Starting phenix.real_space_refine on Sat Mar 16 12:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/03_2024/7rh9_24458.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 9594 2.51 5 N 2387 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 431": "OE1" <-> "OE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3732 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Time building chain proxies: 8.00, per 1000 atoms: 0.54 Number of scatterers: 14680 At special positions: 0 Unit cell: (97.672, 100.198, 121.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2617 8.00 N 2387 7.00 C 9594 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: 5.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 12 sheets defined 69.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.506A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.027A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.645A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 221 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.602A pdb=" N ASN C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.107A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.700A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.883A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.722A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 5.983A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 708 removed outlier: 3.807A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 735 through 746 removed outlier: 3.723A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 3.621A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 932 through 940 removed outlier: 4.163A pdb=" N LEU B 936 " --> pdb=" O ASP B 932 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 960 removed outlier: 6.264A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 964 removed outlier: 3.548A pdb=" N GLN B 964 " --> pdb=" O ALA B 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 964' Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1034 Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.736A pdb=" N LEU B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.554A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 4.883A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.767A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.034A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.906A pdb=" N ASP A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.199A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.833A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 4.684A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 458 through 476 removed outlier: 6.243A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.582A pdb=" N ILE A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 551' Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.564A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.076A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.786A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.510A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.061A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 removed outlier: 3.648A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.977A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.516A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 425 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.679A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 6.195A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 removed outlier: 4.632A pdb=" N ASP D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'C' and resid 496 through 500 Processing sheet with id=AA3, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.225A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 524 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 537 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 526 " --> pdb=" O PHE C 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.532A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.437A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 988 through 990 removed outlier: 6.418A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.689A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.191A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.496A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.138A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU D 524 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 537 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 526 " --> pdb=" O PHE D 535 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2769 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: 4.64 Time building geometry restraints manager: 6.02 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: 4527 1.34 - 1.46: 2690 1.46 - 1.57: 7671 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 15026 Sorted by residual: bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.65e+00 bond pdb=" CA SER D 279 " pdb=" C SER D 279 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.30e-02 5.92e+03 3.40e+00 bond pdb=" C SER D 279 " pdb=" N ARG D 280 " ideal model delta sigma weight residual 1.335 1.318 0.017 1.31e-02 5.83e+03 1.63e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL D 492 " pdb=" CG1 VAL D 492 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 15021 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.60: 233 105.60 - 112.79: 7973 112.79 - 119.99: 5343 119.99 - 127.19: 6657 127.19 - 134.38: 152 Bond angle restraints: 20358 Sorted by residual: angle pdb=" N PHE D 278 " pdb=" CA PHE D 278 " pdb=" C PHE D 278 " ideal model delta sigma weight residual 111.75 116.36 -4.61 1.28e+00 6.10e-01 1.30e+01 angle pdb=" C GLY D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta sigma weight residual 122.46 127.21 -4.75 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C ASN B 830 " pdb=" N SER B 831 " pdb=" CA SER B 831 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C GLY C 558 " pdb=" N ASN C 559 " pdb=" CA ASN C 559 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" C GLY A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 ... (remaining 20353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 8046 16.77 - 33.54: 730 33.54 - 50.31: 107 50.31 - 67.07: 24 67.07 - 83.84: 17 Dihedral angle restraints: 8924 sinusoidal: 3634 harmonic: 5290 Sorted by residual: dihedral pdb=" CA VAL C 469 " pdb=" C VAL C 469 " pdb=" N HIS C 470 " pdb=" CA HIS C 470 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 469 " pdb=" C VAL A 469 " pdb=" N HIS A 470 " pdb=" CA HIS A 470 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL D 469 " pdb=" C VAL D 469 " pdb=" N HIS D 470 " pdb=" CA HIS D 470 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1467 0.032 - 0.065: 529 0.065 - 0.097: 206 0.097 - 0.130: 67 0.130 - 0.162: 7 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ASN D 559 " pdb=" N ASN D 559 " pdb=" C ASN D 559 " pdb=" CB ASN D 559 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ASN A 559 " pdb=" N ASN A 559 " pdb=" C ASN A 559 " pdb=" CB ASN A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA THR B1043 " pdb=" N THR B1043 " pdb=" C THR B1043 " pdb=" CB THR B1043 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2273 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO B 764 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 284 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C PHE A 284 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE A 284 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 285 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 806 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C SER B 806 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 806 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS B 807 " -0.011 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1503 2.75 - 3.29: 15268 3.29 - 3.83: 27125 3.83 - 4.36: 31001 4.36 - 4.90: 52355 Nonbonded interactions: 127252 Sorted by model distance: nonbonded pdb=" OE2 GLU D 515 " pdb=" OH TYR D 517 " model vdw 2.214 2.440 nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.220 2.440 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.250 2.440 nonbonded pdb=" N GLU C 365 " pdb=" OE2 GLU D 365 " model vdw 2.269 2.520 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.275 2.440 ... (remaining 127247 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 156 through 605) selection = chain 'C' selection = (chain 'D' and resid 156 through 605) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.020 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.510 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15026 Z= 0.203 Angle : 0.571 8.779 20358 Z= 0.314 Chirality : 0.041 0.162 2276 Planarity : 0.005 0.075 2523 Dihedral : 