Starting phenix.real_space_refine (version: dev) on Tue Feb 21 11:40:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/02_2023/7rh9_24458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/02_2023/7rh9_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_24458/02_2023/7rh9_24458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/02_2023/7rh9_24458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/02_2023/7rh9_24458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rh9_24458/02_2023/7rh9_24458.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.22, per 1000 atoms: 0.56 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: 5.84 Conformation dependent library (CDL) restraints added in 2.2 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: 0.74 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: 4.41 Time building geometry restraints manager: 6.34 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 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. 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: 0.980 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: 6.530 Check model and map are aligned: 0.220 Process input model: 38.670 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 % 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 *********************** 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 : 1.743 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 1.3810 time to fit residues: 342.8038 Evaluate side-chains 197 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4276 ------------------------------------------------------------------------------- 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: 4.9990 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15026 Z= 0.214 Angle : 0.487 6.983 20358 Z= 0.265 Chirality : 0.039 0.147 2276 Planarity : 0.004 0.063 2523 Dihedral : 3.882 17.433 1991 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.18 % 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: 2.13 (0.19), residues: 1782 helix: 1.89 (0.15), residues: 1145 sheet: 1.75 (0.68), residues: 44 loop : 0.59 (0.26), residues: 593 *********************** 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 223 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.718 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 213 average time/residue: 1.3393 time to fit residues: 312.9952 Evaluate side-chains 199 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2284 time to fit residues: 3.4571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 134 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 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 710 GLN B 714 GLN B 969 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: 0.8417 moved from start: 0.1150 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= 0.134 Angle : 0.421 5.058 20358 Z= 0.229 Chirality : 0.037 0.142 2276 Planarity : 0.003 0.058 2523 Dihedral : 3.690 17.331 1991 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.24 % 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: 2.43 (0.20), residues: 1782 helix: 2.16 (0.15), residues: 1147 sheet: 1.66 (0.68), residues: 44 loop : 0.62 (0.26), residues: 591 *********************** 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: 20 poor density : 199 time to evaluate : 1.855 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 211 average time/residue: 1.3045 time to fit residues: 303.2596 Evaluate side-chains 201 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.5117 time to fit residues: 4.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 84 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 0.1980 chunk 154 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN A 329 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: 0.8433 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 15026 Z= 0.157 Angle : 0.433 5.273 20358 Z= 0.235 Chirality : 0.038 0.144 2276 Planarity : 0.003 0.054 2523 Dihedral : 3.683 17.348 1991 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.12 % 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 (0.19), residues: 1782 helix: 2.27 (0.15), residues: 1147 sheet: 1.74 (0.67), residues: 44 loop : 0.68 (0.26), residues: 591 *********************** 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 210 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.830 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 202 average time/residue: 1.3412 time to fit residues: 298.9401 Evaluate side-chains 196 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.2316 time to fit residues: 3.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 128 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15026 Z= 0.158 Angle : 0.434 5.764 20358 Z= 0.235 Chirality : 0.038 0.142 2276 Planarity : 0.003 0.048 2523 Dihedral : 3.681 17.469 1991 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 1.30 % 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: 2.62 (0.19), residues: 1782 helix: 2.32 (0.15), residues: 1145 sheet: 1.72 (0.66), residues: 44 loop : 0.69 (0.26), residues: 593 *********************** 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 211 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.734 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 201 average time/residue: 1.2760 time to fit residues: 283.3864 Evaluate side-chains 197 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.4306 time to fit residues: 4.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN B 714 GLN B 969 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: 0.8463 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 15026 Z= 0.201 Angle : 0.469 5.736 20358 Z= 0.254 Chirality : 0.038 0.145 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.798 17.650 1991 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.36 % 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 (0.19), residues: 1782 helix: 2.24 (0.15), residues: 1142 sheet: 1.78 (0.67), residues: 44 loop : 0.73 (0.26), residues: 596 *********************** 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 210 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 2.066 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 200 average time/residue: 1.3226 time to fit residues: 292.1007 Evaluate side-chains 194 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1883 time to fit residues: 3.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.1566 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= 0.156 Angle : 0.445 6.424 20358 Z= 0.240 Chirality : 0.038 0.176 2276 Planarity : 0.003 0.044 2523 Dihedral : 3.727 17.805 1991 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 1.30 % 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: 2.61 (0.20), residues: 1782 helix: 2.29 (0.15), residues: 1143 sheet: 1.84 (0.67), residues: 44 loop : 0.72 (0.26), residues: 595 *********************** 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 206 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.783 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 197 average time/residue: 1.2786 time to fit residues: 279.6805 Evaluate side-chains 192 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.1861 time to fit residues: 2.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 15026 Z= 0.127 Angle : 0.423 5.576 20358 Z= 0.227 Chirality : 0.037 0.137 2276 Planarity : 0.003 0.044 2523 Dihedral : 3.607 17.544 1991 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 1.12 % 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: 2.74 (0.20), residues: 1782 helix: 2.40 (0.15), residues: 1144 sheet: 1.75 (0.68), residues: 44 loop : 0.78 (0.26), residues: 594 *********************** 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 207 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.936 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 199 average time/residue: 1.3116 time to fit residues: 288.6087 Evaluate side-chains 194 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.2310 time to fit residues: 3.7602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.1608 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= 0.153 Angle : 0.443 5.835 20358 Z= 0.238 Chirality : 0.038 0.141 2276 Planarity : 0.003 0.044 2523 Dihedral : 3.637 17.414 1991 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.05 % 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: 2.76 (0.20), residues: 1782 helix: 2.41 (0.15), residues: 1143 sheet: 1.75 (0.67), residues: 44 loop : 0.79 (0.26), residues: 595 *********************** 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 200 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.778 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 193 average time/residue: 1.3011 time to fit residues: 278.4587 Evaluate side-chains 194 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.2094 time to fit residues: 3.3894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 86 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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 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: 0.8477 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 15026 Z= 0.248 Angle : 0.515 6.420 20358 Z= 0.278 Chirality : 0.040 0.165 2276 Planarity : 0.004 0.043 2523 Dihedral : 3.916 17.874 1991 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.18 % 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: 2.51 (0.19), residues: 1782 helix: 2.18 (0.15), residues: 1143 sheet: 1.80 (0.65), residues: 44 loop : 0.75 (0.26), residues: 595 ********************** 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 203 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.820 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 195 average time/residue: 1.3055 time to fit residues: 282.0898 Evaluate side-chains 195 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.6732 time to fit residues: 4.8728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098246 restraints weight = 16761.360| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.22 r_work: 0.2912 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 15026 Z= 0.151 Angle : 0.457 8.271 20358 Z= 0.243 Chirality : 0.038 0.140 2276 Planarity : 0.003 0.043 2523 Dihedral : 3.759 18.153 1991 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.81 % 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: 2.64 (0.20), residues: 1782 helix: 2.31 (0.15), residues: 1143 sheet: 1.81 (0.67), residues: 44 loop : 0.74 (0.26), residues: 595 =============================================================================== Job complete usr+sys time: 5090.46 seconds wall clock time: 91 minutes 17.82 seconds (5477.82 seconds total)