Starting phenix.real_space_refine on Sat Mar 16 18:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/03_2024/7rhl_24465.pdb" } resolution = 3.03 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 10005 2.51 5 N 2527 2.21 5 O 2757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1064": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" 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: 15371 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3883 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 474} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3661 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 441} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3916 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3911 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 7.83, per 1000 atoms: 0.51 Number of scatterers: 15371 At special positions: 0 Unit cell: (97.672, 100.198, 160.822, 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 2757 8.00 N 2527 7.00 C 10005 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: 5.55 Conformation dependent library (CDL) restraints added in 2.8 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 70.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.538A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.079A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.851A 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 Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.069A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.903A pdb=" N ASP C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 258' Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.656A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 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 424 removed outlier: 4.896A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) 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: 5.781A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.261A 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 587 removed outlier: 4.487A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'C' and resid 626 through 663 Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.921A 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: 3.835A 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: 3.596A 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 933 through 938 Processing helix chain 'B' and resid 941 through 959 removed outlier: 6.392A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) 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: 3.606A pdb=" N LEU B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1130 Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.560A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.107A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.782A 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: 4.102A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.829A pdb=" N ASP A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.994A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.785A 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: 4.639A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.052A 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: 6.417A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.650A 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 578 through 586 Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'A' and resid 626 through 661 removed outlier: 3.849A pdb=" N SER A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.512A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 4.934A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.842A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.541A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.075A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.796A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.828A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.897A 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 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.804A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 5.922A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 606 Processing helix chain 'D' and resid 626 through 663 removed outlier: 3.777A pdb=" N ILE D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 645 " --> pdb=" O PHE D 641 " (cutoff:3.500A) 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: 6.291A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.891A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 720 " --> pdb=" O ARG B 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.495A 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: 6.346A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.479A 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: 6.739A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.667A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.997A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.209A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3105 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: 4.99 Time building geometry restraints manager: 6.09 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: 4820 1.34 - 1.46: 3855 1.46 - 1.58: 6900 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 15713 Sorted by residual: bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB THR B 842 " pdb=" CG2 THR B 842 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" CB ASN D 559 " pdb=" CG ASN D 559 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CA ASN D 559 " pdb=" CB ASN D 559 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.44e+00 bond pdb=" C