT: D 413 CYS cc_start: 0.8479 (t) cc_final: 0.7820 (p) REVERT: E 380 GLN cc_start: 0.8699 (tt0) cc_final: 0.8284 (tp-100) outliers start: 2 outliers final: 2 residues processed: 361 average time/residue: 0.3168 time to fit residues: 176.1385 Evaluate side-chains 269 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 180 optimal weight: 0.0670 chunk 100 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19990 Z= 0.224 Angle : 0.649 8.102 26950 Z= 0.317 Chirality : 0.045 0.173 3170 Planarity : 0.004 0.058 3434 Dihedral : 8.763 166.013 2788 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.16 (0.16), residues: 2512 helix: -0.59 (0.15), residues: 1028 sheet: -0.08 (0.22), residues: 490 loop : -1.16 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 283 HIS 0.006 0.001 HIS E 316 PHE 0.028 0.002 PHE D 261 TYR 0.020 0.002 TYR B 401 ARG 0.009 0.001 ARG B 253 *********************** 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 364 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 2.367 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: A 105 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 203 GLN cc_start: 0.6463 (tp40) cc_final: 0.6200 (tp40) REVERT: A 259 MET cc_start: 0.5241 (mtt) cc_final: 0.4798 (mtt) REVERT: A 260 MET cc_start: 0.7026 (ptm) cc_final: 0.6682 (ppp) REVERT: B 401 TYR cc_start: 0.8257 (t80) cc_final: 0.7987 (t80) REVERT: C 367 THR cc_start: 0.7217 (p) cc_final: 0.7004 (p) REVERT: D 196 ASP cc_start: 0.8702 (m-30) cc_final: 0.8339 (p0) REVERT: E 21 VAL cc_start: 0.7411 (p) cc_final: 0.7201 (p) REVERT: E 380 GLN cc_start: 0.8690 (tt0) cc_final: 0.8280 (tp-100) REVERT: F 162 THR cc_start: 0.8137 (m) cc_final: 0.7914 (m) REVERT: F 313 ASN cc_start: 0.7270 (t0) cc_final: 0.6995 (t0) REVERT: F 314 ARG cc_start: 0.6786 (ptp-110) cc_final: 0.6356 (ptt90) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3229 time to fit residues: 178.2732 Evaluate side-chains 272 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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: 8.9990 chunk 218 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN C 229 HIS D 146 GLN F 25 HIS F 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19990 Z= 0.159 Angle : 0.613 10.165 26950 Z= 0.296 Chirality : 0.044 0.188 3170 Planarity : 0.003 0.036 3434 Dihedral : 7.997 153.202 2788 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2512 helix: -0.23 (0.16), residues: 1032 sheet: 0.02 (0.23), residues: 464 loop : -1.16 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 283 HIS 0.020 0.001 HIS E 316 PHE 0.014 0.002 PHE D 309 TYR 0.019 0.001 TYR B 401 ARG 0.007 0.000 ARG B 253 *********************** 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 371 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 370 time to evaluate : 2.359 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: A 184 ARG cc_start: 0.7386 (mpt180) cc_final: 0.6356 (ptt180) REVERT: A 203 GLN cc_start: 0.6388 (tp40) cc_final: 0.5729 (tp40) REVERT: A 259 MET cc_start: 0.4442 (mtt) cc_final: 0.4034 (mtp) REVERT: B 178 MET cc_start: 0.7506 (ppp) cc_final: 0.7289 (ppp) REVERT: B 303 MET cc_start: 0.8338 (ppp) cc_final: 0.7435 (ppp) REVERT: B 401 TYR cc_start: 0.8146 (t80) cc_final: 0.7662 (t80) REVERT: C 113 MET cc_start: 0.7476 (ttt) cc_final: 0.7164 (ttt) REVERT: C 367 THR cc_start: 0.7154 (p) cc_final: 0.6925 (p) REVERT: D 141 GLU cc_start: 0.8556 (tt0) cc_final: 0.7542 (tm-30) REVERT: D 196 ASP cc_start: 0.8729 (m-30) cc_final: 0.8328 (p0) REVERT: E 202 ARG cc_start: 0.5149 (mmt90) cc_final: 0.4859 (mmm160) REVERT: E 380 GLN cc_start: 0.8664 (tt0) cc_final: 0.8363 (tp-100) REVERT: F 25 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5911 (m-70) REVERT: F 126 SER cc_start: 0.8983 (m) cc_final: 0.8753 (t) REVERT: F 162 THR cc_start: 0.8125 (m) cc_final: 0.7916 (m) REVERT: F 168 MET cc_start: 0.5470 (ptp) cc_final: 0.5230 (ptm) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.3171 time to fit residues: 181.5955 Evaluate side-chains 286 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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: 0.2980 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS B 121 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 344 HIS ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 19990 