Starting phenix.real_space_refine on Sat Apr 6 00:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmb_22922/04_2024/7kmb_22922.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4159 2.51 5 N 1067 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 37": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 406": "OE1" <-> "OE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 465": "OE1" <-> "OE2" Residue "G TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6509 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.26, per 1000 atoms: 0.65 Number of scatterers: 6509 At special positions: 0 Unit cell: (99.452, 75.118, 111.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1246 8.00 N 1067 7.00 C 4159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 1 " - " ASN F 546 " " NAG B 1 " - " ASN G 343 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 52.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.788A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.796A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.714A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 4.551A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 4.223A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.751A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.608A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.607A pdb=" N GLU F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.569A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 249 removed outlier: 3.707A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.778A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.967A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.543A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 4.140A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 365 through 383 removed outlier: 3.925A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 4.040A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.082A pdb=" N PHE F 438 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.703A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 523 removed outlier: 4.074A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.966A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.632A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 4.132A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 586' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.636A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 365 through 370 removed outlier: 3.675A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 365 through 370' Processing helix chain 'G' and resid 385 through 390 removed outlier: 3.978A pdb=" N ASP G 389 " --> pdb=" O THR G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.508A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'G' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.664A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.023A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.604A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 510 " --> pdb=" O PHE G 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 452 through 454 236 hydrogen bonds defined for protein. 675 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: 1.80 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1771 1.47 - 1.59: 2792 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6689 Sorted by residual: bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG F 705 " pdb=" O5 NAG F 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG F 703 " pdb=" O5 NAG F 703 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 6684 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.87: 219 106.87 - 113.69: 3524 113.69 - 120.51: 2786 120.51 - 127.34: 2470 127.34 - 134.16: 92 Bond angle restraints: 9091 Sorted by residual: angle pdb=" CB MET F 152 " pdb=" CG MET F 152 " pdb=" SD MET F 152 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA MET F 557 " pdb=" CB MET F 557 " pdb=" CG MET F 557 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CB MET F 557 " pdb=" CG MET F 557 " pdb=" SD MET F 557 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N ASP F 499 " pdb=" CA ASP F 499 " pdb=" C ASP F 499 " ideal model delta sigma weight residual 109.81 117.51 -7.70 2.21e+00 2.05e-01 1.21e+01 angle pdb=" CB GLU F 238 " pdb=" CG GLU F 238 " pdb=" CD GLU F 238 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 9086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3596 17.56 - 35.12: 373 35.12 - 52.68: 70 52.68 - 70.24: 17 70.24 - 87.80: 5 Dihedral angle restraints: 4061 sinusoidal: 1750 harmonic: 2311 Sorted by residual: dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.69 66.31 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS F 530 " pdb=" SG CYS F 530 " pdb=" SG CYS F 542 " pdb=" CB CYS F 542 " ideal model delta sinusoidal sigma weight residual -86.00 -122.53 36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" SG CYS G 391 " pdb=" CB CYS G 525 " pdb=" SG CYS G 525 " pdb=" CA CYS G 525 " ideal model delta sinusoidal sigma weight residual 79.00 16.22 62.78 1 2.00e+01 2.50e-03 1.30e+01 ... (remaining 4058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 594 0.036 - 0.072: 267 0.072 - 0.108: 84 0.108 - 0.144: 25 0.144 - 0.180: 7 Chirality restraints: 977 Sorted by residual: chirality pdb=" CB VAL F 364 " pdb=" CA VAL F 364 " pdb=" CG1 VAL F 364 " pdb=" CG2 VAL F 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ASP F 499 " pdb=" N ASP F 499 " pdb=" C ASP F 499 " pdb=" CB ASP F 499 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 974 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 395 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C VAL G 395 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL G 395 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR G 396 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 491 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C