ARG C 277 " pdb=" O ARG C 277 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.33e-02 5.65e+03 1.19e+00 ... (remaining 15708 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.37: 220 105.37 - 112.60: 8183 112.60 - 119.83: 5289 119.83 - 127.06: 7460 127.06 - 134.30: 156 Bond angle restraints: 21308 Sorted by residual: angle pdb=" N PRO B1106 " pdb=" CA PRO B1106 " pdb=" CB PRO B1106 " ideal model delta sigma weight residual 103.00 110.35 -7.35 1.10e+00 8.26e-01 4.47e+01 angle pdb=" CB MET A 604 " pdb=" CG MET A 604 " pdb=" SD MET A 604 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C GLY D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CB LYS D 455 " pdb=" CG LYS D 455 " pdb=" CD LYS D 455 " ideal model delta sigma weight residual 111.30 119.09 -7.79 2.30e+00 1.89e-01 1.15e+01 angle pdb=" N TYR B 865 " pdb=" CA TYR B 865 " pdb=" C TYR B 865 " ideal model delta sigma weight residual 111.69 107.95 3.74 1.23e+00 6.61e-01 9.25e+00 ... (remaining 21303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8454 17.94 - 35.88: 725 35.88 - 53.82: 104 53.82 - 71.76: 30 71.76 - 89.70: 9 Dihedral angle restraints: 9322 sinusoidal: 3634 harmonic: 5688 Sorted by residual: dihedral pdb=" CA ARG B 997 " pdb=" C ARG B 997 " pdb=" N GLU B 998 " pdb=" CA GLU B 998 " ideal model delta harmonic sigma weight residual -180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA THR D 181 " pdb=" C THR D 181 " pdb=" N MET D 182 " pdb=" CA MET D 182 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+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 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1884 0.047 - 0.093: 430 0.093 - 0.140: 88 0.140 - 0.186: 3 0.186 - 0.233: 2 Chirality restraints: 2407 Sorted by residual: chirality pdb=" CA PRO B1106 " pdb=" N PRO B1106 " pdb=" C PRO B1106 " pdb=" CB PRO B1106 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 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 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CB VAL D 350 " pdb=" CA VAL D 350 " pdb=" CG1 VAL D 350 " pdb=" CG2 VAL D 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2404 not shown) Planarity restraints: 2659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 864 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ASN B 864 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN B 864 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR B 865 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 764 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 179 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ASN C 179 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN C 179 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP C 180 " 0.009 2.00e-02 2.50e+03 ... (remaining 2656 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1750 2.75 - 3.29: 15611 3.29 - 3.83: 28015 3.83 - 4.36: 31590 4.36 - 4.90: 53995 Nonbonded interactions: 130961 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.217 2.440 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.237 2.440 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.276 2.440 ... (remaining 130956 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 or resid 625 through 661)) selection = (chain 'C' and resid 156 through 661) selection = (chain 'D' and (resid 156 through 605 or resid 625 through 661)) } 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: 1.110 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: 0.210 Set scattering table: 0.140 Process input model: 40.460 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 0.050 15713 Z= 0.205 Angle : 0.560 10.242 21308 Z= 0.304 Chirality : 0.041 0.233 2407 Planarity : 0.004 0.059 2659 Dihedral : 13.966 89.703 5670 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 1914 helix: 1.45 (0.13), residues: 1290 sheet: 1.69 (0.75), residues: 43 loop : 0.48 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 442 HIS 0.013 0.002 HIS C 422 PHE 0.020 0.002 PHE C 298 TYR 0.019 0.001 TYR D 306 ARG 0.007 0.000 ARG D 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.644 Fit side-chains REVERT: C 604 MET cc_start: 0.6920 (mtt) cc_final: 0.6595 (mtt) REVERT: B 736 ARG cc_start: 0.6355 (ptp90) cc_final: 0.6140 (ptm160) REVERT: B 780 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6055 (pt0) REVERT: B 1071 GLU cc_start: 0.6635 (mp0) cc_final: 0.6301 (mp0) REVERT: A 196 TYR cc_start: 0.8581 (m-80) cc_final: 0.8334 (m-80) REVERT: A 204 ASP cc_start: 0.7982 (m-30) cc_final: 0.7619 (m-30) REVERT: A 601 GLN cc_start: 0.7332 (mm110) cc_final: 0.7118 (mm-40) REVERT: D 351 TYR cc_start: 0.8483 (t80) cc_final: 0.8025 (t80) REVERT: D 422 HIS cc_start: 0.7379 (m170) cc_final: 0.7148 (m170) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2581 time to fit residues: 78.8337 Evaluate side-chains 170 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN C 444 ASN C 601 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN B 864 ASN B1053 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15713 Z= 0.231 Angle : 0.474 6.465 21308 Z= 0.258 Chirality : 0.039 0.187 2407 Planarity : 0.004 0.044 2659 Dihedral : 3.691 19.610 2127 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.56 % Allowed : 4.22 % Favored : 95.22 % 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: 2.33 (0.19), residues: 1914 helix: 2.06 (0.14), residues: 1298 sheet: 0.68 (0.72), residues: 47 loop : 0.53 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.006 0.001 HIS B1049 PHE 0.021 0.002 PHE C 298 TYR 0.017 0.002 TYR C 351 ARG 0.004 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.787 Fit side-chains REVERT: B 1071 GLU cc_start: 0.6636 (mp0) cc_final: 0.6292 (mp0) REVERT: D 265 