Z= 0.295 Angle : 0.706 9.946 26950 Z= 0.349 Chirality : 0.047 0.165 3170 Planarity : 0.004 0.059 3434 Dihedral : 8.012 134.004 2788 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -1.18 (0.16), residues: 2512 helix: -0.50 (0.16), residues: 1034 sheet: -0.25 (0.23), residues: 482 loop : -1.21 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 283 HIS 0.014 0.002 HIS E 316 PHE 0.030 0.002 PHE A 116 TYR 0.019 0.002 TYR C 131 ARG 0.006 0.001 ARG B 336 *********************** 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 333 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.325 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: A 132 GLU cc_start: 0.8612 (pm20) cc_final: 0.7991 (pt0) REVERT: A 184 ARG cc_start: 0.7453 (mpt180) cc_final: 0.6446 (ptt180) REVERT: A 203 GLN cc_start: 0.6359 (tp40) cc_final: 0.5636 (tp40) REVERT: A 259 MET cc_start: 0.4762 (mtt) cc_final: 0.4454 (mtt) REVERT: B 178 MET cc_start: 0.7707 (ppp) cc_final: 0.7456 (ppp) REVERT: C 367 THR cc_start: 0.7263 (p) cc_final: 0.7043 (p) REVERT: D 196 ASP cc_start: 0.8806 (m-30) cc_final: 0.8564 (p0) REVERT: E 202 ARG cc_start: 0.4947 (mmt90) cc_final: 0.4646 (mmm160) REVERT: E 380 GLN cc_start: 0.8669 (tt0) cc_final: 0.8392 (tp-100) REVERT: F 168 MET cc_start: 0.5643 (ptp) cc_final: 0.5278 (ptm) REVERT: F 401 TYR cc_start: 0.8049 (t80) cc_final: 0.7798 (t80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.3028 time to fit residues: 156.9852 Evaluate side-chains 254 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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: 4.9990 chunk 144 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 275 GLN ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19990 Z= 0.171 Angle : 0.623 11.325 26950 Z= 0.302 Chirality : 0.044 0.165 3170 Planarity : 0.003 0.034 3434 Dihedral : 7.347 133.295 2788 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2512 helix: -0.26 (0.16), residues: 1034 sheet: -0.10 (0.23), residues: 472 loop : -1.17 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 283 HIS 0.013 0.001 HIS E 316 PHE 0.014 0.002 PHE F 311 TYR 0.027 0.001 TYR B 401 ARG 0.007 0.000 ARG F 29 *********************** 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 350 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.352 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: A 132 GLU cc_start: 0.8509 (pm20) cc_final: 0.7941 (pt0) REVERT: A 184 ARG cc_start: 0.7443 (mpt180) cc_final: 0.5909 (ptt180) REVERT: A 209 TYR cc_start: 0.6291 (m-80) cc_final: 0.5961 (m-80) REVERT: A 259 MET cc_start: 0.4436 (mtt) cc_final: 0.4087 (mtt) REVERT: A 353 ASP cc_start: 0.6804 (t70) cc_final: 0.6417 (t0) REVERT: A 371 MET cc_start: 0.8315 (mmt) cc_final: 0.8053 (mpp) REVERT: B 178 MET cc_start: 0.7547 (ppp) cc_final: 0.7295 (ppp) REVERT: B 303 MET cc_start: 0.8374 (ppp) cc_final: 0.7823 (ppp) REVERT: C 110 GLU cc_start: 0.7727 (tp30) cc_final: 0.7516 (tp30) REVERT: C 264 MET cc_start: 0.3916 (ppp) cc_final: 0.3539 (ppp) REVERT: C 311 CYS cc_start: 0.8486 (m) cc_final: 0.8180 (m) REVERT: E 202 ARG cc_start: 0.5081 (mmt90) cc_final: 0.4701 (mmm160) REVERT: E 380 GLN cc_start: 0.8670 (tt0) cc_final: 0.8385 (tp-100) REVERT: E 437 PHE cc_start: 0.5659 (p90) cc_final: 0.5374 (p90) REVERT: F 126 SER cc_start: 0.8977 (m) cc_final: 0.8765 (t) REVERT: F 138 ILE cc_start: 0.7015 (mt) cc_final: 0.6704 (mm) REVERT: F 168 MET cc_start: 0.5690 (ptp) cc_final: 0.5346 (ptm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3010 time to fit residues: 166.0062 Evaluate side-chains 276 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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: 4.9990 chunk 231 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 chunk 213 optimal weight: 0.0980 chunk 224 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19990 Z= 0.180 Angle : 0.631 10.881 26950 Z= 0.305 Chirality : 0.044 0.177 3170 Planarity : 0.003 0.031 3434 Dihedral : 7.136 133.990 2788 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 0.05 % Allowed : 0.70 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2512 helix: -0.16 (0.16), residues: 1019 sheet: 0.02 (0.24), residues: 451 loop : -1.18 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 283 HIS 0.015 0.001 HIS E 316 PHE 0.021 0.002 PHE D 309 TYR 0.013 0.001 