VAL F 491 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL F 491 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO F 492 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 491 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO F 492 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 492 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 492 " -0.022 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2005 2.82 - 3.34: 5801 3.34 - 3.86: 10775 3.86 - 4.38: 12487 4.38 - 4.90: 21006 Nonbonded interactions: 52074 Sorted by model distance: nonbonded pdb=" O ALA F 501 " pdb=" OG SER F 507 " model vdw 2.298 2.440 nonbonded pdb=" O ILE F 544 " pdb=" OG SER F 547 " model vdw 2.300 2.440 nonbonded pdb=" O THR F 118 " pdb=" OG1 THR F 122 " model vdw 2.303 2.440 nonbonded pdb=" OG SER G 438 " pdb=" O PRO G 507 " model vdw 2.305 2.440 nonbonded pdb=" O GLU F 406 " pdb=" OG SER F 409 " model vdw 2.342 2.440 ... (remaining 52069 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 15.530 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.004 0.041 6689 Z= 0.236 Angle : 0.741 11.430 9091 Z= 0.367 Chirality : 0.047 0.180 977 Planarity : 0.005 0.039 1167 Dihedral : 14.633 87.805 2558 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -3.57 (0.24), residues: 784 helix: -3.19 (0.17), residues: 348 sheet: -0.40 (0.79), residues: 41 loop : -1.70 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 478 HIS 0.006 0.001 HIS F 540 PHE 0.009 0.001 PHE G 486 TYR 0.018 0.001 TYR G 396 ARG 0.006 0.001 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 121 ASN cc_start: 0.8004 (m110) cc_final: 0.7788 (m110) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1700 time to fit residues: 20.3555 Evaluate side-chains 67 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 373 HIS G 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6689 Z= 0.204 Angle : 0.595 8.716 9091 Z= 0.303 Chirality : 0.042 0.149 977 Planarity : 0.004 0.029 1167 Dihedral : 4.954 46.248 1045 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.16 % Allowed : 9.70 % Favored : 89.15 % 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: -2.02 (0.27), residues: 784 helix: -1.14 (0.25), residues: 343 sheet: -0.34 (0.71), residues: 42 loop : -1.60 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 165 HIS 0.013 0.001 HIS F 540 PHE 0.010 0.001 PHE F 369 TYR 0.022 0.001 TYR F 183 ARG 0.004 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 441 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8358 (tmtt) REVERT: F 498 CYS cc_start: 0.4695 (OUTLIER) cc_final: 0.4488 (t) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.1710 time to fit residues: 17.7132 Evaluate side-chains 71 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 498 CYS Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6689 Z= 0.178 Angle : 0.528 6.421 9091 Z= 0.267 Chirality : 0.041 0.148 977 Planarity : 0.003 0.028 1167 Dihedral : 4.486 38.641 1045 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.01 % Allowed : 13.60 % Favored : 85.38 % 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: -1.31 (0.28), residues: 784 helix: -0.27 (0.27), residues: 344 sheet: -0.58 (0.70), residues: 42 loop : -1.43 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.009 0.001 HIS F 540 PHE 0.012 0.001 PHE F 523 TYR 0.017 0.001 TYR F 183 ARG 0.005 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 332 MET cc_start: 0.6701 (ppp) cc_final: 0.6379 (ptt) REVERT: F 441 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8353 (tmtt) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.1865 time to fit residues: 17.9571 Evaluate side-chains 66 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 440 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6689 Z= 0.286 Angle : 0.599 6.475 9091 Z= 0.307 Chirality : 0.044 0.151 977 Planarity : 0.004 0.052 1167 Dihedral : 4.872 30.207 1045 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.88 % Allowed : 15.05 % Favored : 83.07 % 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: -1.10 (0.29), residues: 784 helix: -0.02 (0.28), residues: 344 sheet: -0.78 (0.70), residues: 42 loop : -1.34 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 610 HIS 0.013 0.002 HIS F 540 PHE 0.013 0.001 PHE F 315 TYR 0.016 0.002 TYR F 183 ARG 0.004 0.001 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: F 23 GLU cc_start: 0.7652 (pt0) cc_final: 0.7430 (pt0) REVERT: F 332 MET cc_start: 0.7019 (ppp) cc_final: 0.6761 (ptt) REVERT: G 355 ARG cc_start: 0.8142 (ttt90) cc_final: 0.7586 (ptm160) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.1828 time to fit residues: 19.2284 Evaluate side-chains 67 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 394 ASN Chi-restraints excluded: chain G residue 422 ASN Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6689 Z= 0.195 Angle : 0.554 6.459 9091 Z= 0.279 Chirality : 0.042 0.155 977 Planarity : 0.003 0.031 1167 Dihedral : 4.494 22.523 1045 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.46 % Allowed : 15.92 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 784 helix: 0.16 (0.28), residues: 349 sheet: -0.93 (0.69), residues: 42 loop : -1.29 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 610 HIS 0.012 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.018 0.001 TYR F 183 ARG 0.003 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.767 Fit side-chains REVERT: F 261 CYS cc_start: 0.7303 (m) cc_final: 0.6917 (m) REVERT: F 332 MET cc_start: 0.6972 (ppp) cc_final: 0.6768 (ptt) REVERT: F 593 THR cc_start: 0.8512 (m) cc_final: 0.8239 (p) REVERT: G 355 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7562 (ptm160) REVERT: G 418 ILE cc_start: 0.9197 (tp) cc_final: 0.8964 (tp) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1863 time to fit residues: 19.5197 Evaluate side-chains 73 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6689 