TRP cc_start: 0.7352 (m100) cc_final: 0.7142 (m100) REVERT: D 283 GLU cc_start: 0.7765 (tt0) cc_final: 0.7512 (tt0) outliers start: 9 outliers final: 8 residues processed: 187 average time/residue: 0.2725 time to fit residues: 75.6835 Evaluate side-chains 177 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15713 Z= 0.171 Angle : 0.441 9.571 21308 Z= 0.236 Chirality : 0.038 0.186 2407 Planarity : 0.003 0.034 2659 Dihedral : 3.584 19.005 2127 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.43 % Allowed : 5.77 % Favored : 93.80 % 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 (0.19), residues: 1914 helix: 2.35 (0.14), residues: 1296 sheet: 0.88 (0.68), residues: 44 loop : 0.52 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 PHE 0.018 0.001 PHE C 298 TYR 0.015 0.001 TYR B 810 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.830 Fit side-chains REVERT: C 381 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (t70) REVERT: B 746 LEU cc_start: 0.6283 (pp) cc_final: 0.5585 (tp) outliers start: 7 outliers final: 3 residues processed: 179 average time/residue: 0.2935 time to fit residues: 78.9079 Evaluate side-chains 172 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 9.9990 chunk 130 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN D 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15713 Z= 0.147 Angle : 0.421 6.980 21308 Z= 0.226 Chirality : 0.037 0.189 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.487 18.424 2127 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.99 % Allowed : 6.58 % Favored : 92.43 % 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: 2.84 (0.19), residues: 1914 helix: 2.52 (0.14), residues: 1297 sheet: 0.95 (0.68), residues: 44 loop : 0.54 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.004 0.001 HIS B 690 PHE 0.018 0.001 PHE C 298 TYR 0.014 0.001 TYR B 810 ARG 0.003 0.000 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.880 Fit side-chains REVERT: C 381 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (t70) REVERT: B 746 LEU cc_start: 0.6318 (pp) cc_final: 0.5553 (tp) REVERT: D 534 GLN cc_start: 0.7823 (mt0) cc_final: 0.7339 (mt0) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.2550 time to fit residues: 72.0157 Evaluate side-chains 178 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 127 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15713 Z= 0.167 Angle : 0.433 7.294 21308 Z= 0.231 Chirality : 0.037 0.204 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.502 17.945 2127 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.99 % Allowed : 7.51 % Favored : 91.50 % 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: 2.89 (0.19), residues: 1914 helix: 2.55 (0.14), residues: 1300 sheet: 0.86 (0.66), residues: 44 loop : 0.58 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.019 0.001 PHE C 298 TYR 0.015 0.001 TYR B 810 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.718 Fit side-chains REVERT: C 381 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (t70) REVERT: B 695 ASP cc_start: 0.6429 (m-30) cc_final: 0.6014 (m-30) REVERT: B 746 LEU cc_start: 0.6370 (pp) cc_final: 0.5615 (tp) REVERT: A 556 LYS cc_start: 0.6682 (mmtm) cc_final: 0.6245 (mttt) REVERT: D 534 GLN cc_start: 0.7821 (mt0) cc_final: 0.7372 (mt0) outliers start: 16 outliers final: 13 residues processed: 179 average time/residue: 0.2624 time to fit residues: 71.5184 Evaluate side-chains 179 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 36 optimal weight: 0.0010 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15713 Z= 0.181 Angle : 0.441 8.152 21308 Z= 0.234 Chirality : 0.038 0.203 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.526 17.873 2127 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.82 % 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: 2.89 (0.19), residues: 1914 helix: 2.55 (0.14), residues: 1300 sheet: 0.94 (0.68), residues: 44 loop : 0.56 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 PHE 0.019 0.001 PHE C 298 TYR 0.015 0.001 TYR B 810 ARG 0.002 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.887 Fit side-chains REVERT: C 381 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (t70) REVERT: B 695 ASP cc_start: 0.6459 (m-30) cc_final: 0.6054 (m-30) REVERT: B 746 LEU cc_start: 0.6375 (pp) cc_final: 0.5633 (tp) REVERT: B 879 MET cc_start: 0.8269 (tpp) cc_final: 0.7980 (tpt) REVERT: A 556 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6246 (mttt) REVERT: D 529 ASP cc_start: 0.5462 (OUTLIER) cc_final: 0.5178 (t0) REVERT: D 534 GLN cc_start: 0.7790 (mt0) cc_final: 0.7380 (mt0) outliers start: 20 outliers final: 15 residues processed: 184 average time/residue: 0.2593 time to fit residues: 72.9725 Evaluate side-chains 184 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15713 Z= 0.160 Angle : 0.435 7.930 21308 Z= 0.231 Chirality : 0.037 0.201 2407 Planarity : 0.003 0.027 2659 Dihedral : 3.497 17.758 2127 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.12 % Allowed : 8.37 % Favored : 90.51 % 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: 2.93 (0.19), residues: 1914 helix: 2.58 (0.14), residues: 1300 sheet: 0.99 (0.70), residues: 44 loop : 0.57 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.020 0.001 PHE A 423 TYR 0.015 0.001 TYR B 810 ARG 0.002 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.776 Fit side-chains REVERT: C 381 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8447 (t70) REVERT: B 695 ASP cc_start: 0.6489 (m-30) cc_final: 0.6091 (m-30) REVERT: B 746 LEU cc_start: 0.6345 (pp) cc_final: 0.5581 (tp) REVERT: B 879 MET cc_start: 0.8258 (tpp) cc_final: 0.7952 (tpt) REVERT: A 556 LYS cc_start: 0.6571 (mmtm) cc_final: 