TYR D 442 ARG 0.008 0.000 ARG F 29 *********************** 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 331 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 2.253 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: A 132 GLU cc_start: 0.8485 (pm20) cc_final: 0.7920 (pt0) REVERT: A 184 ARG cc_start: 0.7381 (mpt180) cc_final: 0.6242 (ptt180) REVERT: A 203 GLN cc_start: 0.6076 (tp40) cc_final: 0.5695 (tp40) REVERT: A 259 MET cc_start: 0.4649 (mtt) cc_final: 0.4352 (mtt) REVERT: B 178 MET cc_start: 0.7571 (ppp) cc_final: 0.7318 (ppp) REVERT: B 303 MET cc_start: 0.8358 (ppp) cc_final: 0.7821 (ppp) REVERT: C 264 MET cc_start: 0.4109 (ppp) cc_final: 0.3683 (ppp) REVERT: C 311 CYS cc_start: 0.8424 (m) cc_final: 0.8130 (m) REVERT: E 202 ARG cc_start: 0.5038 (mmt90) cc_final: 0.4699 (mmm160) REVERT: E 380 GLN cc_start: 0.8651 (tt0) cc_final: 0.8384 (tp-100) REVERT: E 437 PHE cc_start: 0.5799 (p90) cc_final: 0.5468 (p90) REVERT: F 126 SER cc_start: 0.9003 (m) cc_final: 0.8731 (t) REVERT: F 162 THR cc_start: 0.7940 (m) cc_final: 0.7729 (m) REVERT: F 168 MET cc_start: 0.5659 (ptp) cc_final: 0.5322 (ptm) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.3065 time to fit residues: 158.6163 Evaluate side-chains 270 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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: 0.0060 chunk 238 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19990 Z= 0.267 Angle : 0.700 11.258 26950 Z= 0.343 Chirality : 0.046 0.181 3170 Planarity : 0.004 0.086 3434 Dihedral : 7.379 137.223 2788 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 0.09 % Favored : 99.86 % 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: -1.03 (0.16), residues: 2512 helix: -0.31 (0.16), residues: 1013 sheet: -0.15 (0.24), residues: 462 loop : -1.19 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 283 HIS 0.020 0.002 HIS E 316 PHE 0.031 0.002 PHE A 116 TYR 0.034 0.002 TYR B 401 ARG 0.009 0.001 ARG C 249 ********************** 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 317 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 2.906 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: A 132 GLU cc_start: 0.8554 (pm20) cc_final: 0.8096 (pt0) REVERT: A 184 ARG cc_start: 0.7398 (mpt180) cc_final: 0.6274 (ptt180) REVERT: A 203 GLN cc_start: 0.6067 (tp40) cc_final: 0.5631 (tp40) REVERT: A 259 MET cc_start: 0.5173 (mtt) cc_final: 0.4891 (mtt) REVERT: A 306 MET cc_start: 0.7099 (ppp) cc_final: 0.6280 (ptm) REVERT: A 353 ASP cc_start: 0.6669 (t70) cc_final: 0.6462 (t0) REVERT: B 178 MET cc_start: 0.7728 (ppp) cc_final: 0.7267 (ppp) REVERT: B 303 MET cc_start: 0.8498 (ppp) cc_final: 0.8065 (ppp) REVERT: C 264 MET cc_start: 0.4166 (ppp) cc_final: 0.3768 (ppp) REVERT: C 311 CYS cc_start: 0.8491 (m) cc_final: 0.8219 (m) REVERT: E 113 MET cc_start: 0.8247 (tmm) cc_final: 0.7961 (tmm) REVERT: E 202 ARG cc_start: 0.4924 (mmt90) cc_final: 0.4587 (mmm160) REVERT: E 359 MET cc_start: 0.8394 (ttt) cc_final: 0.8126 (ttt) REVERT: E 380 GLN cc_start: 0.8661 (tt0) cc_final: 0.8371 (tp-100) REVERT: E 437 PHE cc_start: 0.5863 (p90) cc_final: 0.5659 (p90) REVERT: F 168 MET cc_start: 0.5661 (ptp) cc_final: 0.5330 (ptm) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2995 time to fit residues: 148.8947 Evaluate side-chains 260 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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: 0.8980 chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109882 restraints weight = 45583.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112179 restraints weight = 27539.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113726 restraints weight = 18726.558| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19990 Z= 0.186 Angle : 0.649 12.416 26950 Z= 0.313 Chirality : 0.044 0.185 3170 Planarity : 0.004 0.041 3434 Dihedral : 7.130 133.617 2788 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2512 helix: -0.21 (0.16), residues: 1013 sheet: -0.07 (0.24), residues: 457 loop : -1.16 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 283 HIS 0.017 0.001 HIS E 316 PHE 0.017 0.002 PHE D 309 TYR 0.018 0.001 TYR E 314 ARG 0.008 0.000 ARG F 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4411.92 seconds wall clock time: 86 minutes 7.83 seconds (5167.83 seconds total)