Z= 0.178 Angle : 0.552 6.932 9091 Z= 0.276 Chirality : 0.042 0.150 977 Planarity : 0.003 0.032 1167 Dihedral : 4.291 19.224 1045 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.04 % Allowed : 15.34 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.29), residues: 784 helix: 0.25 (0.28), residues: 353 sheet: -1.13 (0.68), residues: 42 loop : -1.29 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 610 HIS 0.010 0.001 HIS F 540 PHE 0.012 0.001 PHE F 504 TYR 0.018 0.001 TYR F 183 ARG 0.003 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 LEU cc_start: 0.7800 (tt) cc_final: 0.7540 (mt) REVERT: F 261 CYS cc_start: 0.7283 (m) cc_final: 0.6931 (m) REVERT: F 593 THR cc_start: 0.8528 (m) cc_final: 0.8219 (p) REVERT: G 355 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7553 (ptm160) REVERT: G 418 ILE cc_start: 0.9249 (tp) cc_final: 0.9026 (tp) outliers start: 21 outliers final: 17 residues processed: 77 average time/residue: 0.1610 time to fit residues: 17.6138 Evaluate side-chains 76 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6689 Z= 0.185 Angle : 0.554 6.445 9091 Z= 0.276 Chirality : 0.042 0.153 977 Planarity : 0.003 0.032 1167 Dihedral : 4.202 18.967 1045 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.04 % Allowed : 15.92 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 784 helix: 0.31 (0.29), residues: 355 sheet: -1.09 (0.70), residues: 42 loop : -1.25 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.003 0.001 HIS F 34 PHE 0.013 0.001 PHE F 504 TYR 0.020 0.001 TYR G 365 ARG 0.002 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: F 261 CYS cc_start: 0.7256 (m) cc_final: 0.6876 (m) REVERT: F 593 THR cc_start: 0.8529 (m) cc_final: 0.8219 (p) REVERT: G 355 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7529 (ptm160) REVERT: G 418 ILE cc_start: 0.9271 (tp) cc_final: 0.9065 (tp) outliers start: 21 outliers final: 19 residues processed: 77 average time/residue: 0.1662 time to fit residues: 17.8099 Evaluate side-chains 77 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6689 Z= 0.268 Angle : 0.605 6.914 9091 Z= 0.306 Chirality : 0.044 0.155 977 Planarity : 0.003 0.032 1167 Dihedral : 4.613 24.634 1045 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.18 % Allowed : 16.06 % Favored : 80.75 % 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: -0.89 (0.30), residues: 784 helix: 0.20 (0.28), residues: 355 sheet: -1.15 (0.71), residues: 42 loop : -1.25 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.006 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.017 0.001 TYR F 183 ARG 0.004 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: F 261 CYS cc_start: 0.7100 (m) cc_final: 0.6798 (m) outliers start: 22 outliers final: 19 residues processed: 78 average time/residue: 0.1747 time to fit residues: 18.9368 Evaluate side-chains 79 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0870 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6689 Z= 0.174 Angle : 0.583 6.754 9091 Z= 0.291 Chirality : 0.042 0.158 977 Planarity : 0.003 0.034 1167 Dihedral : 4.180 16.802 1045 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.32 % Allowed : 17.51 % Favored : 80.17 % 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: -0.82 (0.30), residues: 784 helix: 0.23 (0.28), residues: 362 sheet: -1.22 (0.70), residues: 42 loop : -1.19 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 594 HIS 0.003 0.001 HIS F 417 PHE 0.014 0.001 PHE F 504 TYR 0.018 0.001 TYR F 183 ARG 0.002 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: F 261 CYS cc_start: 0.7263 (m) cc_final: 0.6878 (m) REVERT: F 366 MET cc_start: 0.8120 (mmm) cc_final: 0.7889 (tpp) REVERT: F 593 THR cc_start: 0.8500 (m) cc_final: 0.8191 (p) REVERT: G 355 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7801 (ptm160) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1775 time to fit residues: 18.5286 Evaluate side-chains 78 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.0070 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.0050 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6689 Z= 0.181 Angle : 0.578 7.854 9091 Z= 0.290 Chirality : 0.042 0.155 977 Planarity : 0.003 0.034 1167 Dihedral : 4.041 16.959 1045 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.32 % Allowed : 17.51 % Favored : 80.17 % 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: -0.78 (0.30), residues: 784 helix: 0.29 (0.28), residues: 361 sheet: -1.27 (0.69), residues: 42 loop : -1.19 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.003 0.001 HIS F 417 PHE 0.013 0.001 PHE F 504 TYR 0.017 0.001 TYR F 183 ARG 0.002 0.000 ARG G 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 261 CYS cc_start: 0.7184 (m) cc_final: 0.6786 (m) REVERT: F 593 THR cc_start: 0.8517 (m) cc_final: 0.8200 (p) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1792 time to fit residues: 18.9294 Evaluate side-chains 77 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 440 ASN Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 3 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081587 restraints weight = 17473.184| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.83 r_work: 0.3301 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6689 Z= 0.186 Angle : 0.593 12.074 9091 Z= 0.294 Chirality : 0.042 0.157 977 Planarity : 0.003 0.033 1167 Dihedral : 3.936 16.680 1045 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.32 % Allowed : 17.80 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.30), residues: 784 helix: 0.32 (0.28), residues: 362 sheet: -1.10 (0.69), residues: 42 loop : -1.17 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.003 0.001 HIS F 417 PHE 0.013 0.001 PHE F 504 TYR 0.043 0.001 TYR F 50 ARG 0.006 0.000 ARG G 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1776.70 seconds wall clock time: 33 minutes 39.19 seconds (2019.19 seconds total)