0.6224 (mttt) REVERT: D 534 GLN cc_start: 0.7822 (mt0) cc_final: 0.7438 (mt0) outliers start: 18 outliers final: 13 residues processed: 181 average time/residue: 0.2651 time to fit residues: 72.4901 Evaluate side-chains 180 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN D 243 ASN D 422 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15713 Z= 0.272 Angle : 0.506 8.494 21308 Z= 0.268 Chirality : 0.040 0.230 2407 Planarity : 0.003 0.033 2659 Dihedral : 3.754 17.305 2127 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.05 % Allowed : 8.56 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.19), residues: 1914 helix: 2.43 (0.14), residues: 1291 sheet: 0.92 (0.71), residues: 44 loop : 0.51 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 168 HIS 0.007 0.001 HIS B1049 PHE 0.023 0.002 PHE C 298 TYR 0.019 0.002 TYR A 349 ARG 0.003 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 2.030 Fit side-chains REVERT: C 381 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8497 (t70) REVERT: C 498 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8043 (mm-40) REVERT: B 695 ASP cc_start: 0.6541 (m-30) cc_final: 0.6164 (m-30) REVERT: B 703 PHE cc_start: 0.5923 (t80) cc_final: 0.5663 (t80) REVERT: B 746 LEU cc_start: 0.6488 (pp) cc_final: 0.5755 (tp) REVERT: B 879 MET cc_start: 0.8324 (tpp) cc_final: 0.7989 (tpt) REVERT: A 556 LYS cc_start: 0.6633 (mmtm) cc_final: 0.6301 (mttt) REVERT: D 529 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5406 (t70) outliers start: 17 outliers final: 10 residues processed: 189 average time/residue: 0.2689 time to fit residues: 76.8933 Evaluate side-chains 179 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN D 226 GLN D 243 ASN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 HIS D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 15713 Z= 0.144 Angle : 0.437 8.509 21308 Z= 0.230 Chirality : 0.037 0.208 2407 Planarity : 0.003 0.027 2659 Dihedral : 3.556 18.125 2127 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.81 % Allowed : 9.06 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.19), residues: 1914 helix: 2.59 (0.14), residues: 1289 sheet: 0.93 (0.71), residues: 44 loop : 0.57 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 PHE 0.023 0.001 PHE A 423 TYR 0.013 0.001 TYR B 810 ARG 0.002 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 1.874 Fit side-chains REVERT: C 381 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8431 (t70) REVERT: C 430 MET cc_start: 0.8525 (tpp) cc_final: 0.8296 (tpt) REVERT: C 498 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7925 (mm-40) REVERT: B 695 ASP cc_start: 0.6491 (m-30) cc_final: 0.6195 (m-30) REVERT: B 703 PHE cc_start: 0.5741 (t80) cc_final: 0.5486 (t80) REVERT: B 746 LEU cc_start: 0.6332 (pp) cc_final: 0.5592 (tp) REVERT: B 879 MET cc_start: 0.8286 (tpp) cc_final: 0.7960 (tpt) REVERT: A 556 LYS cc_start: 0.6563 (mmtm) cc_final: 0.6246 (mttt) REVERT: D 529 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.5300 (t0) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.2616 time to fit residues: 70.7280 Evaluate side-chains 176 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 190 optimal weight: 40.0000 chunk 175 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN D 226 GLN D 243 ASN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 HIS D 468 ASN D 534 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15713 Z= 0.145 Angle : 0.442 8.265 21308 Z= 0.231 Chirality : 0.037 0.207 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.501 18.021 2127 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.05 % Allowed : 9.00 % Favored : 89.95 % 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: 2.98 (0.19), residues: 1914 helix: 2.63 (0.14), residues: 1289 sheet: 0.93 (0.71), residues: 44 loop : 0.60 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 168 HIS 0.005 0.001 HIS D 422 PHE 0.023 0.001 PHE A 423 TYR 0.015 0.001 TYR B 810 ARG 0.002 0.000 ARG D 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.494 Fit side-chains REVERT: C 381 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (t70) REVERT: C 430 MET cc_start: 0.8538 (tpp) cc_final: 0.8288 (tpt) REVERT: B 703 PHE cc_start: 0.5739 (t80) cc_final: 0.5486 (t80) REVERT: B 746 LEU cc_start: 0.6280 (pp) cc_final: 0.5532 (tp) REVERT: B 879 MET cc_start: 0.8289 (tpp) cc_final: 0.7959 (tpt) REVERT: D 514 ARG cc_start: 0.7110 (ptp90) cc_final: 0.6900 (ptp90) REVERT: D 529 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5255 (t0) outliers start: 17 outliers final: 11 residues processed: 175 average time/residue: 0.2652 time to fit residues: 70.9572 Evaluate side-chains 175 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN B 864 ASN D 226 GLN D 243 ASN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 HIS D 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092317 restraints weight = 22174.851| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.18 r_work: 0.2931 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15713 Z= 0.179 Angle : 0.459 8.575 21308 Z= 0.241 Chirality : 0.038 0.208 2407 Planarity : 0.003 0.031 2659 Dihedral : 3.549 17.780 2127 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.81 % Allowed : 9.31 % 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: 2.94 (0.19), residues: 1914 helix: 2.60 (0.14), residues: 1289 sheet: 0.98 (0.73), residues: 44 loop : 0.57 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 168 HIS 0.005 0.001 HIS B1049 PHE 0.023 0.001 PHE A 423 TYR 0.016 0.001 TYR B 810 ARG 0.002 0.000 ARG C 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.93 seconds wall clock time: 56 minutes 18.01 seconds (3378.01 seconds total)