13.273 83.843 5534 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1782 helix: 1.18 (0.14), residues: 1157 sheet: 1.52 (0.66), residues: 44 loop : 0.36 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 168 HIS 0.009 0.002 HIS D 422 PHE 0.032 0.002 PHE D 382 TYR 0.018 0.002 TYR D 306 ARG 0.006 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.586 Fit side-chains REVERT: C 234 LEU cc_start: 0.7461 (tp) cc_final: 0.7148 (tp) REVERT: C 484 GLU cc_start: 0.6315 (tt0) cc_final: 0.5898 (tt0) REVERT: B 690 HIS cc_start: 0.6111 (m-70) cc_final: 0.5575 (m-70) REVERT: A 422 HIS cc_start: 0.6844 (t-90) cc_final: 0.6303 (t-90) REVERT: A 490 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6802 (mm-30) REVERT: A 521 GLU cc_start: 0.7227 (tt0) cc_final: 0.7004 (tt0) REVERT: A 594 MET cc_start: 0.6264 (tmm) cc_final: 0.5832 (tpp) REVERT: D 262 LYS cc_start: 0.6262 (mptt) cc_final: 0.5758 (mmtm) REVERT: D 399 MET cc_start: 0.8018 (ttm) cc_final: 0.7731 (ttm) REVERT: D 553 LYS cc_start: 0.4058 (tmtt) cc_final: 0.3745 (tptp) REVERT: D 602 ILE cc_start: 0.7654 (mt) cc_final: 0.7352 (mt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 1.3620 time to fit residues: 337.3181 Evaluate side-chains 196 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 710 GLN B 805 ASN B 864 ASN B 969 GLN A 411 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15026 Z= 0.213 Angle : 0.484 6.854 20358 Z= 0.264 Chirality : 0.039 0.149 2276 Planarity : 0.004 0.063 2523 Dihedral : 3.880 17.470 1991 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.05 % Allowed : 7.13 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 1782 helix: 1.90 (0.15), residues: 1145 sheet: 1.73 (0.68), residues: 44 loop : 0.59 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.004 0.001 HIS B1049 PHE 0.020 0.002 PHE D 298 TYR 0.019 0.002 TYR A 349 ARG 0.004 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.714 Fit side-chains REVERT: C 234 LEU cc_start: 0.7443 (tp) cc_final: 0.7144 (tp) REVERT: C 484 GLU cc_start: 0.6400 (tt0) cc_final: 0.5945 (tt0) REVERT: B 690 HIS cc_start: 0.6155 (m-70) cc_final: 0.5613 (m-70) REVERT: B 1006 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: A 422 HIS cc_start: 0.6871 (t-90) cc_final: 0.6316 (t-90) REVERT: A 490 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 516 MET cc_start: 0.8700 (ttt) cc_final: 0.8387 (ttt) REVERT: A 594 MET cc_start: 0.6252 (tmm) cc_final: 0.5866 (tpp) REVERT: D 262 LYS cc_start: 0.6146 (mptt) cc_final: 0.5623 (mmtm) REVERT: D 516 MET cc_start: 0.8561 (ttp) cc_final: 0.8241 (ttp) outliers start: 17 outliers final: 8 residues processed: 213 average time/residue: 1.3085 time to fit residues: 305.8568 Evaluate side-chains 198 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1006 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN B 969 GLN B1006 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15026 Z= 0.148 Angle : 0.429 5.059 20358 Z= 0.234 Chirality : 0.037 0.143 2276 Planarity : 0.003 0.059 2523 Dihedral : 3.720 17.490 1991 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.30 % Allowed : 8.81 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.20), residues: 1782 helix: 2.14 (0.15), residues: 1145 sheet: 1.68 (0.68), residues: 44 loop : 0.64 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 168 HIS 0.003 0.001 HIS B1049 PHE 0.018 0.001 PHE C 298 TYR 0.014 0.001 TYR A 349 ARG 0.002 0.000 ARG D 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.712 Fit side-chains REVERT: C 234 LEU cc_start: 0.7364 (tp) cc_final: 0.7062 (tp) REVERT: C 445 LYS cc_start: 0.6769 (mmtm) cc_final: 0.6510 (mmtm) REVERT: C 509 LYS cc_start: 0.7774 (mtpp) cc_final: 0.7489 (mtpp) REVERT: B 690 HIS cc_start: 0.6151 (m-70) cc_final: 0.5623 (m-70) REVERT: A 235 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7333 (mttm) REVERT: A 422 HIS cc_start: 0.6905 (t-90) cc_final: 0.6373 (t-90) REVERT: A 490 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 516 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: A 594 MET cc_start: 0.6289 (tmm) cc_final: 0.5879 (tpp) REVERT: D 225 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6824 (pt0) REVERT: D 262 LYS cc_start: 0.6238 (mptt) cc_final: 0.5768 (mmtm) REVERT: D 516 MET cc_start: 0.8610 (ttp) cc_final: 0.8396 (ttp) outliers start: 21 outliers final: 7 residues processed: 207 average time/residue: 1.2786 time to fit residues: 290.8378 