Starting phenix.real_space_refine on Thu Feb 15 21:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/02_2024/8fx4_29523_updated.pdb" } resolution = 3.9 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= 0.002 sd= 0.034 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 6 5.49 5 S 68 5.16 5 C 8530 2.51 5 N 2271 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "D GLU 542": "OE1" <-> "OE2" Residue "D ASP 563": "OD1" <-> "OD2" Residue "D ASP 609": "OD1" <-> "OD2" Residue "D ASP 664": "OD1" <-> "OD2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D GLU 688": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "D GLU 719": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13474 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5039 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 17, 'TRANS': 605} Chain breaks: 1 Chain: "B" Number of atoms: 5011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5011 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 17, 'TRANS': 601} Chain breaks: 2 Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1699 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 5 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1663 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.43, per 1000 atoms: 0.55 Number of scatterers: 13474 At special positions: 0 Unit cell: (99.4671, 130.806, 138.981, 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 68 16.00 P 6 15.00 O 2599 8.00 N 2271 7.00 C 8530 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: 5.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 8 sheets defined 41.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 38 through 60 removed outlier: 3.568A pdb=" N LEU A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.591A pdb=" N ASP A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 195 through 202 removed outlier: 3.875A pdb=" N LYS A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 400 through 421 removed outlier: 3.609A pdb=" N ILE A 404 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 405 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 406 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 443 removed outlier: 6.552A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 4.592A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.884A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.699A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 60 removed outlier: 3.758A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.724A pdb=" N ASN B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.879A pdb=" N VAL B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.798A pdb=" N ILE B 404 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 419 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 421 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 4.203A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.799A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 4.127A pdb=" N ARG B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 502 through 505 No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.628A pdb=" N GLN B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 561 through 571 removed outlier: 3.520A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 666 removed outlier: 3.698A pdb=" N SER B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'C' and resid 25 through 57 removed outlier: 3.886A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 112 Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.665A pdb=" N PHE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 182 No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 207 through 227 Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 250 through 265 Processing helix chain 'D' and resid 548 through 550 No H-bonds generated for 'chain 'D' and resid 548 through 550' Processing helix chain 'D' and resid 565 through 583 removed outlier: 3.553A pdb=" N SER D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 630 Processing helix chain 'D' and resid 636 through 652 Processing helix chain 'D' and resid 665 through 674 Processing helix chain 'D' and resid 695 through 703 Processing helix chain 'D' and resid 715 through 728 Processing sheet with id= A, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.921A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 148 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 323 removed outlier: 4.357A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 381 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 356 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 383 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 483 through 485 removed outlier: 3.783A pdb=" N TYR A 485 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 589 through 593 Processing sheet with id= E, first strand: chain 'B' and resid 280 through 283 removed outlier: 4.061A pdb=" N GLU B 280 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 215 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE B 213 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 317 through 322 removed outlier: 3.881A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 577 through 580 removed outlier: 4.367A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 626 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 579 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 590 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 597 through 599 501 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4377 1.34 - 1.46: 2243 1.46 - 1.58: 6962 1.58 - 1.70: 12 1.70 - 1.82: 114 Bond restraints: 13708 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CA ASN A 582 " pdb=" CB ASN A 582 " ideal model delta sigma weight residual 1.536 1.634 -0.098 4.10e-02 5.95e+02 5.71e+00 bond pdb=" CB GLN B 397 " pdb=" CG GLN B 397 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.49e+00 bond pdb=" CA ASN A 46 " pdb=" C ASN A 46 " ideal model delta sigma weight residual 1.522 1.544 -0.021 1.37e-02 5.33e+03 2.46e+00 ... (remaining 13703 not shown) Histogram of bond angle deviations from ideal: 96.88 - 105.48: 202 105.48 - 114.08: 7788 114.08 - 122.68: 9105 122.68 - 131.28: 1314 131.28 - 139.88: 24 Bond angle restraints: 18433 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 97.38 14.62 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA GLN B 397 " pdb=" CB GLN B 397 " pdb=" CG GLN B 397 " ideal model delta sigma weight residual 114.10 125.22 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" CA GLN C 44 " pdb=" CB GLN C 44 " pdb=" CG GLN C 44 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA LYS B 557 " pdb=" CB LYS B 557 " pdb=" CG LYS B 557 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 angle pdb=" C LYS B 552 " pdb=" N MET B 553 " pdb=" CA MET B 553 " ideal model delta sigma weight residual 121.14 113.29 7.85 1.75e+00 3.27e-01 2.01e+01 ... (remaining 18428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7047 17.93 - 35.86: 1084 35.86 - 53.78: 276 53.78 - 71.71: 49 71.71 - 89.64: 22 Dihedral angle restraints: 8478 sinusoidal: 3640 harmonic: 4838 Sorted by residual: dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N ASP C 17 " pdb=" CA ASP C 17 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA D 632 " pdb=" C ALA D 632 " pdb=" N ASN D 633 " pdb=" CA ASN D 633 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS B 477 " pdb=" C LYS B 477 " pdb=" N GLU B 478 " pdb=" CA GLU B 478 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1777 0.069 - 0.139: 238 0.139 - 0.208: 11 0.208 - 0.278: 3 0.278 - 0.347: 1 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB ILE D 607 " pdb=" CA ILE D 607 " pdb=" CG1 ILE D 607 " pdb=" CG2 ILE D 607 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 656 " pdb=" CA VAL A 656 " pdb=" CG1 VAL A 656 " pdb=" CG2 VAL A 656 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2027 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 78 " 0.061 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 79 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 371 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 623 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.29e+00 pdb=" CG TRP D 623 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP D 623 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 623 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 623 " -0.009 2.00e-02 2.50e+03 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 355 2.67 - 3.23: 13446 3.23 - 3.79: 20018 3.79 - 4.34: 25034 4.34 - 4.90: 39472 Nonbonded interactions: 98325 Sorted by model distance: nonbonded pdb=" O ARG B 55 " pdb=" OG SER B 58 " model vdw 2.117 2.440 nonbonded pdb=" OD1 ASP B 546 " pdb=" N GLU B 547 " model vdw 2.155 2.520 nonbonded pdb=" O GLY B 132 " pdb=" OG SER B 135 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASN C 116 " pdb=" OG1 THR C 119 " model vdw 2.206 2.440 nonbonded pdb=" O VAL D 672 " pdb=" OG SER D 675 " model vdw 2.217 2.440 ... (remaining 98320 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 12 through 218 or resid 278 through 613 or resid 617 throu \ gh 690 or resid 801)) selection = (chain 'B' and (resid 12 through 218 or resid 278 through 690 or resid 801)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 2.420 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.490 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 0.175 13708 Z= 0.234 Angle : 0.915 14.618 18433 Z= 0.490 Chirality : 0.046 0.347 2030 Planarity : 0.004 0.084 2345 Dihedral : 18.476 89.640 5332 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.66 % Favored : 91.91 % Rotamer: Outliers : 0.80 % Allowed : 33.00 % Favored : 66.20 % 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: -1.50 (0.21), residues: 1619 helix: 0.35 (0.20), residues: 678 sheet: 0.51 (0.42), residues: 181 loop : -2.77 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 623 HIS 0.007 0.001 HIS A 149 PHE 0.016 0.001 PHE A 39 TYR 0.021 0.001 TYR A 430 ARG 0.006 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 421 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8221 (mtpp) REVERT: A 430 TYR cc_start: 0.7491 (t80) cc_final: 0.7214 (t80) REVERT: A 481 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8632 (mmtt) REVERT: A 501 GLU cc_start: 0.7593 (mp0) cc_final: 0.7364 (mp0) REVERT: A 509 GLU cc_start: 0.6405 (tp30) cc_final: 0.5402 (tp30) REVERT: A 551 LYS cc_start: 0.7642 (ptpp) cc_final: 0.7439 (pttm) REVERT: B 57 GLU cc_start: 0.7862 (tp30) cc_final: 0.7506 (tp30) REVERT: B 279 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6632 (mm-40) REVERT: B 280 GLU cc_start: 0.7697 (pt0) cc_final: 0.6946 (tm-30) REVERT: B 300 GLU cc_start: 0.7555 (mp0) cc_final: 0.7264 (mp0) REVERT: B 304 PHE cc_start: 0.8536 (t80) cc_final: 0.8127 (t80) REVERT: B 312 TRP cc_start: 0.7418 (p-90) cc_final: 0.7136 (p-90) REVERT: B 393 GLU cc_start: 0.7260 (mp0) cc_final: 0.6909 (mp0) REVERT: B 395 LEU cc_start: 0.8045 (tp) cc_final: 0.7720 (tt) REVERT: B 471 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6813 (tm-30) REVERT: B 476 MET cc_start: 0.6600 (mmm) cc_final: 0.6071 (mmm) REVERT: B 553 MET cc_start: 0.7549 (ppp) cc_final: 0.7228 (ppp) REVERT: B 559 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7577 (ttpp) REVERT: B 627 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 20 HIS cc_start: 0.7635 (t-90) cc_final: 0.7363 (t70) REVERT: C 29 PHE cc_start: 0.7187 (m-10) cc_final: 0.6975 (m-80) REVERT: C 36 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.6894 (tmm-80) REVERT: D 627 GLU cc_start: 0.7252 (pp20) cc_final: 0.7026 (pp20) outliers start: 12 outliers final: 8 residues processed: 424 average time/residue: 0.3180 time to fit residues: 182.0946 Evaluate side-chains 412 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 403 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain D residue 634 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 458 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13708 Z= 0.182 Angle : 0.641 9.545 18433 Z= 0.339 Chirality : 0.043 0.202 2030 Planarity : 0.004 0.059 2345 Dihedral : 7.457 83.061 1867 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.28 % Favored : 91.48 % Rotamer: Outliers : 4.89 % Allowed : 27.98 % Favored : 67.14 % 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: -1.29 (0.21), residues: 1619 helix: 0.54 (0.20), residues: 682 sheet: 0.42 (0.43), residues: 169 loop : -2.59 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 623 HIS 0.006 0.001 HIS A 149 PHE 0.025 0.001 PHE C 125 TYR 0.022 0.001 TYR B 305 ARG 0.005 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 416 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8119 (mtpp) REVERT: A 195 GLU cc_start: 0.7628 (tp30) cc_final: 0.7402 (tp30) REVERT: A 303 GLU cc_start: 0.7324 (pp20) cc_final: 0.6951 (pp20) REVERT: A 397 GLN cc_start: 0.7428 (tt0) cc_final: 0.6603 (tm-30) REVERT: A 400 ILE cc_start: 0.8644 (mm) cc_final: 0.8156 (mm) REVERT: A 423 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7007 (mmtm) REVERT: A 424 GLU cc_start: 0.7566 (pm20) cc_final: 0.7366 (tm-30) REVERT: A 430 TYR cc_start: 0.7599 (t80) cc_final: 0.7380 (t80) REVERT: A 449 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.7731 (tpp80) REVERT: A 478 GLU cc_start: 0.7898 (pm20) cc_final: 0.7689 (pm20) REVERT: A 481 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8571 (mmtt) REVERT: A 526 LYS cc_start: 0.7634 (pptt) cc_final: 0.7260 (pptt) REVERT: A 527 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6150 (mt-10) REVERT: B 42 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 154 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6917 (mm-40) REVERT: B 279 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6633 (mm-40) REVERT: B 294 ASP cc_start: 0.7845 (t0) cc_final: 0.7437 (t0) REVERT: B 312 TRP cc_start: 0.7458 (p-90) cc_final: 0.7008 (p-90) REVERT: B 427 LYS cc_start: 0.8807 (mttt) cc_final: 0.8479 (mtmm) REVERT: B 466 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: B 471 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7032 (tm-30) REVERT: B 493 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: B 513 MET cc_start: 0.6626 (mmt) cc_final: 0.6290 (mmt) REVERT: B 559 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7618 (ttpp) REVERT: B 627 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7419 (mm-30) REVERT: B 683 MET cc_start: 0.7935 (mmm) cc_final: 0.7717 (mmm) REVERT: C 29 PHE cc_start: 0.7227 (m-10) cc_final: 0.6958 (m-80) REVERT: C 38 GLU cc_start: 0.7555 (pt0) cc_final: 0.7256 (pt0) REVERT: C 104 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7274 (mm-30) REVERT: C 107 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7271 (mtt-85) REVERT: D 578 MET cc_start: 0.7544 (mmm) cc_final: 0.7299 (mmm) outliers start: 73 outliers final: 42 residues processed: 458 average time/residue: 0.3082 time to fit residues: 193.4342 Evaluate side-chains 446 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 401 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 684 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13708 Z= 0.180 Angle : 0.631 11.204 18433 Z= 0.331 Chirality : 0.043 0.183 2030 Planarity : 0.004 0.058 2345 Dihedral : 6.878 88.106 1854 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer: Outliers : 4.95 % Allowed : 29.52 % Favored : 65.53 % 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: -1.23 (0.21), residues: 1619 helix: 0.63 (0.20), residues: 684 sheet: 0.45 (0.42), residues: 174 loop : -2.62 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 623 HIS 0.005 0.001 HIS B 320 PHE 0.021 0.001 PHE A 361 TYR 0.011 0.001 TYR B 356 ARG 0.008 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 407 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8531 (t0) cc_final: 0.7944 (t0) REVERT: A 153 GLU cc_start: 0.7538 (mp0) cc_final: 0.7184 (mp0) REVERT: A 195 GLU cc_start: 0.7609 (tp30) cc_final: 0.7146 (tp30) REVERT: A 303 GLU cc_start: 0.7435 (pp20) cc_final: 0.7009 (pp20) REVERT: A 397 GLN cc_start: 0.7400 (tt0) cc_final: 0.6506 (tm-30) REVERT: A 400 ILE cc_start: 0.8648 (mm) cc_final: 0.8255 (mm) REVERT: A 423 LYS cc_start: 0.7388 (mmtm) cc_final: 0.6974 (mmtm) REVERT: A 449 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7725 (tpp80) REVERT: A 478 GLU cc_start: 0.7914 (pm20) cc_final: 0.7710 (pm20) REVERT: A 481 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8495 (mmtt) REVERT: A 501 GLU cc_start: 0.7703 (mp0) cc_final: 0.7249 (mp0) REVERT: A 526 LYS cc_start: 0.7623 (pptt) cc_final: 0.7408 (pptt) REVERT: A 527 GLU cc_start: 0.6990 (mt-10) cc_final: 0.5966 (mt-10) REVERT: A 567 MET cc_start: 0.6062 (mmt) cc_final: 0.5711 (tpp) REVERT: B 42 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 93 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: B 95 LYS cc_start: 0.8429 (tttt) cc_final: 0.8188 (ttmm) REVERT: B 98 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 101 ASN cc_start: 0.8067 (t0) cc_final: 0.7617 (t0) REVERT: B 154 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7033 (mm-40) REVERT: B 279 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6489 (mm-40) REVERT: B 312 TRP cc_start: 0.7483 (p-90) cc_final: 0.7160 (p-90) REVERT: B 376 PHE cc_start: 0.8821 (p90) cc_final: 0.7709 (p90) REVERT: B 395 LEU cc_start: 0.8132 (tp) cc_final: 0.7808 (tt) REVERT: B 427 LYS cc_start: 0.8839 (mttt) cc_final: 0.8510 (mtmm) REVERT: B 466 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: B 471 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 476 MET cc_start: 0.6396 (mmm) cc_final: 0.5765 (mmm) REVERT: B 493 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8014 (mm-40) REVERT: B 513 MET cc_start: 0.6712 (mmt) cc_final: 0.6160 (mmt) REVERT: B 569 GLU cc_start: 0.7626 (pm20) cc_final: 0.7266 (pm20) REVERT: B 576 GLU cc_start: 0.7626 (mp0) cc_final: 0.7303 (mp0) REVERT: B 627 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 683 MET cc_start: 0.7927 (mmm) cc_final: 0.7671 (mmm) REVERT: C 29 PHE cc_start: 0.7222 (m-10) cc_final: 0.6856 (m-80) REVERT: C 31 TRP cc_start: 0.8639 (OUTLIER) cc_final: 0.7649 (m-90) REVERT: C 38 GLU cc_start: 0.7552 (pt0) cc_final: 0.7305 (pt0) REVERT: C 40 MET cc_start: 0.7519 (tpt) cc_final: 0.7255 (tpt) REVERT: C 104 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 107 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7234 (mtt-85) REVERT: C 222 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7809 (pm20) REVERT: D 533 MET cc_start: 0.7987 (ptp) cc_final: 0.7650 (ptp) REVERT: D 585 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7542 (mmmm) outliers start: 74 outliers final: 48 residues processed: 442 average time/residue: 0.3409 time to fit residues: 207.8114 Evaluate side-chains 453 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 399 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13708 Z= 0.200 Angle : 0.634 11.236 18433 Z= 0.335 Chirality : 0.043 0.185 2030 Planarity : 0.004 0.057 2345 Dihedral : 6.773 88.833 1852 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.20 % Favored : 90.67 % Rotamer: Outliers : 6.56 % Allowed : 28.78 % Favored : 64.66 % 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: -1.13 (0.21), residues: 1619 helix: 0.71 (0.20), residues: 680 sheet: 0.43 (0.42), residues: 174 loop : -2.52 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 289 HIS 0.006 0.001 HIS B 320 PHE 0.018 0.001 PHE A 329 TYR 0.020 0.001 TYR A 430 ARG 0.009 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 417 time to evaluate : 1.706 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 30 ASN cc_start: 0.8524 (t0) cc_final: 0.8172 (t0) REVERT: A 53 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8179 (mtpp) REVERT: A 155 TYR cc_start: 0.7480 (m-80) cc_final: 0.6963 (m-80) REVERT: A 189 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8202 (mm-40) REVERT: A 195 GLU cc_start: 0.7574 (tp30) cc_final: 0.6002 (tp30) REVERT: A 199 LYS cc_start: 0.8603 (pttm) cc_final: 0.7870 (pttm) REVERT: A 303 GLU cc_start: 0.7557 (pp20) cc_final: 0.7239 (pp20) REVERT: A 386 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 397 GLN cc_start: 0.7404 (tt0) cc_final: 0.6508 (tm-30) REVERT: A 400 ILE cc_start: 0.8682 (mm) cc_final: 0.8362 (mm) REVERT: A 449 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7749 (tpp80) REVERT: A 478 GLU cc_start: 0.7924 (pm20) cc_final: 0.7701 (pm20) REVERT: A 481 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8524 (mmtt) REVERT: A 487 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 501 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: A 509 GLU cc_start: 0.7034 (tp30) cc_final: 0.6483 (tp30) REVERT: A 527 GLU cc_start: 0.6954 (mt-10) cc_final: 0.5874 (mm-30) REVERT: A 567 MET cc_start: 0.6178 (mmt) cc_final: 0.5755 (tpp) REVERT: A 582 ASN cc_start: 0.7982 (p0) cc_final: 0.7735 (p0) REVERT: A 649 LYS cc_start: 0.7879 (pptt) cc_final: 0.7248 (mmtm) REVERT: B 42 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6862 (mm-30) REVERT: B 70 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7221 (mp0) REVERT: B 93 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7539 (mmt) REVERT: B 95 LYS cc_start: 0.8488 (tttt) cc_final: 0.8222 (ttmm) REVERT: B 98 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8070 (tp) REVERT: B 101 ASN cc_start: 0.8064 (t0) cc_final: 0.7586 (t0) REVERT: B 142 LYS cc_start: 0.8444 (mttt) cc_final: 0.7819 (mtmm) REVERT: B 154 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6857 (mm-40) REVERT: B 279 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6570 (mm-40) REVERT: B 294 ASP cc_start: 0.7886 (t0) cc_final: 0.7477 (t0) REVERT: B 312 TRP cc_start: 0.7531 (p-90) cc_final: 0.7084 (p-90) REVERT: B 376 PHE cc_start: 0.8801 (p90) cc_final: 0.7979 (p90) REVERT: B 395 LEU cc_start: 0.8168 (tp) cc_final: 0.7931 (tt) REVERT: B 397 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6820 (tm-30) REVERT: B 426 TYR cc_start: 0.8476 (t80) cc_final: 0.8127 (t80) REVERT: B 427 LYS cc_start: 0.8858 (mttt) cc_final: 0.8538 (mtmm) REVERT: B 466 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: B 476 MET cc_start: 0.6398 (mmm) cc_final: 0.5880 (mmm) REVERT: B 493 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: B 513 MET cc_start: 0.6767 (mmt) cc_final: 0.6468 (mmt) REVERT: B 569 GLU cc_start: 0.7757 (pm20) cc_final: 0.7529 (pm20) REVERT: B 627 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7402 (mm-30) REVERT: B 683 MET cc_start: 0.7986 (mmm) cc_final: 0.7723 (mmm) REVERT: C 29 PHE cc_start: 0.7249 (m-10) cc_final: 0.6852 (m-80) REVERT: C 31 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.7619 (m-90) REVERT: C 40 MET cc_start: 0.7507 (tpt) cc_final: 0.7215 (tpt) REVERT: C 48 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 104 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7130 (mm-30) REVERT: C 107 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7139 (mtt-85) REVERT: D 529 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5680 (ptmm) REVERT: D 533 MET cc_start: 0.7950 (ptp) cc_final: 0.7662 (ptp) REVERT: D 578 MET cc_start: 0.7450 (mmm) cc_final: 0.7071 (mmm) REVERT: D 585 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7534 (mmmm) REVERT: D 724 LYS cc_start: 0.8313 (tmmt) cc_final: 0.8113 (tmmt) outliers start: 98 outliers final: 61 residues processed: 470 average time/residue: 0.2962 time to fit residues: 190.9567 Evaluate side-chains 485 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 414 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.0670 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 0.0050 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13708 Z= 0.165 Angle : 0.643 11.915 18433 Z= 0.330 Chirality : 0.042 0.199 2030 Planarity : 0.004 0.057 2345 Dihedral : 6.619 88.535 1852 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.60 % Favored : 92.28 % Rotamer: Outliers : 5.29 % Allowed : 30.92 % Favored : 63.79 % 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: -1.06 (0.22), residues: 1619 helix: 0.79 (0.21), residues: 684 sheet: 0.33 (0.41), residues: 182 loop : -2.51 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 623 HIS 0.004 0.001 HIS A 149 PHE 0.014 0.001 PHE C 260 TYR 0.013 0.001 TYR B 305 ARG 0.009 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 415 time to evaluate : 1.654 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 30 ASN cc_start: 0.8481 (t0) cc_final: 0.8118 (t0) REVERT: A 72 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6644 (mtmm) REVERT: A 107 LYS cc_start: 0.7847 (tppp) cc_final: 0.7626 (ttmm) REVERT: A 115 GLU cc_start: 0.7798 (tp30) cc_final: 0.7461 (tp30) REVERT: A 153 GLU cc_start: 0.7517 (mp0) cc_final: 0.7137 (mp0) REVERT: A 195 GLU cc_start: 0.7563 (tp30) cc_final: 0.6770 (tp30) REVERT: A 199 LYS cc_start: 0.8634 (pttm) cc_final: 0.8389 (pttm) REVERT: A 303 GLU cc_start: 0.7542 (pp20) cc_final: 0.7185 (pp20) REVERT: A 397 GLN cc_start: 0.7314 (tt0) cc_final: 0.6476 (tm-30) REVERT: A 400 ILE cc_start: 0.8644 (mm) cc_final: 0.8340 (mm) REVERT: A 423 LYS cc_start: 0.7519 (mmtm) cc_final: 0.7065 (mmmt) REVERT: A 449 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.8059 (mtp85) REVERT: A 478 GLU cc_start: 0.7919 (pm20) cc_final: 0.7705 (pm20) REVERT: A 509 GLU cc_start: 0.7041 (tp30) cc_final: 0.6556 (tp30) REVERT: A 567 MET cc_start: 0.6004 (mmt) cc_final: 0.5616 (tpp) REVERT: A 582 ASN cc_start: 0.7949 (p0) cc_final: 0.7704 (p0) REVERT: A 637 THR cc_start: 0.8067 (p) cc_final: 0.7741 (p) REVERT: A 641 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7624 (mmmm) REVERT: A 649 LYS cc_start: 0.7838 (pptt) cc_final: 0.7225 (mmtm) REVERT: B 42 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 70 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7139 (mp0) REVERT: B 93 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: B 95 LYS cc_start: 0.8399 (tttt) cc_final: 0.8123 (ttmm) REVERT: B 98 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 101 ASN cc_start: 0.8052 (t0) cc_final: 0.7570 (t0) REVERT: B 142 LYS cc_start: 0.8396 (mttt) cc_final: 0.7811 (mtmm) REVERT: B 154 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6946 (mm-40) REVERT: B 279 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6591 (mm110) REVERT: B 294 ASP cc_start: 0.7883 (t0) cc_final: 0.7470 (t0) REVERT: B 312 TRP cc_start: 0.7453 (p-90) cc_final: 0.7111 (p-90) REVERT: B 376 PHE cc_start: 0.8754 (p90) cc_final: 0.7783 (p90) REVERT: B 395 LEU cc_start: 0.8116 (tp) cc_final: 0.7792 (tt) REVERT: B 427 LYS cc_start: 0.8845 (mttt) cc_final: 0.8505 (mtmm) REVERT: B 466 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: B 471 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6973 (tm-30) REVERT: B 472 TYR cc_start: 0.8429 (t80) cc_final: 0.8201 (t80) REVERT: B 493 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: B 576 GLU cc_start: 0.7637 (mp0) cc_final: 0.7362 (mp0) REVERT: B 627 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 8 ASP cc_start: 0.6904 (m-30) cc_final: 0.6641 (m-30) REVERT: C 29 PHE cc_start: 0.7261 (m-10) cc_final: 0.6986 (m-80) REVERT: C 31 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7601 (m-90) REVERT: C 40 MET cc_start: 0.7438 (tpt) cc_final: 0.7138 (tpt) REVERT: C 46 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: C 104 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7101 (mm-30) REVERT: C 107 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7299 (mtt-85) REVERT: C 111 LYS cc_start: 0.8308 (mmmm) cc_final: 0.7949 (mttt) REVERT: C 133 LYS cc_start: 0.6605 (mtpt) cc_final: 0.6300 (mmtm) REVERT: D 533 MET cc_start: 0.7937 (ptp) cc_final: 0.7569 (ptp) REVERT: D 578 MET cc_start: 0.7423 (mmm) cc_final: 0.7056 (mmm) REVERT: D 585 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7524 (mmmm) REVERT: D 662 CYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5390 (p) REVERT: D 699 LEU cc_start: 0.7184 (mm) cc_final: 0.6941 (mm) REVERT: D 724 LYS cc_start: 0.8325 (tmmt) cc_final: 0.8027 (tmmt) outliers start: 79 outliers final: 53 residues processed: 457 average time/residue: 0.3015 time to fit residues: 187.7398 Evaluate side-chains 472 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 410 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 686 PHE Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13708 Z= 0.184 Angle : 0.651 13.712 18433 Z= 0.337 Chirality : 0.043 0.223 2030 Planarity : 0.004 0.056 2345 Dihedral : 6.599 88.297 1852 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.83 % Favored : 91.04 % Rotamer: Outliers : 6.09 % Allowed : 30.92 % Favored : 62.99 % 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: -1.03 (0.22), residues: 1619 helix: 0.84 (0.21), residues: 681 sheet: 0.26 (0.41), residues: 182 loop : -2.49 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.004 0.001 HIS A 149 PHE 0.023 0.001 PHE A 361 TYR 0.013 0.001 TYR A 305 ARG 0.010 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 412 time to evaluate : 1.714 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 30 ASN cc_start: 0.8474 (t0) cc_final: 0.8099 (t0) REVERT: A 41 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8217 (tmm-80) REVERT: A 53 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8148 (mtpp) REVERT: A 72 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6695 (mtmm) REVERT: A 107 LYS cc_start: 0.7868 (tppp) cc_final: 0.7640 (ttmm) REVERT: A 115 GLU cc_start: 0.7836 (tp30) cc_final: 0.7463 (tp30) REVERT: A 153 GLU cc_start: 0.7518 (mp0) cc_final: 0.7162 (mp0) REVERT: A 155 TYR cc_start: 0.7452 (m-80) cc_final: 0.6922 (m-80) REVERT: A 189 GLN cc_start: 0.8610 (mm110) cc_final: 0.8205 (mm-40) REVERT: A 195 GLU cc_start: 0.7656 (tp30) cc_final: 0.6196 (tp30) REVERT: A 199 LYS cc_start: 0.8610 (pttm) cc_final: 0.7811 (pttm) REVERT: A 303 GLU cc_start: 0.7563 (pp20) cc_final: 0.7200 (pp20) REVERT: A 386 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 397 GLN cc_start: 0.7337 (tt0) cc_final: 0.6480 (tm-30) REVERT: A 400 ILE cc_start: 0.8668 (mm) cc_final: 0.8387 (mm) REVERT: A 449 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7747 (mtp85) REVERT: A 450 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7948 (mmp80) REVERT: A 478 GLU cc_start: 0.7962 (pm20) cc_final: 0.7737 (pm20) REVERT: A 501 GLU cc_start: 0.7427 (mp0) cc_final: 0.7067 (mp0) REVERT: A 509 GLU cc_start: 0.6973 (tp30) cc_final: 0.6605 (tp30) REVERT: A 567 MET cc_start: 0.6021 (mmt) cc_final: 0.5609 (tpp) REVERT: A 637 THR cc_start: 0.8085 (p) cc_final: 0.7809 (p) REVERT: A 649 LYS cc_start: 0.7874 (pptt) cc_final: 0.7259 (mmtm) REVERT: B 42 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 93 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7434 (mmt) REVERT: B 95 LYS cc_start: 0.8400 (tttt) cc_final: 0.8165 (ttmt) REVERT: B 98 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 101 ASN cc_start: 0.8050 (t0) cc_final: 0.7584 (t0) REVERT: B 142 LYS cc_start: 0.8416 (mttt) cc_final: 0.7794 (mtmm) REVERT: B 154 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6946 (mm-40) REVERT: B 279 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6609 (mm110) REVERT: B 294 ASP cc_start: 0.7880 (t0) cc_final: 0.7440 (t0) REVERT: B 312 TRP cc_start: 0.7485 (p-90) cc_final: 0.7125 (p-90) REVERT: B 376 PHE cc_start: 0.8733 (p90) cc_final: 0.7736 (p90) REVERT: B 395 LEU cc_start: 0.8105 (tp) cc_final: 0.7782 (tt) REVERT: B 426 TYR cc_start: 0.8509 (t80) cc_final: 0.8138 (t80) REVERT: B 427 LYS cc_start: 0.8875 (mttt) cc_final: 0.8514 (mtmm) REVERT: B 466 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7857 (mpp) REVERT: B 481 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8369 (mmtt) REVERT: B 493 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: B 499 PHE cc_start: 0.8130 (m-80) cc_final: 0.7505 (m-80) REVERT: B 513 MET cc_start: 0.6645 (mmt) cc_final: 0.6066 (mmt) REVERT: B 514 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.7121 (p) REVERT: B 576 GLU cc_start: 0.7627 (mp0) cc_final: 0.7261 (mp0) REVERT: B 627 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 8 ASP cc_start: 0.6932 (m-30) cc_final: 0.6668 (m-30) REVERT: C 31 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7588 (m-90) REVERT: C 40 MET cc_start: 0.7433 (tpt) cc_final: 0.7119 (tpt) REVERT: C 46 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: C 104 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 107 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7343 (mtt-85) REVERT: C 111 LYS cc_start: 0.8316 (mmmm) cc_final: 0.7959 (mttt) REVERT: C 133 LYS cc_start: 0.6615 (mtpt) cc_final: 0.6302 (mmtm) REVERT: D 529 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5486 (ptmm) REVERT: D 533 MET cc_start: 0.8047 (ptp) cc_final: 0.7540 (ptp) REVERT: D 578 MET cc_start: 0.7464 (mmm) cc_final: 0.7087 (mmm) REVERT: D 585 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7524 (mmmm) REVERT: D 662 CYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5510 (p) REVERT: D 699 LEU cc_start: 0.7233 (mm) cc_final: 0.6985 (mm) REVERT: D 724 LYS cc_start: 0.8289 (tmmt) cc_final: 0.7969 (tmmt) outliers start: 91 outliers final: 64 residues processed: 465 average time/residue: 0.3085 time to fit residues: 196.2535 Evaluate side-chains 482 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 405 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13708 Z= 0.183 Angle : 0.685 14.416 18433 Z= 0.348 Chirality : 0.043 0.214 2030 Planarity : 0.004 0.056 2345 Dihedral : 6.573 88.211 1852 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.91 % Rotamer: Outliers : 5.96 % Allowed : 31.79 % Favored : 62.25 % 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: -1.06 (0.22), residues: 1619 helix: 0.79 (0.21), residues: 681 sheet: 0.26 (0.41), residues: 182 loop : -2.47 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 289 HIS 0.006 0.001 HIS B 632 PHE 0.022 0.001 PHE A 361 TYR 0.021 0.001 TYR A 305 ARG 0.008 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 407 time to evaluate : 1.577 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 30 ASN cc_start: 0.8455 (t0) cc_final: 0.8078 (t0) REVERT: A 41 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8214 (tmm-80) REVERT: A 72 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6681 (mtmm) REVERT: A 107 LYS cc_start: 0.7871 (tppp) cc_final: 0.7645 (ttmm) REVERT: A 153 GLU cc_start: 0.7508 (mp0) cc_final: 0.7130 (mp0) REVERT: A 155 TYR cc_start: 0.7444 (m-80) cc_final: 0.6946 (m-80) REVERT: A 195 GLU cc_start: 0.7665 (tp30) cc_final: 0.7004 (tp30) REVERT: A 303 GLU cc_start: 0.7564 (pp20) cc_final: 0.7179 (pp20) REVERT: A 386 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 397 GLN cc_start: 0.7353 (tt0) cc_final: 0.6529 (tm-30) REVERT: A 400 ILE cc_start: 0.8675 (mm) cc_final: 0.8413 (mm) REVERT: A 449 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7721 (mtp85) REVERT: A 487 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7733 (p) REVERT: A 567 MET cc_start: 0.6000 (mmt) cc_final: 0.5603 (tpp) REVERT: A 637 THR cc_start: 0.8100 (p) cc_final: 0.7865 (p) REVERT: A 649 LYS cc_start: 0.7897 (pptt) cc_final: 0.7268 (mmtm) REVERT: B 42 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 57 GLU cc_start: 0.7749 (tp30) cc_final: 0.7308 (tp30) REVERT: B 93 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: B 98 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 101 ASN cc_start: 0.8053 (t0) cc_final: 0.7531 (t0) REVERT: B 142 LYS cc_start: 0.8301 (mttt) cc_final: 0.7753 (mtmm) REVERT: B 154 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6787 (mm-40) REVERT: B 186 LYS cc_start: 0.7651 (mmtp) cc_final: 0.7152 (mmtt) REVERT: B 279 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6652 (mm110) REVERT: B 294 ASP cc_start: 0.7861 (t0) cc_final: 0.7424 (t0) REVERT: B 312 TRP cc_start: 0.7468 (p-90) cc_final: 0.6985 (p-90) REVERT: B 344 PHE cc_start: 0.7582 (m-80) cc_final: 0.7352 (m-80) REVERT: B 376 PHE cc_start: 0.8764 (p90) cc_final: 0.7802 (p90) REVERT: B 395 LEU cc_start: 0.8082 (tp) cc_final: 0.7741 (tt) REVERT: B 426 TYR cc_start: 0.8501 (t80) cc_final: 0.8151 (t80) REVERT: B 427 LYS cc_start: 0.8879 (mttt) cc_final: 0.8514 (mtmm) REVERT: B 466 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: B 493 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8000 (mm-40) REVERT: B 499 PHE cc_start: 0.8125 (m-80) cc_final: 0.7487 (m-80) REVERT: B 513 MET cc_start: 0.6653 (mmt) cc_final: 0.6027 (mmt) REVERT: B 514 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7035 (p) REVERT: B 576 GLU cc_start: 0.7609 (mp0) cc_final: 0.7277 (mp0) REVERT: B 627 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 8 ASP cc_start: 0.6914 (m-30) cc_final: 0.6679 (m-30) REVERT: C 29 PHE cc_start: 0.7345 (m-10) cc_final: 0.7126 (m-80) REVERT: C 31 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.7602 (m-90) REVERT: C 40 MET cc_start: 0.7416 (tpt) cc_final: 0.7124 (tpt) REVERT: C 46 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: C 104 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7207 (mm-30) REVERT: C 107 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7423 (mtt-85) REVERT: C 111 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7961 (mttt) REVERT: D 529 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5592 (ptmm) REVERT: D 533 MET cc_start: 0.8008 (ptp) cc_final: 0.7803 (ptp) REVERT: D 578 MET cc_start: 0.7530 (mmm) cc_final: 0.7119 (mmm) REVERT: D 585 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7549 (mmmm) REVERT: D 662 CYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5503 (p) REVERT: D 699 LEU cc_start: 0.7234 (mm) cc_final: 0.6990 (mm) REVERT: D 724 LYS cc_start: 0.8290 (tmmt) cc_final: 0.7947 (tmmt) outliers start: 89 outliers final: 62 residues processed: 460 average time/residue: 0.3024 time to fit residues: 191.5998 Evaluate side-chains 479 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 403 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.0770 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13708 Z= 0.184 Angle : 0.689 15.177 18433 Z= 0.350 Chirality : 0.043 0.213 2030 Planarity : 0.004 0.063 2345 Dihedral : 6.515 88.001 1852 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.59 % Favored : 91.29 % Rotamer: Outliers : 6.22 % Allowed : 31.73 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1619 helix: 0.73 (0.20), residues: 687 sheet: 0.32 (0.41), residues: 190 loop : -2.47 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 289 HIS 0.004 0.001 HIS A 149 PHE 0.020 0.001 PHE A 361 TYR 0.025 0.001 TYR B 305 ARG 0.015 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 407 time to evaluate : 1.579 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 30 ASN cc_start: 0.8468 (t0) cc_final: 0.8059 (t0) REVERT: A 53 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8181 (mtpp) REVERT: A 72 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6631 (mtmm) REVERT: A 93 MET cc_start: 0.7803 (mpp) cc_final: 0.7590 (mpp) REVERT: A 107 LYS cc_start: 0.7874 (tppp) cc_final: 0.7644 (ttmm) REVERT: A 153 GLU cc_start: 0.7511 (mp0) cc_final: 0.7154 (mp0) REVERT: A 155 TYR cc_start: 0.7445 (m-80) cc_final: 0.6950 (m-80) REVERT: A 303 GLU cc_start: 0.7568 (pp20) cc_final: 0.7181 (pp20) REVERT: A 330 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6655 (mtm-85) REVERT: A 334 PHE cc_start: 0.7659 (m-10) cc_final: 0.7356 (m-10) REVERT: A 386 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7751 (mp) REVERT: A 397 GLN cc_start: 0.7333 (tt0) cc_final: 0.6523 (tm-30) REVERT: A 400 ILE cc_start: 0.8673 (mm) cc_final: 0.8426 (mm) REVERT: A 449 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7690 (mtp85) REVERT: A 471 GLU cc_start: 0.7520 (mp0) cc_final: 0.7204 (mp0) REVERT: A 487 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7714 (p) REVERT: A 567 MET cc_start: 0.5833 (mmt) cc_final: 0.5462 (tpp) REVERT: A 607 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8250 (mtpt) REVERT: A 649 LYS cc_start: 0.7893 (pptt) cc_final: 0.7240 (mmtm) REVERT: B 42 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6826 (mm-30) REVERT: B 93 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7396 (mmt) REVERT: B 95 LYS cc_start: 0.8324 (tttt) cc_final: 0.8113 (tttt) REVERT: B 98 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 101 ASN cc_start: 0.8043 (t0) cc_final: 0.7528 (t0) REVERT: B 142 LYS cc_start: 0.8329 (mttt) cc_final: 0.7786 (mtmm) REVERT: B 154 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6756 (mm-40) REVERT: B 279 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6714 (mm-40) REVERT: B 294 ASP cc_start: 0.7730 (t0) cc_final: 0.7263 (t0) REVERT: B 344 PHE cc_start: 0.7600 (m-80) cc_final: 0.7397 (m-80) REVERT: B 376 PHE cc_start: 0.8770 (p90) cc_final: 0.7828 (p90) REVERT: B 395 LEU cc_start: 0.8102 (tp) cc_final: 0.7793 (tt) REVERT: B 426 TYR cc_start: 0.8575 (t80) cc_final: 0.8243 (t80) REVERT: B 427 LYS cc_start: 0.8872 (mttt) cc_final: 0.8508 (mtmm) REVERT: B 466 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: B 471 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6934 (tm-30) REVERT: B 493 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: B 499 PHE cc_start: 0.8129 (m-80) cc_final: 0.7491 (m-80) REVERT: B 513 MET cc_start: 0.6674 (mmt) cc_final: 0.6032 (mmt) REVERT: B 514 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7009 (p) REVERT: B 519 GLU cc_start: 0.7098 (tt0) cc_final: 0.6873 (tm-30) REVERT: B 627 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7420 (mm-30) REVERT: C 8 ASP cc_start: 0.6901 (m-30) cc_final: 0.6633 (m-30) REVERT: C 29 PHE cc_start: 0.7303 (m-10) cc_final: 0.7069 (m-80) REVERT: C 31 TRP cc_start: 0.8709 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: C 40 MET cc_start: 0.7389 (tpt) cc_final: 0.7118 (tpt) REVERT: C 46 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: C 104 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7179 (mm-30) REVERT: C 107 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7391 (mtt-85) REVERT: C 111 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7950 (mttt) REVERT: C 118 ASP cc_start: 0.6872 (t0) cc_final: 0.6350 (t0) REVERT: D 529 LYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5516 (ptmm) REVERT: D 533 MET cc_start: 0.7939 (ptp) cc_final: 0.7720 (ptp) REVERT: D 578 MET cc_start: 0.7472 (mmm) cc_final: 0.7059 (mmm) REVERT: D 585 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7506 (mmmm) REVERT: D 662 CYS cc_start: 0.5621 (OUTLIER) cc_final: 0.5368 (p) REVERT: D 699 LEU cc_start: 0.7238 (mm) cc_final: 0.7005 (mm) REVERT: D 724 LYS cc_start: 0.8339 (tmmt) cc_final: 0.7993 (tmmt) outliers start: 93 outliers final: 67 residues processed: 461 average time/residue: 0.2951 time to fit residues: 185.8435 Evaluate side-chains 486 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 405 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 146 optimal weight: 0.0270 chunk 150 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 458 HIS ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13708 Z= 0.191 Angle : 0.724 15.653 18433 Z= 0.367 Chirality : 0.043 0.212 2030 Planarity : 0.004 0.069 2345 Dihedral : 6.477 87.767 1852 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.72 % Rotamer: Outliers : 5.69 % Allowed : 32.60 % Favored : 61.71 % 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: -1.04 (0.22), residues: 1619 helix: 0.77 (0.21), residues: 680 sheet: 0.35 (0.40), residues: 192 loop : -2.48 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 623 HIS 0.004 0.001 HIS A 149 PHE 0.029 0.001 PHE A 429 TYR 0.028 0.001 TYR B 305 ARG 0.018 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 403 time to evaluate : 1.710 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 30 ASN cc_start: 0.8467 (t0) cc_final: 0.8029 (t0) REVERT: A 72 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6385 (ptpp) REVERT: A 93 MET cc_start: 0.7789 (mpp) cc_final: 0.7547 (mpp) REVERT: A 107 LYS cc_start: 0.7871 (tppp) cc_final: 0.7653 (ttmm) REVERT: A 153 GLU cc_start: 0.7506 (mp0) cc_final: 0.7138 (mp0) REVERT: A 303 GLU cc_start: 0.7511 (pp20) cc_final: 0.7106 (pp20) REVERT: A 330 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6554 (mtm-85) REVERT: A 334 PHE cc_start: 0.7648 (m-10) cc_final: 0.7316 (m-10) REVERT: A 386 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 397 GLN cc_start: 0.7316 (tt0) cc_final: 0.6508 (tm-30) REVERT: A 400 ILE cc_start: 0.8676 (mm) cc_final: 0.8423 (mm) REVERT: A 431 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 449 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.8044 (mtp85) REVERT: A 450 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7876 (mmp80) REVERT: A 471 GLU cc_start: 0.7500 (mp0) cc_final: 0.7220 (mp0) REVERT: A 487 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 509 GLU cc_start: 0.7025 (tp30) cc_final: 0.6631 (tp30) REVERT: A 567 MET cc_start: 0.5820 (mmt) cc_final: 0.5465 (tpp) REVERT: A 606 MET cc_start: 0.7678 (mmm) cc_final: 0.7270 (mmm) REVERT: A 607 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8179 (mtpt) REVERT: A 649 LYS cc_start: 0.7893 (pptt) cc_final: 0.7267 (mmtm) REVERT: B 42 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 57 GLU cc_start: 0.7743 (tp30) cc_final: 0.7299 (tp30) REVERT: B 93 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7341 (mmt) REVERT: B 95 LYS cc_start: 0.8311 (tttt) cc_final: 0.8081 (tttt) REVERT: B 98 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 101 ASN cc_start: 0.8042 (t0) cc_final: 0.7524 (t0) REVERT: B 142 LYS cc_start: 0.8260 (mttt) cc_final: 0.7754 (mtmm) REVERT: B 154 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6681 (mm-40) REVERT: B 279 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6648 (mm110) REVERT: B 294 ASP cc_start: 0.7750 (t0) cc_final: 0.7304 (t0) REVERT: B 344 PHE cc_start: 0.7804 (m-80) cc_final: 0.7550 (m-80) REVERT: B 376 PHE cc_start: 0.8735 (p90) cc_final: 0.7664 (p90) REVERT: B 395 LEU cc_start: 0.8074 (tp) cc_final: 0.7730 (tt) REVERT: B 426 TYR cc_start: 0.8565 (t80) cc_final: 0.8221 (t80) REVERT: B 427 LYS cc_start: 0.8869 (mttt) cc_final: 0.8508 (mtmm) REVERT: B 466 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: B 471 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 493 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7969 (mm-40) REVERT: B 499 PHE cc_start: 0.8119 (m-80) cc_final: 0.7482 (m-80) REVERT: B 513 MET cc_start: 0.6697 (mmt) cc_final: 0.6154 (mmt) REVERT: B 519 GLU cc_start: 0.7130 (tt0) cc_final: 0.6909 (tm-30) REVERT: B 557 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8477 (mmmt) REVERT: B 627 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 8 ASP cc_start: 0.6895 (m-30) cc_final: 0.6634 (m-30) REVERT: C 29 PHE cc_start: 0.7332 (m-10) cc_final: 0.7096 (m-80) REVERT: C 31 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: C 40 MET cc_start: 0.7404 (tpt) cc_final: 0.7088 (tpt) REVERT: C 46 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: C 104 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7208 (mm-30) REVERT: C 107 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7345 (mtt-85) REVERT: C 111 LYS cc_start: 0.8306 (mmmm) cc_final: 0.7948 (mttt) REVERT: C 118 ASP cc_start: 0.6841 (t0) cc_final: 0.6454 (t0) REVERT: D 529 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5555 (ptmm) REVERT: D 578 MET cc_start: 0.7475 (mmm) cc_final: 0.7096 (mmm) REVERT: D 585 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7478 (mmmm) REVERT: D 662 CYS cc_start: 0.5622 (OUTLIER) cc_final: 0.5347 (p) REVERT: D 699 LEU cc_start: 0.7219 (mm) cc_final: 0.6974 (mm) REVERT: D 724 LYS cc_start: 0.8350 (tmmt) cc_final: 0.7995 (tmmt) outliers start: 85 outliers final: 61 residues processed: 451 average time/residue: 0.3123 time to fit residues: 192.0660 Evaluate side-chains 472 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 398 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 2.9990 chunk 94 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 458 HIS B 30 ASN B 461 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13708 Z= 0.280 Angle : 0.783 15.753 18433 Z= 0.406 Chirality : 0.046 0.225 2030 Planarity : 0.005 0.089 2345 Dihedral : 6.902 89.433 1852 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.38 % Favored : 89.56 % Rotamer: Outliers : 5.42 % Allowed : 33.00 % Favored : 61.58 % 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: -1.22 (0.21), residues: 1619 helix: 0.56 (0.20), residues: 673 sheet: 0.34 (0.42), residues: 183 loop : -2.48 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 289 HIS 0.010 0.001 HIS B 320 PHE 0.024 0.002 PHE A 329 TYR 0.027 0.002 TYR B 305 ARG 0.024 0.001 ARG A 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 420 time to evaluate : 1.650 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 30 ASN cc_start: 0.8496 (t0) cc_final: 0.8118 (t0) REVERT: A 53 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8181 (mtpp) REVERT: A 72 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6587 (pttm) REVERT: A 93 MET cc_start: 0.7787 (mpp) cc_final: 0.7564 (mpp) REVERT: A 153 GLU cc_start: 0.7565 (mp0) cc_final: 0.7223 (mp0) REVERT: A 155 TYR cc_start: 0.7482 (m-80) cc_final: 0.6865 (m-80) REVERT: A 300 GLU cc_start: 0.7100 (pp20) cc_final: 0.6376 (pt0) REVERT: A 303 GLU cc_start: 0.7592 (pp20) cc_final: 0.7180 (pp20) REVERT: A 330 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6705 (mtm-85) REVERT: A 334 PHE cc_start: 0.7826 (m-10) cc_final: 0.7485 (m-10) REVERT: A 338 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7567 (mmp80) REVERT: A 342 ASP cc_start: 0.7729 (p0) cc_final: 0.7331 (p0) REVERT: A 386 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 397 GLN cc_start: 0.7405 (tt0) cc_final: 0.6540 (tm-30) REVERT: A 400 ILE cc_start: 0.8700 (mm) cc_final: 0.8493 (mm) REVERT: A 431 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 449 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8055 (mtp85) REVERT: A 471 GLU cc_start: 0.7483 (mp0) cc_final: 0.6989 (mp0) REVERT: A 487 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 509 GLU cc_start: 0.6869 (tp30) cc_final: 0.6603 (tp30) REVERT: A 567 MET cc_start: 0.6040 (mmt) cc_final: 0.5655 (tpp) REVERT: A 606 MET cc_start: 0.7621 (mmm) cc_final: 0.7221 (mmm) REVERT: A 607 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8197 (mtpt) REVERT: A 629 ASN cc_start: 0.8243 (t0) cc_final: 0.8027 (t0) REVERT: A 649 LYS cc_start: 0.7965 (pptt) cc_final: 0.7299 (mmtm) REVERT: B 42 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6880 (mm-30) REVERT: B 57 GLU cc_start: 0.7791 (tp30) cc_final: 0.7356 (tp30) REVERT: B 70 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7117 (mp0) REVERT: B 93 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: B 98 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 101 ASN cc_start: 0.8051 (t0) cc_final: 0.7512 (t0) REVERT: B 142 LYS cc_start: 0.8348 (mttt) cc_final: 0.7814 (mtmm) REVERT: B 154 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6659 (mm-40) REVERT: B 294 ASP cc_start: 0.7804 (t0) cc_final: 0.7328 (t0) REVERT: B 312 TRP cc_start: 0.7539 (p-90) cc_final: 0.7080 (p-90) REVERT: B 376 PHE cc_start: 0.8780 (p90) cc_final: 0.8019 (p90) REVERT: B 395 LEU cc_start: 0.8234 (tp) cc_final: 0.8022 (tt) REVERT: B 426 TYR cc_start: 0.8647 (t80) cc_final: 0.8384 (t80) REVERT: B 466 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: B 481 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8456 (mmtt) REVERT: B 493 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: B 576 GLU cc_start: 0.7694 (mp0) cc_final: 0.7380 (mp0) REVERT: B 627 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7297 (mm-30) REVERT: C 8 ASP cc_start: 0.7053 (m-30) cc_final: 0.6785 (m-30) REVERT: C 29 PHE cc_start: 0.7401 (m-10) cc_final: 0.7030 (m-80) REVERT: C 31 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: C 40 MET cc_start: 0.7463 (tpt) cc_final: 0.7160 (tpt) REVERT: C 46 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: C 104 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7421 (mm-30) REVERT: C 107 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7249 (mtt-85) REVERT: C 111 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8002 (mttt) REVERT: C 118 ASP cc_start: 0.7222 (t0) cc_final: 0.6892 (t0) REVERT: D 529 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5573 (ptmm) REVERT: D 574 ILE cc_start: 0.8367 (mm) cc_final: 0.8140 (mm) REVERT: D 578 MET cc_start: 0.7540 (mmm) cc_final: 0.7197 (mmm) REVERT: D 585 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7519 (mmmm) REVERT: D 621 ASP cc_start: 0.8264 (p0) cc_final: 0.8050 (p0) REVERT: D 699 LEU cc_start: 0.7341 (mm) cc_final: 0.7102 (mm) REVERT: D 724 LYS cc_start: 0.8330 (tmmt) cc_final: 0.7965 (tmmt) outliers start: 81 outliers final: 57 residues processed: 462 average time/residue: 0.3034 time to fit residues: 192.4263 Evaluate side-chains 486 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 418 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 39 optimal weight: 0.0870 chunk 119 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 279 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115202 restraints weight = 24867.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119001 restraints weight = 13444.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121572 restraints weight = 8499.239| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13708 Z= 0.215 Angle : 0.771 15.741 18433 Z= 0.391 Chirality : 0.045 0.236 2030 Planarity : 0.004 0.062 2345 Dihedral : 6.633 87.609 1849 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 4.62 % Allowed : 33.94 % Favored : 61.45 % 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: -1.21 (0.21), residues: 1619 helix: 0.58 (0.20), residues: 673 sheet: 0.25 (0.42), residues: 177 loop : -2.44 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 623 HIS 0.005 0.001 HIS B 320 PHE 0.020 0.001 PHE C 260 TYR 0.026 0.001 TYR B 305 ARG 0.019 0.000 ARG A 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3727.84 seconds wall clock time: 68 minutes 19.60 seconds (4099.60 seconds total)