Evaluate side-chains 204 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 243 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN B1006 GLN A 329 ASN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15026 Z= 0.134 Angle : 0.417 5.052 20358 Z= 0.226 Chirality : 0.037 0.139 2276 Planarity : 0.003 0.056 2523 Dihedral : 3.632 17.322 1991 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.18 % Allowed : 9.93 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.20), residues: 1782 helix: 2.28 (0.15), residues: 1147 sheet: 1.70 (0.68), residues: 44 loop : 0.66 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 PHE 0.017 0.001 PHE C 298 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG D 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.720 Fit side-chains REVERT: C 234 LEU cc_start: 0.7431 (tp) cc_final: 0.7129 (tp) REVERT: C 445 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6563 (mmtt) REVERT: C 484 GLU cc_start: 0.6378 (tt0) cc_final: 0.5863 (tt0) REVERT: C 509 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7582 (mtpp) REVERT: B 690 HIS cc_start: 0.6143 (m-70) cc_final: 0.5625 (m-70) REVERT: B 853 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7667 (ttpt) REVERT: A 490 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 516 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8380 (ttt) REVERT: A 594 MET cc_start: 0.6277 (tmm) cc_final: 0.5874 (tpp) REVERT: D 262 LYS cc_start: 0.6284 (mptt) cc_final: 0.5774 (mmtm) REVERT: D 553 LYS cc_start: 0.4334 (tmtt) cc_final: 0.4111 (tptp) outliers start: 19 outliers final: 6 residues processed: 208 average time/residue: 1.3056 time to fit residues: 298.0879 Evaluate side-chains 199 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS C 496 GLN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15026 Z= 0.255 Angle : 0.503 6.340 20358 Z= 0.273 Chirality : 0.040 0.152 2276 Planarity : 0.004 0.053 2523 Dihedral : 3.935 17.919 1991 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.80 % Allowed : 10.36 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.19), residues: 1782 helix: 2.12 (0.15), residues: 1141 sheet: 1.67 (0.65), residues: 44 loop : 0.61 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.005 0.002 HIS B1049 PHE 0.022 0.002 PHE C 298 TYR 0.022 0.002 TYR C 349 ARG 0.005 0.001 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.981 Fit side-chains REVERT: C 234 LEU cc_start: 0.7387 (tp) cc_final: 0.7126 (tp) REVERT: C 445 LYS cc_start: 0.6652 (mmtm) cc_final: 0.6402 (mmtm) REVERT: C 484 GLU cc_start: 0.6436 (tt0) cc_final: 0.5877 (tt0) REVERT: B 690 HIS cc_start: 0.6227 (m-70) cc_final: 0.5686 (m-70) REVERT: B 991 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7664 (mttp) REVERT: A 337 ILE cc_start: 0.8092 (pt) cc_final: 0.7849 (pt) REVERT: A 490 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 516 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8524 (ttt) REVERT: A 594 MET cc_start: 0.6258 (tmm) cc_final: 0.5866 (tpp) REVERT: D 262 LYS cc_start: 0.6316 (mptt) cc_final: 0.5723 (mmtm) REVERT: D 608 LEU cc_start: 0.5783 (mm) cc_final: 0.5556 (mm) outliers start: 29 outliers final: 12 residues processed: 206 average time/residue: 1.2440 time to fit residues: 282.0273 Evaluate side-chains 200 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 ASN B 969 GLN B1006 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15026 Z= 0.144 Angle : 0.430 5.577 20358 Z= 0.233 Chirality : 0.037 0.139 2276 Planarity : 0.003 0.047 2523 Dihedral : 3.746 18.281 1991 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.05 % Allowed : 11.54 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.20), residues: 1782 helix: 2.28 (0.15), residues: 1143 sheet: 1.80 (0.67), residues: 44 loop : 0.64 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 168 HIS 0.004 0.001 HIS B1049 PHE 0.016 0.001 PHE C 298 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.822 Fit side-chains REVERT: C 234 LEU cc_start: 0.7391 (tp) cc_final: 0.7124 (tp) REVERT: C 305 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7691 (ppp) REVERT: C 484 GLU cc_start: 0.6474 (tt0) cc_final: 0.5924 (tt0) REVERT: B 690 HIS cc_start: 0.6230 (m-70) cc_final: 0.5702 (m-70) REVERT: B 897 MET cc_start: 0.8194 (ttt) cc_final: 0.7967 (mtp) REVERT: B 991 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7626 (mttp) REVERT: A 337 ILE cc_start: 0.8057 (pt) cc_final: 0.7853 (pt) REVERT: A 490 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 516 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8429 (ttt) REVERT: A 594 MET cc_start: 0.6233 (tmm) cc_final: 0.5845 (tpp) REVERT: D 262 LYS cc_start: 0.6308 (mptt) cc_final: 0.5759 (mmtm) REVERT: D 305 MET cc_start: 0.7714 (ttp) cc_final: 0.7471 (ptp) REVERT: D 553 LYS cc_start: 0.4387 (tmtt) cc_final: 0.4019 (tmtt) outliers start: 17 outliers final: 9 residues processed: 197 average time/residue: 1.2894 time to fit residues: 279.2414 Evaluate side-chains 194 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 125 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN B1006 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15026 Z= 0.127 Angle : 0.416 5.695 20358 Z= 0.224 Chirality : 0.037 0.133 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.608 17.876 1991 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.12 % Allowed : 12.03 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.20), residues: 1782 helix: 2.38 (0.15), residues: 1146 sheet: 1.81 (0.68), residues: 44 loop : 0.68 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 PHE 0.015 0.001 PHE B 870 TYR 0.012 0.001 TYR C 354 ARG 0.002 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.846 Fit side-chains REVERT: C 234 LEU cc_start: 0.7365 (tp) cc_final: 0.7076 (tp) REVERT: C 305 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7637 (ppp) REVERT: C 484 GLU cc_start: 0.6395 (tt0) cc_final: 0.5834 (tt0) REVERT: B 690 HIS cc_start: 0.6235 (m-70) cc_final: 0.5719 (m-70) REVERT: B 721 ILE cc_start: 0.7809 (mm) cc_final: 0.7593 (pp) REVERT: B 897 MET cc_start: 0.8162 (ttt) cc_final: 0.7956 (mtp) REVERT: B 991 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7607 (mttp) REVERT: A 337 ILE cc_start: 0.8021 (pt) cc_final: 0.7814 (pt) REVERT: A 422 HIS cc_start: 0.6866 (t-90) cc_final: 0.6289 (t-90) REVERT: A 490 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6795 (mm-30) REVERT: A 516 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (ttt) REVERT: A 594 MET cc_start: 0.6265 (tmm) cc_final: 0.5870 (tpp) REVERT: D 262 LYS cc_start: 0.6331 (mptt) cc_final: 0.5784 (mmtm) outliers start: 18 outliers final: 8 residues processed: 201 average time/residue: 1.3003 time to fit residues: 287.5981 Evaluate side-chains 198 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 516 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 0.0040 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN B1006 GLN A 551 ASN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15026 Z= 0.163 Angle : 0.441 5.759 20358 Z= 0.238 Chirality : 0.038 0.139 2276 Planarity : 0.003 0.044 2523 Dihedral : 3.663 17.824 1991 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.30 % Allowed : 12.53 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.20), residues: 1782 helix: 2.38 (0.15), residues: 1143 sheet: 1.76 (0.67), residues: 44 loop : 0.73 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.017 0.001 PHE D 298 TYR 0.016 0.001 TYR A 349 ARG 0.003 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.616 Fit side-chains REVERT: C 234 LEU cc_start: 0.7356 (tp) cc_final: 0.7079 (tp) REVERT: C 305 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7697 (ppp) REVERT: C 484 GLU cc_start: 0.6420 (tt0) cc_final: 0.5853 (tt0) REVERT: B 690 HIS cc_start: 0.6226 (m-70) cc_final: 0.5699 (m-70) REVERT: B 721 ILE cc_start: 0.7872 (mm) cc_final: 0.7643 (pp) REVERT: B 991 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7628 (mttp) REVERT: A 337 ILE cc_start: 0.8066 (pt) cc_final: 0.7859 (pt) REVERT: A 422 HIS cc_start: 0.6897 (t-90) cc_final: 0.6318 (t-90) REVERT: A 490 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 516 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8435 (ttt) REVERT: A 594 MET cc_start: 0.6263 (tmm) cc_final: 0.5873 (tpp) REVERT: D 262 LYS cc_start: 0.6331 (mptt) cc_final: 0.5739 (mmtm) REVERT: D 582 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.5944 (mpm) outliers start: 21 outliers final: 11 residues processed: 198 average time/residue: 1.2574 time to fit residues: 274.1010 Evaluate side-chains 199 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 144 optimal weight: 0.0060 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1006 GLN A 551 ASN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15026 Z= 0.157 Angle : 0.441 6.094 20358 Z= 0.237 Chirality : 0.038 0.140 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.665 17.812 1991 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.36 % Allowed : 12.41 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.20), residues: 1782 helix: 2.38 (0.15), residues: 1143 sheet: 1.73 (0.67), residues: 44 loop : 0.71 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.004 0.001 HIS B1049 PHE 0.017 0.001 PHE D 298 TYR 0.014 0.001 TYR A 349 ARG 0.003 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.830 Fit side-chains REVERT: C 234 LEU cc_start: 0.7355 (tp) cc_final: 0.7086 (tp) REVERT: C 305 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7678 (ppp) REVERT: C 484 GLU cc_start: 0.6390 (tt0) cc_final: 0.5838 (tt0) REVERT: B 690 HIS cc_start: 0.6248 (m-70) cc_final: 0.5718 (m-70) REVERT: B 721 ILE cc_start: 0.7877 (mm) cc_final: 0.7648 (pp) REVERT: B 991 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7627 (mttp) REVERT: A 337 ILE cc_start: 0.8078 (pt) cc_final: 0.7866 (pt) REVERT: A 422 HIS cc_start: 0.6892 (t-90) cc_final: 0.6312 (t-90) REVERT: A 490 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 516 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (ttt) REVERT: A 594 MET cc_start: 0.6261 (tmm) cc_final: 0.5876 (tpp) REVERT: A 606 ASP cc_start: 0.6024 (m-30) cc_final: 0.5781 (m-30) REVERT: D 262 LYS cc_start: 0.6329 (mptt) cc_final: 0.5734 (mmtm) REVERT: D 582 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.5931 (mpm) outliers start: 22 outliers final: 13 residues processed: 197 average time/residue: 1.2696 time to fit residues: 275.1467 Evaluate side-chains 202 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1006 GLN A 551 ASN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15026 Z= 0.144 Angle : 0.435 5.615 20358 Z= 0.234 Chirality : 0.038 0.138 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.631 17.742 1991 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.05 % Allowed : 12.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.20), residues: 1782 helix: 2.41 (0.15), residues: 1145 sheet: 1.73 (0.67), residues: 44 loop : 0.68 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.003 0.001 HIS B1049 PHE 0.016 0.001 PHE B 870 TYR 0.014 0.001 TYR B 787 ARG 0.002 0.000 ARG D 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.695 Fit side-chains REVERT: C 234 LEU cc_start: 0.7401 (tp) cc_final: 0.7107 (tp) REVERT: C 305 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7665 (ppp) REVERT: C 484 GLU cc_start: 0.6401 (tt0) cc_final: 0.5839 (tt0) REVERT: B 690 HIS cc_start: 0.6274 (m-70) cc_final: 0.5772 (m-70) REVERT: B 721 ILE cc_start: 0.7867 (mm) cc_final: 0.7641 (pp) REVERT: B 991 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7623 (mttp) REVERT: A 337 ILE cc_start: 0.8071 (pt) cc_final: 0.7860 (pt) REVERT: A 340 PRO cc_start: 0.7936 (Cg_endo) cc_final: 0.7685 (Cg_exo) REVERT: A 422 HIS cc_start: 0.6898 (t-90) cc_final: 0.6315 (t-90) REVERT: A 490 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6802 (mm-30) REVERT: A 516 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8433 (ttt) REVERT: A 594 MET cc_start: 0.6259 (tmm) cc_final: 0.5874 (tpp) REVERT: A 606 ASP cc_start: 0.6015 (m-30) cc_final: 0.5766 (m-30) REVERT: D 262 LYS cc_start: 0.6300 (mptt) cc_final: 0.5725 (mmtm) outliers start: 17 outliers final: 11 residues processed: 197 average time/residue: 1.2615 time to fit residues: 273.4046 Evaluate side-chains 198 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS B 969 GLN B1006 GLN A 498 GLN A 551 ASN D 419 GLN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094823 restraints weight = 16770.231| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.26 r_work: 0.2868 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15026 Z= 0.270 Angle : 0.522 5.639 20358 Z= 0.283 Chirality : 0.041 0.158 2276 Planarity : 0.004 0.044 2523 Dihedral : 3.968 18.248 1991 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.30 % Allowed : 12.97 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 1782 helix: 2.13 (0.15), residues: 1146 sheet: 1.74 (0.63), residues: 44 loop : 0.61 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 168 HIS 0.005 0.002 HIS B1049 PHE 0.022 0.002 PHE C 298 TYR 0.023 0.002 TYR C 349 ARG 0.006 0.001 ARG C 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5157.24 seconds wall clock time: 92 minutes 7.08 seconds (5527.08 seconds total)